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2024-03-07 21:09:18

罕见病脊髓性肌萎缩致病基因SMN1 - 知乎

罕见病脊髓性肌萎缩致病基因SMN1 - 知乎切换模式写文章登录/注册罕见病脊髓性肌萎缩致病基因SMN1赛业生物cyagen​咨询业务+v:cyagen-class(备注知乎)想获得国自然选题思路,提高国自然基金申请命中率?想调整研究方向,获得学术研究突破口?有机会发高分文章?你需要了解学科发展态势和未来走向!赛业生物专栏《Gene of the Week》每周会根据热点研究领域介绍一个基因,详细为您介绍基因基本信息、研究概况和应用背景等,助您保持学术研究敏锐度,提高科学研究效率,期待您的持续关注哦。今天我们要讲的主角是人类遗传病脊髓性肌萎缩致病基因SMN1。SMN1基因研究概况运动神经元存活基因1(survival motor neuron gene 1, SMN1)编码与之同名的蛋白。该蛋白与人类遗传病脊髓性肌萎缩(Spinal Muscular Atrophy, SMA)密切相关,该疾病大多数情况下会导致新生儿2周岁之前死亡。SMN1的单拷贝失活(无症状)现象在亚洲人群中大约是1/50,这就造成了1/10000左右的新生儿发病率(不同人种地域的突变频率有所区别)。SMN1是剪接体的组成部分,剪接体复合物在小核糖核蛋白 (snRNPs)的组装中起着催化剂的作用,因此在pre-mRNA的剪接中起着重要的作用。从其命名就可以看出,该蛋白在维持运动神经元的生存方面不可或缺。图1. SMN1结构。图中显示人类SMN1成熟的mRNA和蛋白线性化的结构区域。箭头指示的是翻译起始和终止位点。不同区域内部的数字表示氨基酸数量。下方则是对该基因的不同功能区进行注释。信息来源:10.4155/FMC.14.63.人类SMN基因分为SMN1和SMN2, SMN1基因位于端粒侧,转录后产生全长mRNA,SMN2基因位于着丝粒侧,SMN2基因与SMN1基因在外显剪接增强子处有一个核苷酸的差异,从而使得转录后的SMN2缺失第7个外显子,编码截断的SMN蛋白,截断的SMN蛋白丧失全长SMN蛋白的功能,并且在细胞内迅速降解。生理状态下,SMN2 mRNA的第7个外显子在有些情况下并不是全部缺失,SMN2基因仍然能够产生一小部分(10-15%) 全长mRNA,这部分mRNA可编码具有正常功能的SMN蛋白。不过,仍有一部分SMN2的转录(大约10-15%左右)能够突破封锁生成完整的mRNA,进而合成有功能的蛋白。研究发现95%的SMA是由SMN1基因发生突变引起的,SMA患者体内由于SMN1基因的缺失,不能产生足够的SMN蛋白。在疾病状态下,体内SMN蛋白主要来源于SMN2基因,由于SMN2基因只有少部分可产生功能性SMN蛋白,因此SMA主要是由体内SMN蛋白的缺乏而引起。图2. SMN1与SMA。信息来源:10.1001/archneurol.2011.74.根据前面所述的SMA致病机理,SMA的治疗方案有两条不同的路径。其一是直接通过载体将能够编码正常SMN1的基因导入,也就是图3左侧Zolgensma药物所采用的疗法,该方法也成为了第三个上市的AAV介导的基因治疗方案;第二种就是通过反义核苷酸促进患者身体内仍然存在的SMN2的正常表达(抑制7号外显子的剪切)来实现。希望在不远的将来,基因治疗能为SMA患者带来福音,彻底治愈该疾病。图3. SMA的基因治疗。信息来源:10.3390/ijms21249589.在过去的几十年里,基因治疗在治疗遗传性疾病方面取得了重大进展。以基因组学或蛋白组学的方式找到致病基因,再结合细胞水平或动物水平验证,用这种模式产出的高质量文章层出不穷。推荐文献:1. Howell MD, Singh NN, Singh RN. Advances in therapeutic development for spinal muscular atrophy. Future Med Chem. 2014 Jun;6(9):1081-99. doi: 10.4155/fmc.14.63. PMID: 25068989; PMCID: PMC4356243.2. Kolb SJ, Kissel JT. Spinal muscular atrophy: a timely review. Arch Neurol. 2011 Aug;68(8):979-84. doi: 10.1001/archneurol.2011.74. Epub 2011 Apr 11. PMID: 21482919; PMCID: PMC3860273.3. Chiu W, Hsun Y-H, Chang K-J, Yarmishyn AA, Hsiao Y-J, Chien Y, et al. Current Genetic Survey and Potential Gene-Targeting Therapeutics for Neuromuscular Diseases. IJMS. 2020 Dec 16;21(24):9589.发布于 2021-02-24 11:14研究方向生物基因组学​赞同 5​​添加评论​分享​喜欢​收藏​申请

消息通知服务 SMN_消息提醒_推送消息_应用服务-华为云

消息通知服务 SMN_消息提醒_推送消息_应用服务-华为云

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消息通知服务 SMN

消息通知服务 SMN

提供云上应用和服务消息传送到多种终端的消息发布订阅服务

提供云上应用和服务消息传送到多种终端的消息发布订阅服务

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华为云上超过60+服务使用SMN发送消息

为什么选择华为云消息通知服务 SMN

消息发送快速简便,使用门槛低

消息发送快速简便,使用门槛低

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可将消息以10+种协议方式送达客户终端

消息通知服务,支持10+协议消息推送,满足不同企业的个性化需求,包含邮件,短信,语音,HTTP/HTTPS,FunctionGraph函数、FunctionGraph工作流,企业微信群,钉钉群,飞书群,Welink群。

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与云服务的集成

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多通道告警事件通知

多通道告警事件通知

SMN服务支持多种消息推送方式,可将告警事件通知等消息发送到不同终端。例如将CES的告警按重要性分级通知到邮件,短信,语音,钉钉/企业微信群等。

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一个主题下添加不同类型的订阅终端,一次推送可将一个消息推送到不同的终端。

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订阅终端用户确认订阅后,才会收到消息,避免无效消息打扰。

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弹性云服务器 ECS

对象存储服务 OBS

云监控服务 CES

与云服务的集成

与云服务的集成

将SMN作为消息连接不同的云服务,例如将云服务的消息(如OBS桶中对象的事件消息)通知到其他云服务(如FunctionGraph),实现云服务间的消息互联。

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弹性云服务器 ECS

对象存储服务 OBS

云监控服务 CES

错峰流控

错峰流控

上下游系统处理能力有差异时,可以使用SMN转储系统间的通信数据,提供消息堆积缓冲能力,减少下游系统的压力

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弹性云服务器 ECS

对象存储服务 OBS

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携手数百万客户持续业务创新

携手数百万客户持续业务创新

美图

顺丰科技

迷你创想

基于SMN的消息通知能力,实时通知资源变化到CMDB系统

美图通过自建CMDB管理公司全部IT资源,华为云Config服务感知华为云上资源变化,通过SMN服务Https通知能力将资源变化消息通知到美图CMDB系统,及时更新资源信息。

了解详情

事件告警分级通知,提升运维效率

根据告警事件严重性,通过SMN服务的邮件,手机短信,语音不同方式,分级通知到运维人员,提升运维效率。

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告警通知到企业即时通讯工具,方便运维管理

华为云SMN服务将云上告警消息转发到客户办公用运维组飞书群,消息一次通知到整个团队。企业人员变化跟随办公即时通讯群,不需要在华为云上管理消息接收人。

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产品介绍

图解消息通知服务?

什么是消息通知服务?

消息通知服务应用场景

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快速入门

快速入门

消息通知服务入门指引

发布JSON消息

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用户指南

用户指南

主题管理

订阅管理

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常见问题

常见问题

消息通知服务支持的传输协议有哪些?

消息通知服务的使用如何收费和计费?

消息通知服务的主题名称有何格式要求?

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即刻开启快速简便的消息通知之旅

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提供云上及本地资源的立体化监控平台

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提供全局资源配置管理,配置检测能力

弹性云服务器 ECS

可随时自动获取、可弹性伸缩的云服务器

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意大利品牌知多少|Santa Maria Novella:高贵的妆,撩人的香 - 知乎

意大利品牌知多少|Santa Maria Novella:高贵的妆,撩人的香 - 知乎切换模式写文章登录/注册意大利品牌知多少|Santa Maria Novella:高贵的妆,撩人的香意风意风着眼的商品均是100%进口自意大利,每个品牌都享有意大利原厂的经销授权书。今天意风带来的主角是个颇具神秘&传奇色彩的品牌。说它神秘,是因为它几乎没有任何的宣传广告,却在“小红书”上被誉为“去意大利必败圣品之一”;说它传奇,则是因为这家开在教堂里的药妆品牌最早是“王室特供品”,被称为全世界最古老的药妆品牌之一。说到这,主角的大名呼之欲出—一个与佛罗伦萨圣母玛利亚教堂同名的意国古老药妆品牌:Santa Maria Novella。品牌简介名称:Santa Maria Novella(简称SMN)国籍:意大利创始年代:1612年创始人:修道院的修士主打产品:药妆、香薰、宠物香氛、摆件、配饰、食品等定位:价位经济的“高大上”品牌历程SMN的发家史细数起来可要追溯到13世纪,比文艺复兴的时间还要早。彼时,SMN还只是一家专职为托斯卡纳贵族—美第奇家族制作化妆品、日用品和药品的药妆店(关于美第奇家族的八卦感兴趣的小伙伴可以自行度娘,要知道这个家族在是号称昔日能够左右世界经济的欧洲四大家族之一)。因此,店里使用的都是相当考究的纯天然原料,绝不使用杀虫剂和除草剂,并且经过反复而精细的调试和配制,很多产品都是经由修道士们遵循流传多年的古法而制成。后来,辉煌了200多年的美第奇王朝绝了子嗣土崩瓦解了,但是为大家族服务了多年的SMN却源远流长地被传承了下来,开始对外营业,并且发扬光大,一度成为戴安娜王妃、宋美龄女士最爱的药妆品牌,名人粉丝也是一波接一波:据说SMN是全智贤来佛罗伦萨必逛的店。如今,SMN在佛罗伦萨的店铺仍然位于Santa Maria Novella教堂内,如果不是摆放着货架和收银机,相信多数偶然踏入这里的人都会以为这里是座芳香博物馆;事实上,除了药妆店它真的就是一间芳香展示厅,同时,也是一个可以坐下来享受SMN专供草药茶的Tea House。别忘了在SMN享用一壶曼妙的草药茶过去神秘而高贵的王室药妆店摇身一变成为普罗大众都能一亲芳泽的亲民品牌,除了意大利本土外,如今在法国、俄罗斯、英国、西班牙、南非、美国、巴拿马、中国香港&台湾、韩国、日本、印尼、泰国、澳大利亚都能找到SMN的专卖店--刚好在旅途中的姑娘们可千万别错过噢(具体店铺地址可查询官网)!推荐理由事实上,这是个根本就不需要任何宣传也能分分钟卖断货的品牌;所以,今天【推荐理由】的版块意风就只跟大家说一句:高贵的妆配上撩人的香,还给贴上如此亲民的价,错过找不到第二家……推荐购买直接来看看SMN的明星产品们吧,价格给大家参考美国售价:明星产品No.1 玫瑰保湿水500ML, $60玫瑰保湿水应该是光顾SMN的姑娘们人手必备的产品头牌了。这款玫瑰水蕴含玫瑰花精华、天然荷尔蒙、维生素C&油脂,渗透能力超强,除了超赞的保湿效果外,用久了还能发现肤色明显提亮变白。需要一说的是,敏感类肌肤初用的几天内可能会有刺痛或微热感,不过不用怕,这只是玫瑰水在拼命渗透肌肤的正常表现。此外,它还可以作为严重过敏性肌肤患者与皮肤直接接触物品的清洗剂,据说用牛奶洗澡的宋美龄每天都会在衣物和床单上喷洒此物。对了,玫瑰水都是用厚实的玻璃装瓶的,包装质感很好但是分量也增加不少。不过相信我,拧开瓶盖的一瞬间,你一定会被浓浓的玫瑰花香迷住,然后妥妥爱上它……明星产品No.2 洁面手工皂$35这款洁面皂用起来相当温和,其成分是纯天然的花草精华、椰子油和天然奶脂,依据古法传承其制作过程完全不使用机器,经过60天的阴干手工制造完成,有瞬间滋养干燥皮肤的神奇功效。这东西好携带并且价格又如此公道,简直是自用或者伴手礼的最佳选择!明星产品No.3 金盏花面霜$65这款也是网络上强烈推荐的好东西。金盏花本来就是好东西,有疗伤的神效,所以这款面霜对于舒缓日晒与发炎造成的发痒、发红症状都有超强的功效(简直就是海滩必备)。面霜中所含的大豆与脂肪酸能有效修复受损肌肤,荷荷巴精油与杏仁油又能充分保湿滋润皮肤,并且味道也是香香的,所以每天使用都是极好哒。当然,价格比起前两款产品来说略高,但仍然很亲民。除了这三款明星产品外,SMN家的香薰类产品也是值得一买的,身体用的&家用的产品应有尽有。石榴味道的香水,想想都觉得香气迷人 $125薰衣草香薰袋,衣柜抽屉的好帮手$35SMN家居然有专门给喵星人和汪星人研制的除臭香氛和洗涤剂,简直就是各位铲屎官们的福音~试想下,当你家喵和汪跑过的时候,散发着迷人的玫瑰香是一种什么感受……玫瑰香型宠物除臭剂$20泡沫免洗宠物清洁剂$40还要给物件控们发个福利,SMN除了各种“美美香香”外,还卖一些配件和饰品(官网上都能搜罗到)。金壶$620对了,再啰嗦一句,SMN家的东西都能在购买后选择礼盒包装,当然,这项服务是收费哒(米国一个盒子官方收费6.5刀)。文末奉上个小贴士,去佛罗伦萨的小伙伴们别忘了记录地址噢,门口比较小,很容易走过却错过:地址:Via della Scala, 16 – 50123 营业时间:9:00-20:00店里有中文导购手册,进去了别忘了先拿一本,就算是一句外文不会说的朋友,也能按图指给店员帮你找到,在买买买的道路上又多了一项便利……发布于 2017-09-22 13:01意大利药妆​赞同 16​​4 条评论​分享​喜欢​收藏​申请

SMN1和SMN2基因有什么区别 - 知乎

SMN1和SMN2基因有什么区别 - 知乎切换模式写文章登录/注册SMN1和SMN2基因有什么区别biofount科研试剂什么是SMN1基因?SMN1基因一般称为运动神经元存活基因。 它也被称为 gems 1 的一个组成部分。该基因编码人类中一种名为 SMN 蛋白的特定蛋白质。 该基因位于5号染色体的端粒区。此外,SMN1基因还位于5号染色体q13的一部分,称为反向复制区,长500 kbp。 该重复区域包含至少 4 个基因(例如 SMN2 基因)和重复元件。 此外,倒置重复区域由于其复杂性而易于重排和删除。 SMN1 和 SMN2 基因几乎相同。 但这两个基因有一个关键的序列差异,即外显子 7 中的单核苷酸转换(C 到 T)。图1.SMN1基因SMN1 基因的突变会导致一种称为脊髓性肌萎缩症的神经肌肉疾病。 然而,SMN2 基因的缺失不会导致这种疾病。 此外,SMN1 和 SMN2 基因的突变共同导致胚胎死亡。什么是SMN2基因?SMN2基因通常被称为运动神经元存活2。该基因在人类中产生两种类型的蛋白质; 正常的全长 SMN 蛋白和截短的 SMN 蛋白。 由于该基因外显子 7 中 C 向 T 的转变,从大多数 SMN2 mRNA 转录物中产生了截短的、无功能的 SMN 蛋白。 然而,来自 SMN2 基因的 10% 到 15% 的 SMN2 mRNA 转录物可以产生功能性的全长 SMN 蛋白。 因此,突变导致的 SMN1 基因功能丧失部分由 SMN 2 基因合成的 SMN 蛋白所补偿。此外,SMN 2 基因中的核苷酸取代导致大约 80-90% 的截短和不稳定蛋白质,以及 10-20% 的全长蛋白质,这与 SMN1 基因产生的蛋白质非常相似。 除此之外,由于该基因是该疾病的修饰因子,因此发现三个或更多 SMN2 拷贝的存在与较轻的脊髓性肌萎缩症表型相关。SMN1 和 SMN2 基因有什么区别?SMN1基因突变确实会导致脊髓性肌萎缩症,而SMN2基因突变不会导致脊髓性肌萎缩症。 因此,这是 SMN1 和 SMN2 基因之间的关键区别。 此外,SMN1 总是产生全长 SMN 蛋白,而 SMN 2 基因产生大约 80-90% 的截短和不稳定的 SMN 蛋白以及 10-20% 的全长 SMN 蛋白。发布于 2023-03-20 09:22・IP 属地天津生物科技化学试剂​赞同 2​​添加评论​分享​喜欢​收藏​申请

请问SMn(F)在线性空间中有什么特殊含义吗,有一道题直接给出这种表示没有任何说明? - 知乎

请问SMn(F)在线性空间中有什么特殊含义吗,有一道题直接给出这种表示没有任何说明? - 知乎首页知乎知学堂发现等你来答​切换模式登录/注册线性代数请问SMn(F)在线性空间中有什么特殊含义吗,有一道题直接给出这种表示没有任何说明?关注者7被浏览3,043关注问题​写回答​邀请回答​好问题​添加评论​分享​7 个回答默认排序知乎用户数域F上的n阶对称矩阵。在课本例5.21有说。我也刚找到(ಡωಡ)发布于 2015-11-20 23:51​赞同 6​​2 条评论​分享​收藏​喜欢收起​匿名用户呃,是校友?^_^把作业发到知乎上问。。发布于 2015-12-15 20:33​赞同 1​​添加评论​分享​收藏​喜欢

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SMN1基因敲除小鼠与脊髓性肌萎缩症(SMA) | 赛业生物科技有限公司

SMN1基因敲除小鼠与脊髓性肌萎缩症(SMA) | 赛业生物科技有限公司

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8月:脊髓性肌萎缩症(SMA)关爱月

 

脊髓性肌萎缩症(SMA)是一种具高致亡性、致残性的罕见病,被称为两岁以下婴幼儿的头号遗传病杀手。自1996年起,包括欧洲、美国、加拿大、澳大利亚等地在内的全球脊髓性肌萎缩症(SMA)群体将每年的8月定为SMA关爱月,并在这个月里举行各种疾病宣传活动,提升社会公众对SMA这一罕见疾病的了解,以及对SMA群体的关爱支持。

 

绝大部分SMA患者(95%)是因SMN1基因第7号外显子纯合缺失所致病,另外5%患者的致病因也与这一基因的第7号外显子有关。鉴于“7”这个数字对SMA的特殊意义,2018年北京市美儿SMA关爱中心倡导发起在原来国际普遍接受的8月为SMA宣传月的基础上,将8月7日定为国际SMA关爱日,提高各界社会公众对SMA患者的重视及关爱。今天的《Gene of the Week》就让我们一起了解SMA及其致病基因SMN1吧!

图1. 国际SMA关爱日LOGO。这是由两条出现断裂的DNA螺旋结构组成数字“7”主图案,代表SMA主要是由致病基因上第7号外显子缺失所致。红蓝两主色分别代表了对SMA群体的持续关爱和对疾病的不懈探索研究。配合英文文字“World SMA Awareness Day”和国际化的设计风格构成了承载完整信息的“国际SMA关爱日”LOGO。

 

基因基本信息

表1. SMN1的基本信息

备注:标有√的意为赛业红鼠资源库有该种保存状态的小鼠

 

SMN1基因研究概况

运动神经元存活基因1(survival motor neuron gene 1, SMN1)编码与之同名的蛋白。该蛋白与人类遗传病脊髓性肌萎缩(Spinal Muscular Atrophy, SMA)密切相关,该疾病大多数情况下会导致新生儿2周岁之前死亡。SMN1的单拷贝失活(无症状)现象在亚洲人群中大约是1/50,这就造成了1/10000左右的新生儿发病率(不同人种地域的突变频率有所区别)。SMN1是剪接体的组成部分,剪接体复合物在小核糖核蛋白 (snRNPs)的组装中起着催化剂的作用,因此在pre-mRNA的剪接中起着重要的作用。从其命名就可以看出,该蛋白在维持运动神经元的生存方面不可或缺。

图2. SMN1结构。图中显示人类SMN1成熟的mRNA和蛋白线性化的结构区域。箭头指示的是翻译起始和终止位点。不同区域内部的数字表示氨基酸数量。下方则是对该基因的不同功能区进行注释。信息来源:10.4155/FMC.14.63.

 

人类SMN基因分为SMN1和SMN2, SMN1基因位于端粒侧,转录后产生全长mRNA,SMN2基因位于着丝粒侧,SMN2基因与SMN1基因在外显剪接增强子处有一个核苷酸的差异,从而使得转录后的SMN2缺失第7个外显子,编码截断的SMN蛋白,截断的SMN蛋白丧失全长SMN蛋白的功能,并且在细胞内迅速降解。生理状态下,SMN2 mRNA的第7个外显子在有些情况下并不是全部缺失,SMN2基因仍然能够产生一小部分(10-15%) 全长mRNA,这部分mRNA可编码具有正常功能的SMN蛋白。不过,仍有一部分SMN2的转录(大约10-15%左右)能够突破封锁生成完整的mRNA,进而合成有功能的蛋白。研究发现95%的SMA是由SMN1基因发生突变引起的,SMA患者体内由于SMN1基因的缺失,不能产生足够的SMN蛋白。在疾病状态下,体内SMN蛋白主要来源于SMN2基因,由于SMN2基因只有少部分可产生功能性SMN蛋白,因此SMA主要是由体内SMN蛋白的缺乏而引起。

图3. SMN1与SMA。

信息来源:10.1001/archneurol.2011.74.

 

根据前面所述的SMA致病机理,SMA的治疗方案有两条不同的路径。其一是直接通过载体将能够编码正常SMN1的基因导入,也就是图4左侧Zolgensma药物所采用的疗法,该方法也成为了第三个上市的AAV介导的基因治疗方案;第二种就是通过反义核苷酸促进患者身体内仍然存在的SMN2的正常表达(抑制7号外显子的剪切)来实现。

图4. SMA的基因治疗。

信息来源:10.3390/ijms21249589.

 

今年6月,全球首个SMA口服药物——利司扑兰口服溶液用散(Risdiplam Powder for Oral Solution)在获得国家药监局的优先审评资格认定后,仅用1年便在中国正式获批,让SMA的治疗进入了口服治疗的新阶段,为SMA患者带来全新的治疗选择和希望。希望在不远的将来,基因治疗能为SMA患者带来福音,彻底治愈该疾病。

 

赛业生物一站式服务平台助力基因治疗研究

作为一家基于模式动物的国际化创新性CRO平台,赛业生物深知罕见病是全人类共同面临的公共健康问题,并希望通过自己在专业领域的技术专长助力罕见病基因治疗研究。赛业生物积累了大量的生物信息及基因编辑方面的数据,在模式动物持续的深耕也让我们在基因编辑技术方面一直走在行业前沿,结合赛业生物在人工智能领域的深度探索,我们可以给科学家们提供更高效的基因功能解析与基因治疗解决方案。

赛业生物罕见病基因治疗一站式解决方案可为研究罕见病及开发下游基因治疗的客户提供从突变基因的致病风险评估到小鼠模型制作,到表型分析,到基因治疗方案,到AAV载体设计直至小鼠模型药效验证的全套服务,免费的致病突变位点致病风险预测,免费提供罕见病模型构建方案及免费提供罕见病基因治疗下游验证方案。如您正在从事罕见病相关研究,欢迎点击图片填写罕见病基因相关信息,我们收到信息后,将有专业同事与您联系。

 

推荐文献:

1. Howell MD, Singh NN, Singh RN. Advances in therapeutic development for spinal muscular atrophy. Future Med Chem. 2014 Jun;6(9):1081-99. doi: 10.4155/fmc.14.63. PMID: 25068989; PMCID: PMC4356243.

2. Kolb SJ, Kissel JT. Spinal muscular atrophy: a timely review. Arch Neurol. 2011 Aug;68(8):979-84. doi: 10.1001/archneurol.2011.74. Epub 2011 Apr 11. PMID: 21482919; PMCID: PMC3860273.

3. Chiu W, Hsun Y-H, Chang K-J, Yarmishyn AA, Hsiao Y-J, Chien Y, et al. Current Genetic Survey and Potential Gene-Targeting Therapeutics for Neuromuscular Diseases. IJMS. 2020 Dec 16;21(24):9589.

 

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A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II | Nature Communications

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II | Nature Communications

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A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II

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Published: 16 September 2022

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II

Yanli Liu 

ORCID: orcid.org/0000-0003-0197-76171,2,3 na1 na2, Aman Iqbal3 na1, Weiguo Li2,3 na1, Zuyao Ni4 na1, Yalong Wang5 na1, Jurupula Ramprasad1, Karan Joshua Abraham 

ORCID: orcid.org/0000-0002-6221-49156, Mengmeng Zhang1, Dorothy Yanling Zhao4, Su Qin3,7, Peter Loppnau3, Honglv Jiang1, Xinghua Guo4, Peter J. Brown 

ORCID: orcid.org/0000-0002-8454-03673, Xuechu Zhen1, Guoqiang Xu 

ORCID: orcid.org/0000-0002-4753-47691, Karim Mekhail 

ORCID: orcid.org/0000-0002-6084-020X6, Xingyue Ji1, Mark T. Bedford 

ORCID: orcid.org/0000-0002-8899-10505, Jack F. Greenblatt4 & …Jinrong Min 

ORCID: orcid.org/0000-0001-5210-31302,3,8 na2 Show authors

Nature Communications

volume 13, Article number: 5453 (2022)

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MethylationSmall moleculesTranscriptionX-ray crystallography

AbstractSurvival of motor neuron (SMN) functions in diverse biological pathways via recognition of symmetric dimethylarginine (Rme2s) on proteins by its Tudor domain, and deficiency of SMN leads to spinal muscular atrophy. Here we report a potent and selective antagonist with a 4-iminopyridine scaffold targeting the Tudor domain of SMN. Our structural and mutagenesis studies indicate that both the aromatic ring and imino groups of compound 1 contribute to its selective binding to SMN. Various on-target engagement assays support that compound 1 specifically recognizes SMN in a cellular context and prevents the interaction of SMN with the R1810me2s of RNA polymerase II subunit POLR2A, resulting in transcription termination and R-loop accumulation mimicking SMN depletion. Thus, in addition to the antisense, RNAi and CRISPR/Cas9 techniques, potent SMN antagonists could be used as an efficient tool to understand the biological functions of SMN.

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IntroductionSurvival of motor neuron (SMN), a Tudor domain-containing protein, is a core component of the SMN complex, which is essential for biogenesis of small nuclear ribonucleoproteins (snRNPs) by assembling the heptameric Sm ring onto spliceosomal snRNA1. The Tudor domain of SMN (Fig. 1a) binds to arginine symmetric-dimethylated (Rme2s) Sm proteins, and this interaction plays a critical role in snRNP assembly2,3. Considering the importance of SMN in the fundamental process of snRNP assembly, it is not surprising that complete loss of SMN is lethal. The human genome contains 2 genes, SMN1 and SMN2, which produce the identical SMN protein. Homozygous deletion or mutation of SMN1 coupled with a single nucleotide substitution at position 6 of exon 7 (C6T) of SMN2 is responsible for spinal muscular atrophy (SMA)4, the most common genetic cause of infant death with a frequency of 1 in ~10,000 births5.Fig. 1: Compound 1 preferentially binds to SMN among assayed methylarginine or methyllysine binders.a Domain structure of SMN. b Molecular structure of compound 1. c Binding affinities of compound 1 to selected modified histone readers measured by ITC. ITC data shown are representative of two independent experiments. The names of non-Tudor domains were shown in the parentheses. Source data are provided as a Source Data file.Full size imageIn addition to its role in snRNP assembly, SMN is also involved in regulation of nuclear architecture6,7, local axonal translation in neurons8, and transcription termination9. SMN regulates nuclear architecture by interacting with arginine methylated coilin, a Cajal body (CB) specific protein. Cajal bodies (CBs) and gemini of Cajal bodies (Gems) are the twin subcellular organelles in the nucleus of proliferative cells such as embryonic cells, or metabolically active cells such as motor neurons. Coilin harbors symmetrically dimethylated arginine residues6,7. Sufficient arginine methylation of coilin is required for its binding to SMN, which is stored in Gems and accompanies snRNP to CBs during differentiation of the human neuroblastoma cell line SH-SY5Y10. SMN is also reported to regulate local axonal translation via the miR-183/mTOR pathway in neurons8. Specifically, the miR-183 level is increased and local axonal translation of mTor is reduced in SMN-deficient neurons. In an SMA mouse model, suppression of the miR-183 expression in the spinal motor neurons strengthens motor function and increases survival of Smn-mutant mice, which uncovers another potential mechanism responsible for SMA pathology8. SMN also interacts with symmetric-dimethylated R1810 at the C-terminal domain (CTD) of RNA polymerase II (RNAP II) subunit POLR2A (R1810me2s-POLR2A) via its Tudor domain to regulate transcription termination9. In SMA patients, abnormal transcription termination such as pause of RNAP II and R-loop (DNA-RNA hybrids) accumulation in the termination region may facilitate neurodegeneration9. Taken together, SMN functions in different biological pathways, and the Tudor domain of SMN plays a critical role in executing these functions by mediating arginine methylation-dependent interactions. In spite of the extensive study of SMN and its associated SMA disease, it is still unclear how SMN protects motor neurons in the spinal cord against degeneration.In this work, we set out to design SMN-selective chemical probes that would specifically occupy the methylarginine binding pocket and disrupt the Tudor domain-mediated and arginine methylation-dependent interactions. These SMN-specific chemical probes could be used to better understand biological functions of SMN in different pathways and molecular etiology of SMA.ResultsIdentification of an SMN-selective small molecule antagonistIn this study, we obtained an SMN-selective antagonist by serendipity when we tried to screen inhibitors against the histone H3K9me3 binding tandem Tudor domain (TTD) of UHRF1 (Fig. 1b, Supplementary Fig. 1a and Supplementary Table 1). In this fluorescence-based peptide displacement screen for UHRF1, we found 5 hits, among which compound 1 was confirmed by isothermal titration calorimetry (ITC) (Kd ~16 µM, Supplementary Fig. 1b, c). As we know, many proteins bind to lysine and arginine methylated histones/proteins, including the Tudor Royal superfamily (Tudor, chromodomain, PWWP and MBT) of proteins and some CW-type (cystine and tryptophan) and PHD-type (plant homeodomain) zinc finger containing proteins11,12,13,14, and all of these proteins utilize an aromatic cage to recognize the methyllysine or methylarginine residue. In order to investigate the binding selectivity of compound 1, we screened it against selected methylarginine or methyllysine-binding Tudor domains and methyllysine/methylarginine-binding non-Tudor domains (Fig. 1c). UHRF1_TTD was the only assayed methyllysine binder that bound to compound 1 measurably, and compound 1 bound more tightly to the methylarginine binding Tudor domains of SMN, SMNDC1, and TDRD3 than to the methyllysine binding Tudor domain of UHRF1_TTD (Fig. 1c and Supplementary Fig. 2). SMN, SMNDC1 and TDRD3 are the only three known methylarginine binding proteins of single canonical Tudor domain. Moreover, the highly homologous Tudor domains of SMN and SMNDC1 bound to compound 1 with a ~4-fold selectivity over that of TDRD3 (Fig. 1c).Compound 1 specifically engages SMN in a cellular contextTo verify the cellular on-target engagement of compound 1, we subcloned SMN into the mammalian expression vector mCherry2-C1 to express the N-terminally mCherry tagged SMN fluorescent protein, and conjugated compound 1 to 9-(2-carboxy-2-cyanovinyl)julolidine (CCVJ), a fluorescent molecular rotor as previously reported15 to generate CCVJ-Cmpd 1, which presents switched-on fluorescence upon binding to SMN, or to biotin to generate a biotin conjugate compound 1 (biotin-Cmpd 1) for cellular lysate pulldown assays16 (Fig. 2a and Supplementary Fig. 3). Our ITC results showed that these two modified compounds still bound to SMN (Supplementary Fig. 4). When the fluorescence-switching CCVJ-Cmpd 1 binds to SMN, restriction of the fluorescent molecule rotations would trigger emission of strong green fluorescence signals15, which is confirmed in solution (Supplementary Fig. 5). Upon treatment of U2OS cells with CCVJ-Cmpd 1, the green fluorescent compound 1 colocalized with the red fluorescent mCherry-SMN, which was not observed with the SMN cage mutant (Fig. 2b), indicating that compound 1 binds to the aromatic cage of SMN specifically.Fig. 2: Cellular on-target engagement of compound 1.a Chemical structure of CCVJ conjugated compound 1 (CCVJ-Cmpd 1) and biotin conjugated compound 1 (biotin-Cmpd 1). b mCherry-SMN (red) colocalizes with CCVJ-Cmpd 1 (green), which is lost when the cage residue W102 is mutated in SMN. Scale bar: 10 μm. c Compound 1, but not negative compound 15, prevents the pulldown of SMN by biotin-labeled compound 1 from cell lysates. d SMN cage mutants disrupt or weaken the interaction between SMN and biotin-Cmpd 1 in cell lysates. The U2OS cell lysate was incubated with 20 μM of biotin-Cmpd 1 overnight at 4 °C in figures c and d. Data shown are representative of three independent experiments in (b–d). e On-target engagement of compound 1 was analyzed by chemical proteomics. Volcano plot shows significantly displaced proteins from immobilized biotin-Cmpd 1 pulldowns by competition with 200 μM compound 1 relative to DMSO (FDR q value = 0.01, S0 = 0. 1, two-tailed Student’s t-test and n = 3 biological replicates). Significantly depleted protein colored and labeled in red, major potential prey proteins labeled in blue. FC: fold change. Source data are provided as a Source Data file.Full size imageTo further confirm the cellular binding of compound 1 to SMN, we performed pulldown assays of cell lysates by using the biotin-labeled compound 1 (biotin-Cmpd 1). Our results showed that SMN could be efficiently captured, while neither TDRD3 nor SND1 could be detected (Fig. 2c and Supplementary Fig. 6). The biotin-Cmpd 1 could be competed out by the presence of unlabeled compound 1, but not the negative control compound 15 in the lysates (Fig. 2c). Furthermore, the biotin-Cmpd 1 could not efficiently pull down the SMN cage mutants (Fig. 2d). Affinity-purification and mass spectrometry (AP-MS) based proteomic analysis of the biotin-Cmpd 1 pulldown samples identified SMN as the most significant protein target (with the largest fold change, log2 FC = −8.9). Their interaction was efficiently blocked by the competition of compound 1 (Fig. 2e). The second to forth AP-MS potential prey proteins are GEMIN1 (log2 FC = −6.9), GEMIN6 (log2 FC = −5.4) and GEMIN2 (log2 FC = −5.2), the three major components of the SMN complex17,18, further indicating that compound 1 selectively and specifically binds to endogenous SMN in the cells. Taken together, these data provide convincing evidence that compound 1 binds to the full-length SMN protein specifically in a cellular context.Structural basis of selective compound 1 binding to SMNIn order to understand the structural basis of compound 1 recognition by these reader proteins, we determined the crystal structures of compound 1 in complex with SMN, TDRD3 and UHRF1, respectively (Fig. 3, Supplementary Figs. 7–9 and Table 1). In the complex structure of SMN-compound 1, compound 1 binds to the aromatic cage formed by W102, Y109, Y127 and Y130, which otherwise accommodates dimethylarginine of its physiological ligands (Fig. 3a–c and Supplementary Fig. 7a, b). W102 and Y130 sandwich compound 1 rings. In addition, compound 1 forms a hydrogen bond between its imino group and the side chain of N132. This hydrogen bond boosts the ligand binding ability of SMN, because mutating N132 to alanine significantly reduced its binding affinity (Fig. 3d).Fig. 3: Structural basis of preferential binding of compound 1 to SMN.a Cartoon mode of the complex structure of Tudor domain of SMN and compound 1. The Tudor domain of SMN was colored in green, with the interacting residues shown in sticks and the intermolecular hydrogen bonds indicated by red dashes. b Electrostatic potential surface representation of the complex of Tudor domain of SMN and compound 1. c Cartoon mode of the complex structure of Tudor domain of SMN and Rme2s. d Binding affinities of compound 1 to different SMN Tudor mutants determined by ITC. Shown are representative of two independent experiments. e Sequence alignment of selected Tudor domains. The compound 1 interacting residues were highlighted in red background. Structure figures were generated in PyMOL. Surface representations were calculated with the built-in protein contact potential function of PyMOL. Source data are provided as a Source Data file.Full size imageTable 1 Data collection and refinement statisticsFull size tableIn the TDRD3-compound 1 structure, the binding mode is largely conserved (Supplementary Figs. 7c, d and 8), but Y566 of TDRD3 might not stack with the compound as effectively as W102 in SMN (Fig. 3e and Supplementary Fig. 10), which may explain weaker binding affinity of TDRD3 to compound 1 (Fig. 1c). Consistent with this hypothesis, the W102Y mutant of SMN showed a binding affinity to compound 1 similar to wild-type TDRD3, and the Y566W mutant of TDRD3 displayed a binding affinity to compound 1 similar to wild-type SMN (Fig. 3d and Supplementary Fig. 11). Although we did not determine the corresponding complex structure of SND1, the structure-based sequence alignment revealed that W102 of SMN corresponds to F740 of SND1 (Fig. 3e and Supplementary Fig. 10). Consistent with this, the W102F mutant of SMN only weakly bound to compound 1, while the F740W mutant of SND1 displayed a significantly enhanced binding affinity to compound 1 (Fig. 3d and Supplementary Fig. 11). In addition, the W102A and Y130A mutants of SMN did not bind to compound 1 (Fig. 3d). This lack of binding is consistent with our failure to observe binding for the other tested proteins. On the other hand, the mutations of the SMN cage residues Y109 and Y127 weakened, but did not abrogate the binding of SMN to compound 1 (Fig. 3d). Hence, the sandwich stacking interactions of compound 1 by W102 and Y130 of SMN play a more critical role in the specific compound 1 recognition by SMN.UHRF1 recognizes compound 1 via an arginine-binding pocketTo uncover the specific interactions between UHRF1_TTD and compound 1, we also solved the crystal structure of UHRF1_TTD in complex with compound 1 (Supplementary Figs. 7e, f and 9). Two UHRF1_TTD molecules are present in each asymmetric unit of the UHRF1-compound 1 complex structure (Supplementary Fig. 9a), but we only observed the expected disc-shaped electron density of compound 1 in the histone H3K9me3-binding cage of one UHRF1_TTD molecule, while we found a differently shaped blob in the histone H3K9me3-binding cage of the other UHRF1_TTD molecule (Supplementary Fig. 9b). In the complex structure of UHRF1_TTD-PHD and the H3K9me3 peptide (PDB code: 3ASK), an arginine residue R296 in the linker between the TTD and PHD domains of UHRF1 is found in a pocket formed by D142, E153, A208, M224, W238 and F278 from the TTD domain19 (Supplementary Figs. 1a and 9c). R296 is locked in the pocket by forming a salt bridge with D142. Intriguingly, we found the disc-shaped density that resembles compound 1 in the R296-binding pockets of both UHRF1_TTD molecules, and compound 1 is stacked between the indole ring system of W238 and the guanidinium group of R209 in both UHRF1_TTD molecules (Supplementary Fig. 9b, d).Several lines of evidence suggested that the R296-binding pocket is the major binding site and the methyllysine-binding aromatic cage is just a minor or non-specific binding site. First, when we mutated the aromatic cage residues of UHRF1_TTD that have been shown to be critical for histone H3K9me3 binding to alanine, the binding affinity of compound 1 is not affected significantly. In contrast, when we mutated the R296-binding pocket residues, the binding is totally disrupted (Supplementary Fig. 9e). Second, the electron density inside the H3K9me3 aromatic cage is either smear and can be modeled in multiple orientations of compound 1, which implies that compound 1 does not bind to the cage specifically, or is of no defined density shape (Supplementary Fig. 9b). Third, the aromatic cage has a propensity to accommodate small molecules non-specifically. For instance, some molecules in buffer have been found in the aromatic cage of TDRD320. For the case of UHRF1_TTD, some ethylene glycol molecules from the crystallization buffer are found in the H3K9me3 aromatic cage and the R296-binding pocket of the apo-UHRF1_TTD structure21 (Supplementary Fig. 9f). Fourth, in the SMN-compound 1 complex structure, compound 1 is stacked between the aromatic rings of W102 and Y130. However, the three aromatic residues in the aromatic cage of UHRF1 are perpendicular to each other, which could not stack the compound like SMN does (Supplementary Fig. 9g). Taken together, UHRF1 used the R296-binding pocket to specifically bind to compound 1, and this R296-binding pocket could serve as a therapeutic venue for designing potent small molecule allosteric regulators of the UHRF1 functions. Based on the structural information we obtained from our UHRF1_TTD-compound 1 complex and the UHRF1_TTD-PHD-H3K9me3 complex (PDB code: 3ASK), it is conceivable that the compound 1 binding pocket of UHRF1 is occupied by R296 of the full-length UHRF1 protein, which would prevent compound 1 from chemiprecipitating UHRF1 from the U2OS cell lysate.The imino group of compound 1 plays a critical role in binding to SMNTo explore if we could identify more potent compounds than compound 1, we procured commercially available analogs of compound 1 that include single, double and triple ring molecules and measured their binding affinities to SMN or UHRF1, respectively (Table 2). SMN bound to all the four triple-ring compounds with affinities between 2.6 and 31 μM (Table 2 and Supplementary Fig. 12). The four triple-ring compounds have a 4-iminopyridine scaffold in common, and none of them is more potent than the original hit. Although the binding affinities of SMN and these compounds are not high, SMN binds to these compounds much stronger than its physiological ligands such as symmetric dimethylarginine or R1810me2s-POLR2A, which showed a binding affinity of 476 μM22 or 175 μM9, respectively.Table 2 Binding affinities of compound 1 analogs reveal the importance of the triple-ring and imino group of compound 1Full size tableDue to the electronic similarity between the N-methyl and 4-imino sites on the 4-iminopyridine core, we did not expect to resolve the orientation of compound 1 based on electron density alone, and could not exclude the possibility that the imino group would instead protrude into the solvent. However, the positive binding results of 1-substituted pyridine cores to SMN presented here could confirm that N132 does interact with the imino group and substituents on the pyridine nitrogen would point away from the Tudor domain, as larger 1-substituents would otherwise clash inside the aromatic cage. In addition, the modifications at the N-methyl site of compound 1, such as CCVJ-Cmpd 1 and biotin-Cmpd 1, did not disrupt the interaction of SMN and the modified compounds, which further validates our statement that SMN binds to the 4-imino group of compound 1 to entail a hydrogen bond between the 4-imino group and N132. Indeed, our crystal structure of SMN in complex with compound 4 also confirms that the imino group of compound 4 forms a hydrogen bond with N132 (Supplementary Figs. 7g, h and 13a, b).In addition to triple-ring compounds 1 to 4, SMN also bound to two of twelve double-ring compounds, compounds 5 and 6 (Table 2 and Supplementary Fig. 12). Both compounds retain the imino group, which pinpoints the importance of the imino group-mediated hydrogen bond in the compound binding and is consistent with our crystal structures of SMN in complex with compounds 1, 4, and 6 (Fig. 3 and Supplementary Figs. 7 and 13). None of the single-ring compounds bound to SMN, which may not be able to provide strong enough π–π stacking interaction to hold the compounds. UHRF1, however, did not bind to any other three-ring compounds, because the substituents on the pyridine nitrogen of these compounds are too large to accommodate the more enclosed arginine-binding pocket of UHRF1.SMN antagonists disrupt the SMN-RNAP II interactionWe previously showed that R1810 in the CTD of the mammalian RNAP II subunit POLR2A is symmetrically dimethylated by PRMT5 and the R1810 methylated CTD directly recruits the Tudor-domain protein SMN, which contributes to the assembly of an R-loop resolving complex on the RNAP II CTD9. Hence, we asked whether these small molecule antagonists might be able to disrupt the interaction of SMN with RNAP II in cells. To test this possibility, we treated the HEK293 cells with a series of concentrations of either compound 1, compound 2 or negative control compound 15 for 72 h, and then performed immunoprecipitation using the cell extracts. We demonstrated that coimmunoprecipitation of SMN with GFP fusion protein of POLR2D, a component of RNAP II, was inhibited by compound 1 and compound 2 on a dose-dependent manner, but not by negative compound 15 or DMSO (Fig. 4a). Furthermore, the coimmunoprecipitation of POLR2A with SMN was also disrupted on the treatment of compound 1 and compound 2, whereas no significant effect was observed for the cells treated with DMSO as a control (Supplementary Fig. 14). These results provide convincing evidence that the small molecule antagonists compound 1 or compound 2 of SMN disrupts the interaction between SMN and the RNAP II complex. Since 20 µM of either compound 1 or compound 2 is enough to exhibit significant inhibition of the interaction between SMN and POLR2A (Supplementary Fig. 14), we used this concentration in the following assays.Fig. 4: Effects of SMN antagonists on the interaction between SMN and RNAP II, RNAP II pause, and R-loop accumulation.a SMN antagonists disrupt binding of SMN to RNAP II. Data shown are representative of three independent experiments. b Illustration of ACTB gene and the qPCR amplification positions. c SMN antagonists reduce SMN association at ACTB gene locus. Quantification of SMN qPCR data from ChIP experiments using SMN antibody at the indicated ACTB amplification positions. The SMN levels in DMSO controls were set as 100%. d SMN antagonists lead to RNAP II pause. Quantification of RNAP II qPCR data from ChIP experiments using POLR2A antibody at the indicated ACTB amplification positions. e SMN knockout (KO) leads to R-loop accumulation. Representative single-plane images of Z-stacks of the R-loop levels in scramble vs SMN KO cells of three independent experiments. Scale bar: 5 μm. f Global nuclear R-loop accumulation in SMN KO cells. g SMN antagonists cause global nuclear R-loop accumulation. h SMN antagonists lead to R-loop accumulation at ACTB gene locus. Quantified DNA immunoprecipitation using primers along ACTB locus by using GFP antibody, in cell extracts that were transfected with GFP-RNase H1 R-loop-binding domain (GFP-HB) fusion construct for R-loop detection. a–h HEK293 cells; c, d, h data were presented as the mean ± S.E.M. of three independent experiments (*P < 0.05, **P < 0.01, ***P < 0.001 for the two-tailed Student’s t-test); f, g scatter plots representing data from single-cell and R-loop immunofluorescence analysis (number of cells = 377, 332, 295, 262, 265 for scramble, SMN KO, DMSO, Cmpd 1, Cmpd 2 condition, respectively; Mean ± Quartiles; ****P < 0.0001 for the two-tailed Mann–Whitney test; a.u.: arbitrary units). Source data are provided as a Source Data file.Full size imageSMN antagonists disrupt SMN gene occupancy and lead to RNAP II pauseOur previous ChIP study has shown that SMN occupies the ACTB (β-actin) gene from its promoter to the termination regions with the highest level of occupancy at the 3′-end of the gene9. PRMT5 depletion or POLR2A R1810 mutation leads to a decreased SMN occupancy9. To examine whether the small molecule antagonists of SMN have any effects on the SMN occupancy at its target genes during transcription, the SMN ChIP assay was performed using the primers along the ACTB gene (Fig. 4b). Similar to the effects of PRMT5 depletion or POLR2A R1810 mutation, treatment of either compound 1 or compound 2 significantly reduced the occupancy levels of SMN along the ACTB gene (Fig. 4c). Given that POLR2A CTD R1810A mutation or depletion of SMN leads to the accumulation of RNPA II at genes9, the SMN antagonists might have similar effects. To explore this possibility, we performed RNAP II ChIP experiments and found that addition of either compound 1 or compound 2 (20 µM, 72 h) significantly increased the occupancy levels of RNAP II at the promoter regions and 3′-end of the ACTB gene as detected by quantitative PCR (qPCR) (Fig. 4d). These results indicate that the SMN antagonists could cause the accumulation of RNAP II at both the promoter and 3′ pause site of its target genes.SMN depletion or its inhibition causes R-loop accumulationOur previous studies demonstrated that PRMT5 or SMN depletion, or POLR2A R1810 mutation leads to R-loop accumulation at the ACTB gene9. Here, we further confirmed that CRISPR/Cas9 mediated SMN knockout increased global R-loop accumulation in HEK293 cells as detected by immunofluorescence staining (Fig. 4e, f and Supplementary Fig. 15). Overexpression of RNase H1 significantly decreased the levels of R-loops in the SMN knockout cells, validating the authenticity of the R-loop signals (Supplementary Fig. 16). Similar to the SMN knockout, treatment with either compound 1 or compound 2 significantly increased R-loop levels in comparison to the DMSO controls (Fig. 4g), indicating the global effects of SMN antagonists in R-loop accumulation. Consistently, treatment of either compound 1 or compound 2 significantly increased R-loop signals at the 3′-end of the ACTB gene (Fig. 4h).DiscussionIn this study, we identified some low micromolar antagonists with a 4-iminopyridine scaffold targeting the Tudor domain of SMN, and compound 1 shows >4-fold selectivity over other tested methyllysine or methylarginine binding domains. Although the binding affinity of SMN and compound 1 is not high, SMN binds to compound 1 60–180-fold more tightly than its physiological ligands such as symmetric dimethylarginine or R1810me2s-POLR2A (Kd of 2.6 μM for compound 1 vs 476 μM for symmetric dimethylarginine22 or 175 μM for R1810me2s-POLR2A9). We then utilized different cellular on-target engagement assays to validate that compound 1 specifically recognizes SMN in a cellular context, and showed that compound 1 would prevent the interaction of SMN with R1810me2s of DNA-directed RNA polymerase II subunit POLR2A and result in transcription termination and R-loop accumulation. Hence, compound 1 is a potent and selective antagonist of SMN.Our structural and mutagenesis studies provide mechanistic insights into the selectivity of compound 1 for SMN. Our protein-compound complex structures uncover that compound 1 is an antagonist targeting methylated arginine binding protein and the sandwich stacking interactions of compound 1 by W102 and Y130 of SMN play a critical role in the compound 1 recognition. The larger binuclear ring structure of tryptophan provides a stronger π–π interaction with compound 1 than tyrosine or phenylalanine. In order to explore if mutating Y130 to tryptophan would increases its binding to compound 1 further, we made a Y130W mutant, which renders the protein to become insoluble, presumably due to steric clash around the aromatic cage. In addition, our structural study uncovers that UHRF1 used an arginine-binding pocket to specifically bind to compound 1, which indicates that the arginine-binding pocket could serve as a therapeutic venue for designing potent small molecule allosteric regulators of the UHRF1 functions.Although the causative link between SMN deficiency and SMA was established 20 years ago4, it remains elusive how deficiency of a protein, which is ubiquitously expressed and causes widespread defects in pre-mRNA splicing in cell culture and mouse models of SMA, would result in a cell-type-specific phenotype: motor neuron dysfunction23. A Drosophila model suggests that involvement of SMN in snRNP biogenesis does not explain locomotion and viability defects of Smn null mutants, implying that SMN may have other functions contributing to the etiology of SMA24. Indeed, in addition to its role in snRNP assembly, SMN is also involved in regulation of nuclear architecture by interacting with arginine methylated coilin6,7, local axonal translation in neurons by participating in miR-183/mTOR pathway8, and transcription termination by interacting with arginine methylated POLR2A9. All of these findings may have important implications for understanding the cell-specific functions of SMN, and shed light on the molecular mechanism of SMA pathology6,7,8,10. SMN was also proposed to have other functions. It interacts with the mSin3A/HDAC transcription corepressor complex and thus represses transcription in an HDAC-dependent manner25. In contrast, by interacting with the nuclear transcription activator E2 of papillomavirus, SMN positively regulates E2-dependent transcription26. The Tudor domain of SMN recognizes arginine methylated Epstein-Barr virus nuclear antigen 2 (EBNA2), the main viral transactivator of Epstein-Barr virus (EBV)4, and regulates EBV-mediated B-cell transformation27. Infection with the EBV can lead to a number of human diseases including Hodgkin’s and Burkitt’s lymphomas. SMN interacts with the fused in sarcoma (FUS) protein, a genetic factor in amyotrophic lateral sclerosis, which links the two motor neuron diseases28.In order to facilitate the elucidation of the biological functions of SMN in different pathways and molecular etiology of SMA, we set out to develop SMN-specific chemical probes, and identified compound 1, a 2.6 μM antagonist. Although compound 1 could not be claimed as a chemical probe, compound 1 and even weaker binding compound 2 bind to SMN much stronger than its physiological ligand R1810me2s-POLR2A, and our cellular studies still display that these SMN antagonists prevent SMN interaction with R1810me2s-POLR2A, resulting in the over-accumulation of active RNAP II and R-loop, mimicking depletion of SMN. These small molecule compounds specifically compete with methylated arginine for the binding pocket of SMN. Application of these small molecules has the advantage of maintaining the normal cellular SMN levels without disrupting methylarginine independent functions of SMN. Thus, in addition to the antisense, RNAi and CRISPR/Cas9 techniques, these potent SMN antagonists may be used as efficient tools in the study of SMN biology and its related neurological diseases.MethodsProtein expression and purificationThe coding DNA fragments of following Tudor domains were cloned into pET28-MHL vector: SMN (aa 82–147), UHRF1 (aa 126–285), SMNDC1 (aa 53–130), TDRD3 (aa 554–611), SND1 (aa 650–910), TDRD2 (aa 327–420), FXR1 (aa 2–132), PHF1 (aa 28–87), SGF29 (aa 115–293), JMJD2A (aa 897–1101), 53BP1 (aa 1483–1606), SETDB1 (aa 190–410), LBR (aa 1–67), ZGPAT (aa 120–271). The coding regions of chromodomain of CBX7 (aa 8–62), PWWP domain of DNMT3A (aa 275–417), WD40 repeats of WDR5 (aa 24–334) and CW domain of ZCWPW2 (aa 21–78) were also subcloned into pET28-MHL vector to generate N-terminally His-tagged fusion protein. The MBT repeats of L3MBTL1 (aa 200–522) and L3MBTL2 (aa 170–625) were subcloned into pET28GST-LIC vector to generate N-terminally GST-His-tagged fusion protein. All the plasmids were generated by ligase independent cloning (Vazyme Biotech, C112 or ABclonal Technology, RK21020). The recombinant proteins were overexpressed in E. coli BL21 (DE3) Codon plus RIL (Stratagene, 230280) at 15 °C under induction of 0.25 mM IPTG (isopropyl-β-D-thiogalactoside) and purified by affinity chromatography on Ni-nitrilotriacetate resin (Qiagen, or Nanjing Qingning Bio-Technology Co., Ltd.) followed by TEV (for the N-terminally His-tagged fusion protein) or thrombin (for the N-terminally GST-His-tagged fusion protein) protease treatment to cleave the tag. The buffer condition for Ni-affinity chromatography is as following: lysis buffer: 20 mM Tris-HCl, pH 7.5, 250 mM NaCl, 5% glycerol and 5 mM β-mercaptoethanol; wash buffer: 20 mM Tris-HCl, pH 7.5, 1 M NaCl and 40 mM imidazole; elution buffer: 20 mM Tris-HCl, pH 7.5, 250 mM NaCl and 250 mM imidazole; dialysis buffer: 20 mM Tris-HCl, pH 7.5, 150 mM NaCl and 5 mM β-mercaptoethanol. The proteins were further purified by Superdex75 or Superdex200 gel-filtration column (GE Healthcare) in a buffer containing 20 mM Tris-HCl, pH 7.5, 150 mM NaCl and 1 mM DTT. For crystallization experiments, purified proteins were concentrated to 18 mg/mL for SMN, 23 mg/mL for UHRF1 and 10 mg/mL for TDRD3 in the gel-filtration buffer. All the mutations were introduced with the QuikChange II XL site-directed mutagenesis kit (Stratagene, 200522) and confirmed by DNA sequencing. Mutant proteins were also expressed in E. coli BL21 (DE3) Codon plus RIL and purified using the same procedures described above. The molecular weight of all protein samples was measured by mass spectrometry.For mammalian expression, the coding DNAs of full-length SMN, SND1 and TDRD3 were cloned into mCherry2-C1 or GFP-C1 vector through digestions with restriction endonucleases Hind III/BamH I and ligation with T4 DNA ligase. All the mutations of full-length SMN were introduced with the QuikChange II XL site-directed mutagenesis kit (Stratagene, 200522) and confirmed by DNA sequencing. All the primers used in this research were shown in Supplementary Table 2.Small molecule fragment-based screening of UHRF1 tandem Tudor domainA small molecule fragment library with 2040 compounds was screened against TTD of UHRF1 by fluorescein polarization-based peptide displacement assay according to previous reports29. Briefly, the screening was performed in 10 μL at a protein concentration of 8 μM premixed with a 40 nM FITC-labeled H3K9me3 peptide (aa 1–25, Tufts University Core Services), and then adding a single concentration of 2 mM compound in a buffer of 20 mM Tris-HCl, pH 8.8, 50 mM NaCl, and 0.01% Triton X-100. The hits were further confirmed by dose response analysis with 1 mM as the highest concentration with 11 sequential 2-fold dilutions. All the assays were performed in duplicate in 384-well plates (Greiner, 784290), using the Synergy 4 microplate reader (BioTek), with an excitation wavelength of 485 nm and an emission wavelength of 528 nm. Data were corrected by background of the free labeled peptides and analyzed by GraphPad Prism version 5 software. All the compounds were purchased from Maybridge, Sigma or Specs company.Chemical synthesis and compound characterizationSynthesis of CCVJ and biotin conjugated compound 1 (CCVJ-Cmpd 1 and biotin-Cmpd 1) and their characterization are described in the Supplementary Methods.Isothermal titration calorimetry (ITC)For the ITC measurement, the concentrated proteins were diluted into 20 mM Tris-HCl, pH 7.5, 150 mM NaCl (ITC buffer); the lyophilized compounds were dissolved in the same buffer, and the pH value was adjusted by adding 2 M NaOH or 2 M HCl. The compounds that could not be dissolved in the ITC buffer were dissolved in DMSO with the accessible highest concentration. Compound concentrations were calculated from the mass and the volume of the solvent. For the ITC assay with compound dissolved in DMSO, the protein was diluted by ITC buffer containing same final concentration of DMSO. All measurements were performed in duplicate at 25 °C, using a VP-ITC (MicroCal, Inc.), an iTC-200 (MicroCal, Inc.), or a Nano-ITC (TA, Inc.) microcalorimeter. The protein with a concentration of 50–100 μM was placed in the cell chamber, and the compounds with a concentration of 0.5–2 mM in syringe was injected in 25, 20, or 20 successive injections with a spacing of 180, 150, or 120 s for VP-ITC, iTC-200, or Nano-ITC, respectively, as previously described30,31,32. iTC-200 or Nano-ITC data were consistent with those from the VP-ITC instrument, based on ITC results of SMN-compound 1 detected by using all the instruments. Control experiments were performed under identical conditions to determine the heat signals that arise from injection of the compounds into the buffer. Data were fitted using the single-site binding model within the Origin software 7.0 package (MicroCal, Inc.) or the independent model within the Nano-Analyze software package (TA, Inc.).Protein crystallizationFor the complex crystal of SMN-compound 1, SMN was crystallized in a buffer containing 2 M ammonium sulfate, 0.2 M potassium/sodium tartrate, 0.1 M sodium citrate, pH 5.6, and soaked with compound 1 at a molar ratio of 1:5 for 24 h. For the complex crystals of UHRF1-compound 1, SMN-compound 4/6, and TDRD3-compound 1, purified proteins were mixed with the compounds at a molar ratio of 1:5 and co-crystallized using the sitting drop vapor diffusion method at 18 °C by mixing 0.5 μL of the protein with 0.5 μL of the reservoir solution. The complex of UHRF1-compound 1 was crystallized in a buffer containing 20% PEG 3350, 0.2 M magnesium nitrate; SMN-compound 4 was crystallized in a buffer containing 1.8 M sodium acetate, pH 7.0, 0.1 M Bis-Tris propane, pH 7.0; SMN-compound 6 was crystallized in a buffer containing 2 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5; and TDRD3-compound 1 was crystallized in a buffer containing 1.2 M sodium citrate, 0.1 M Tris-HCl, pH 8.5. Before flash-freezing crystals in liquid nitrogen, crystals were soaked in a cryoprotectant consisting of 85% reservoir solution and 15% glycerol.Data collection and structure determinationThe program PHASER33 was used for molecular replacement (MR) when needed. Models were interactively rebuilt, refined and validated using COOT34, REFMAC35 and MOLPROBITY36,37 software, respectively. MarvinSketch (Chemaxon.com) was used for the calculation of some SMILES strings during preparation of small molecule geometry restraints. PDB_EXTRACT38 and CCTBX39 library were used during preparation of the crystallographic models for PDB deposition and publication. Diffraction data and model refinement statistics for the structures are displayed in Table 1. Some structure determination details for specific structures are as follows. SMN in complex with compound 1: Diffraction images were collected on a copper rotating anode source and initially reduced to merged intensities with DENZO/SCALEPACK40/AIMLESS41. For later refinement steps, data were reduced with XDS42/AIMLESS. The crystal structure was solved by placement of atomic coordinates from isomorphous PDB entry 1MHN43 in the asymmetric unit. Geometry restraints for compound 1 were prepared on the GRADE server44,45. SMN in complex with compound 4: Diffraction data were collected at APS/NE-CAT beam line 24-ID-E and reduced with XDS/AIMLESS. The structure was solved by MR with diffraction data from an additional, isomorphous crystal and coordinates from PDB entry 4QQ6 (SMN in complex with compound 1, above). Geometry restraints for compound 4 were prepared with PRODRG46. Anisotropic displacement parameters were analyzed on the PARVATI server47. SMN in complex with compound 6: Diffraction data were collected on a rotating copper anode source and reduced with XDS/AIMLESS. The structure was solved by MR with coordinates from PDB entry 4QQ6. Geometry restraints for compound 6 were prepared with ELBOW48, which in turn used MOGUL. UHRF1 in complex with compound 1: Diffraction data were collected at APS/SBC-CAT beamline 19ID and reduced to merged intensities with XDS/AIMLESS. The structure was solved by MR with coordinates derived from PDB entry 3DB349. TDRD3 in complex with compound 1: Diffraction data were collected at CLS/CMCF beamline 08ID and reduced to intensities with DENZO/SCALEPACK. Intensities were converted to the MTZ format with COMBAT50 or, alternatively, POINTLESS51 before symmetry-related intensities were merged with AIMLESS. The structure was solved by MR with coordinates from PDB entry 3PMT20.Fluorescence analysisU2OS cells (ATCC, HTB-96) were plated in a 35 mm FluoroDish with a 0.17 mm coverslip bottom (World Precision Instruments, FD35-100) for 12–24 h and transfected with 1.0 μg mCherry-SMN WT (wild-type) or mutant plasmids. Media was changed 4–6 h after transfection and cells were cultured for another 24 h. 10 μM CCVJ-Cmpd 1 was added for 24 h treatment. Then the treated cells were rinsed by PBS and the media replaced with phenol-free FluoroBright DMEM (Thermo Fisher, A1896701) for analysis by using Zeiss LSM880 microscopy.Pulldown and western blottingU2OS cells were lysed in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 7.6, 1% Triton, 0.1% sodium deoxycholate, 1 mM EDTA) containing protease inhibitors (Roche, 05892791001). The cell lysate was incubated with 20 μM biotin-Cmpd 1 overnight at 4 °C, then 30 μL streptavidin beads (Thermo Fisher, 20353) was added and incubated at 4 °C for 1 h. The beads were then washed with RIPA buffer for 3 times, 10 min/time and loading buffer was added and boiled for 5 min for elution. The eluted samples were separated by SDS-PAGE for western blotting (SMN monoclonal antibody, BD Transduction Laboratories, 610646, clone No. 8, dilution of 1:1000; TDRD3 rabbit monoclonal antibody, Cell signaling, 5492, clone No. 5492, dilution of 1:1000; SND1 polyclonal antibody, Bethyl, A302-883A, dilution of 1:2000; RFP polyclonal antibody, Abcam, ab62341, dilution of 1:1000; GFP monoclonal antibody, Santa Cruz Biotechnology, sc-9996, dilution of 1:1000; Streptavidin-Horseradish Peroxidase (HRP), Invitrogen, SA10001, dilution of 1:5000) as previously described52,53. For the competition analysis, 200 μM biotin-free compound 1 or compound 15 was added at the same time when the biotin-Cmpd 1 was incubated with the cell lysates.Affinity-purification and mass spectrometry (AP-MS)The samples for AP-MS were prepared following pulldown procedure as previously described with minor modifications54. Briefly, U2OS cells were lysed in RIPA buffer and the cell lysate was equally divided into two groups: (1) DMSO group (control group): the cell lysate was incubated with 20 μM biotin-labeled compound 1; (2) Cpmd 1 group (sample group): the cell lysate was incubated with 20 μM biotin-labeled compound 1 and 200 μM free compound 1. Each group contains three biological replicates. They were incubated overnight at 4 °C, then 30 μL streptavidin beads (Thermo Fisher, 20353) was added and incubated at 4 °C for 1 h. The beads were then washed with RIPA buffer for 3 times, 10 min/time.Beads were rinsed twice with 50 mM TEAB, pH 7.55, before eluting proteins with 25 μL of 5% SDS, 50 mM TEAB, pH 7.55. The sample was then centrifuged at 17,000 × g for 10 min to remove any debris. Proteins were reduced with 20 mM TCEP (Thermo Fisher, 77720) and incubated at 65 °C for 30 min. The sample was cooled to room temperature and 1 μL of 0.5 M iodoacetamide acid was added and allowed to react for 20 min in dark. Phosphoric acid (12%, 2.75 μL) was added to the protein solution, followed by adding 165 μL of binding buffer (90% methanol, 100 mM TEAB, pH 7.1). The resulting solution was added to S-Trap spin column (protifi.com) and passed through the column using a bench top centrifuge (30 s spin at 4000 × g). The spin column was washed with 400 μL of binding buffer and centrifuged. This step was repeated two more times. Then trypsin was added to the protein mixture at a mass ratio of 1:25 in 50 mM TEAB, pH 8.0, and the sample was incubated at 37 °C for 4 h. Peptides were eluted with 80 μL of 50 mM TEAB, followed by 80 μL of 0.2% formic acid, and finally 80 μL of 50% acetonitrile, 0.2% formic acid. The combined peptide solution was then dried in a speed vac and resuspended in 2% acetonitrile, 0.1% formic acid, 97.9% water and placed in an autosampler vial.Samples were analyzed by nanoLC-MS/MS (nanoRSLC, Thermo Fisher) using an Aurora series (Ion Opticks) reversed phase HPLC column (25 cm length × 75 µm inner diameter) and directly injected to an Orbitrap Eclipse (Thermo Fisher) using a 120 min gradient (mobile phase A = 0.1% formic acid, mobile phase B = 99.9% acetonitrile with 0.1% formic acid; hold 2% B for 5 min, 2–6% B in 0.1 min, 6–25% in 100 min, 25–50% in 15 min) at a flow rate of 350 nL/min. Eluted peptide ions were analyzed using a data-dependent acquisition (DDA) method with resolution settings of 120,000 and 15,000 (at m/z 200) for MS1 and MS2 scans, respectively. DDA-selected peptides were fragmented using stepped high energy collisional dissociation (27, 32, and 37%).The data of AP-MS were analyzed as a previously described method with minor modifications55. Briefly, the raw MS files were searched with MaxQuant software (version 1.6.1.1, www.maxquant.org)56 against the UniProt human protein database (www.uniprot.org) concatenated with common contaminants and the decoy database. The mass tolerance for precursor ions was set to 20 ppm and 4.5 ppm for the first and main search, respectively. The cysteine carbamidomethylation was set as fixed modification and methionine oxidation and N-terminal acetylation as variable modifications. Enzyme specificity was set to trypsin and a maximum missed cleavage was set as 2. The 1% false discovery rate (FDR) at both peptide and protein levels was applied for the analysis. Relative protein quantification was based on the label-free quantification incorporated in the MaxQuant software. The iBAQ intensity of proteins was obtained for the control and experimental samples. The missing iBAQ intensity was replaced by a random number, which was calculated from a normal distribution with a width of 0.3 and a downshift of 1.8 defined by Perseus software (version 1.6.5.0). The P-value was calculated by performing two-sample Student’s t-test. Log2 FC (Cmpd 1/DMSO) and −Log10 (P-value) from three biological replicates were used to construct the volcano plot using OriginPro 9.0.Cell cultureHEK293 cells (ATCC, CRL-1573) were grown in DMEM (SLRI media facility) plus 10% FBS (Sigma, F1051). For analysis of SMN chemical antagonists, HEK293 cells were treated with DMSO or a series of concentrations (0, 2, 6, 10, 20, 30, 40, and 80 μM) of compound 1, compound 2 or negative compound 15 for 72 h. CRISPR-mediated SMN1 gene knockout was performed according to our previous study9. Briefly, 2 μg of CRISPR/Cas9 plasmid (pCMV-Cas9-GFP), which expresses scrambled guide RNA, or guide RNA that targets the SMN1 gene exon1 (gRNA target sequence: ATTCCGTGCTGTTCCGGCGCGG) or exon3 (gRNA target sequence: GTGACATTTGTGAAACTTCGGG) was transfected into HEK293 cells. Cells were sorted by BD FACSAria flow cytometry at Donnelly Center, University of Toronto 24 h after transfection, and single GFP-positive cells were seeded into a 48-well plate. The expression levels of SMN in each clone were detected by immunofluorescence. The transfection of GFP-RNase H1 R-loop-binding domain (GFP-HB) for R-loop detection into HEK293 cells was performed with the FuGENE Transfection reagent (Roche, E269A).Immunoprecipitation (IP) and western blottingThe experiments were performed following procedure as previously described with minor modifications57. Briefly, HEK293 cells were subjected to three freeze-thaw cycles in high-salt lysis buffer (10 mM Tris-HCl, pH 7.9, 10% glycerol, 420 mM NaCl, 0.1% Nonidet P-40, 2 mM EDTA, 2 mM DTT, 10 mM NaF, 0.25 mM Na3VO4, and 1× protease inhibitor mixture (Sigma, P8340)), followed by centrifugation at 18,400 × g for 1 h at 4 °C to remove insoluble materials. The supernatant cell lysates were sonicated with five on and off cycles of 0.3 s/0.7 s per mL and incubated for 30 min at 4 °C with 12.5–25 units/mL benzonase nuclease (Sigma, E1014) to remove RNA and DNA, followed by centrifugation at 18,400 × g for 30 min at 4 °C. The supernatant cell lysates were incubated with 2 μg of antibody overnight at 4 °C, followed by the addition of 20 μL of Dynabeads Protein G beads (Invitrogen, 10004D) for an additional incubation for 4 h. After washing with low-salt buffer (10 mM Tris-HCl, pH 7.9, 100 mM NaCl, and 0.1% Nonidet P-40) 3 times, 10 min/time, associated proteins were eluted into protein-loading buffer and separated by Tris 4–20% SDS-polyacrylamide (Mini-PROTEAN TGX Precast Protein Gel, BioRad, 4561096), and transferred to nitrocellulose or PVDF membranes (Immu-Blot PVDF, BioRad, 1620112 or 1620177). Transferred samples were immunoblotted with primary antibodies (POLR2A, Abcam, ab5408, monoclonal antibody, clone No. 4H8; SMN, Santa Cruz Biotechnology, sc-15320, polyclonal antibody; ACTB, Sigma, A5441, monoclonal antibody, clone No. AC-15; GFP, Invitrogen, G10362, rabbit monoclonal antibody; TUBB, Santa Cruz Biotechnology, sc-9104, polyclonal antibody) at a dilution of 1:2000 to 1:5000, followed by horseradish peroxidase-conjugated goat anti-mouse or mouse anti-rabbit secondary antibody (Jackson Immuno Research, 115-035-174 or 211-032-171) at a dilution of 1:10,000. Western blot detection was performed with enhanced chemiluminescence (Pierce ECL Western Blotting Substrate, Thermo Fisher, 32209). For analysis of SMN chemical antagonists, HEK293 cells were treated with DMSO, compound 1 or compound 2 with a series of concentrations for 72 h, before being processed for IP and western blotting.Chromatin immunoprecipitation (ChIP)ChIP was performed using the EZ-ChIP™ A - Chromatin Immunoprecipitation Kit (Millipore, 17-371) according to the manufacturer’s instruction. Antibodies were used with a range of 1–2 μg, and IgG (Millipore, polyclonal antibody, 12-370) was used as a background control. After immunoprecipitation, genomic DNA was de-crosslinked in ChIP elution buffer containing 5 M NaCl at 65 °C overnight and purified with the Qiaex II kit (Qiagen, 20021), and eluted in water for PCR amplification. Immunoprecipitated and input DNAs were used as templates for qPCR. The qPCR primer sequences for ACTB gene are the same as described earlier9 and shown in the Supplementary Table 2. For analysis of SMN chemical antagonists, HEK293 cells were treated with DMSO, compound 1 or compound 2 (a final concentration of 20 μM) for 72 h, before processing for ChIP.Immunofluorescence and microscopic R-loop quantificationGlobal nuclear R-loop detection was ascertained via immunofluorescence using the S9.6 antibody (Kerafast, ENH001)58. At 24 h prior to immunofluorescence, 40,000 cells were seeded on to Poly-L-Lysine (PLL) coated coverslips. Cells were fixed using 1% formaldehyde for 15 min, washed three times with PBS, permeabilized with 0.3% Triton X-100 and washed again three times with PBS. Coverslips were blocked using 5% BSA for 1 h at room temperature and transferred to humidified chambers for antibody incubations. Coverslips were incubated with 60 μL of monoclonal S9.6 antibody (Kerafast, ENH001, 1:500) for 1 h at room temperature. After washing with PBS, cells were incubated with a secondary goat anti-mouse Alexa Fluor 488 antibody (Thermo Fisher, A11001, 1:1000) for 1 h in a dark chamber. Following further washing and DAPI staining, coverslips were mounted onto microscope slides using DAKO fluorescent mounting medium (Agilent, S302380-2) and then sealed with nail polish. For RNase H1 overexpression analysis, scramble and SMN knockout cells were seeded in 6-well plates and transfected 24 h later with 0.9 μg pcDNA3-Empty vector or pcDNA3-RNase H1. At 48 h post-transfection, cells were harvested and re-seeded onto PLL-coated coverslips. The coverslips were processed for immunofluorescence 24 h later using the primary antibodies monoclonal S9.6 (Kerafast, ENH001, 1:500), or polyclonal anti-RNase H1 (Proteintech, 15606-1-AP, 1:500) and the secondary antibodies goat anti-mouse Alexa Fluor 488 (Thermo Fisher, A11001, 1:1000) or goat anti-rabbit Alexa Fluor 568 (Thermo Fisher, A11011, 1:1000) to quantify R-loop and confirm RNase H1 overexpression, respectively. For the analysis of SMN chemical antagonists, HEK293 cells were treated with DMSO, compound 1 or compound 2 at a final concentration of 20 μM for 72 h before processing for S9.6 immunofluorescence.We employed a Nikon C2+ confocal microscope coupled to NIS-elements AR software (Nikon). For R-loop microscopy in HEK293 cells, random fields identified by DAPI staining were captured at 100× magnification. For any given image, 5–6 2D imaging planes were acquired along the z-axis to generate 3D confocal image stacks. DAPI was used to stain nuclei and S9.6 intensity values for individual cells were obtained as maximum intensity planes via the NIS-elements AR software (Nikon). Representative single-plane images from z-stacks were adjusted for background and contrast in Photoshop (Adobe).Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article.

Data availability

The coordinates and structure factors generated in this study have been deposited in the Protein Data Bank (PDB) with accession codes 4QQ6 (SMN-compound 1), 4QQD (UHRF1-compound 1), 7W2P (SMN-compound 4), 7W30 (SMN-compound 6), 6V9T (TDRD3-compound 1). The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the iProX partner repository59 with the dataset identifier PXD034927 (Identification of the target proteins for compound 1 in U2OS cells). The structural data used in this study are available in the Protein Data Bank (PDB) under accession codes 1MHN43 (SMN Tudor domain structure), 3DB349 (UHRF1-H3K9me3 complex), 3PMT20 (TDRD3 Tudor domain structure), 3ASK19 (UHRF1-H3K9me3 complex), 5YYA21 (UHRF1 bound to ethylene glycol). The uncropped and unprocessed versions of blots, all original ITC curves, synthesis and characterization of CCVJ and biotin conjugated compound 1 (CCVJ-Cmpd 1 and biotin-Cmpd 1) generated in this study are provided in the Supplementary Information and the Source Data file. Source data are provided with this paper.

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Download referencesAcknowledgementsWe thank Dr. Wolfram Tempel for data collection and structure determination, Dr. John R. Walker for reviewing some of the crystal structures, and Dr. Dalia Barsyte-Lovejoy, Dr. Magdalena M Szewczyk and Dr. Hui Peng for technical assistance. This work was supported by the National Key R&D Program of China (2019YFA0802401, G.X.), the NSERC grant RGPIN-2021-02728 (J.M.), the National Natural Science Foundation of China (32271309, Y. L. and 81773608, X.J.), the Priority Academic Program Development of the Jiangsu Higher Education Institutes (PAPD), the CPRIT grant RP180804 (M.T.B.), and the NIH grant GM126421 (M.T.B.). The Structural Genomics Consortium is a registered charity (no: 1097737) that receives funds from Bayer AG, Boehringer Ingelheim, Bristol Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute [OGI-196], EU/EFPIA/OICR/McGill/KTH/Diamond Innovative Medicines Initiative 2 Joint Undertaking [EUbOPEN grant 875510], Janssen, Merck KGaA (aka EMD in Canada and US), Pfizer and Takeda. Some diffraction experiments were performed at the Structural Biology Center and Northeastern Collaborative Access Team (NIGMS grant P30 GM124165) and Structural Biology Center beam lines at the Advanced Photon Source at Argonne National Laboratory. ANL is operated by the University of Chicago Argonne, LLC, for the U.S. Department of Energy Office of Biological and Environmental Research under contract DE-AC02-06CH11357. Diffraction experiments described in this paper were also performed by using beamline 08ID-1 at the Canadian Light Source, which is supported by the Canada Foundation for Innovation, Natural Sciences and Engineering Research Council of Canada, the University of Saskatchewan, the Government of Saskatchewan, Western Economic Diversification Canada, the National Research Council Canada, and the Canadian Institutes of Health Research. The Mass Spectrometry Facility is supported in part by Cancer Prevention Research Institute of Texas (CPRIT) grant number RP190682.Author informationAuthor notesThese authors contributed equally: Yanli Liu, Aman Iqbal, Weiguo Li, Zuyao Ni, Yalong Wang.These authors jointly supervised this work: Yanli Liu, Jinrong Min.Authors and AffiliationsJiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, ChinaYanli Liu, Jurupula Ramprasad, Mengmeng Zhang, Honglv Jiang, Xuechu Zhen, Guoqiang Xu & Xingyue JiHubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, ChinaYanli Liu, Weiguo Li & Jinrong MinStructural Genomics Consortium, University of Toronto, Toronto, ON, CanadaYanli Liu, Aman Iqbal, Weiguo Li, Su Qin, Peter Loppnau, Peter J. Brown & Jinrong MinDonnelly Centre, University of Toronto, Toronto, ON, CanadaZuyao Ni, Dorothy Yanling Zhao, Xinghua Guo & Jack F. GreenblattDepartment of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USAYalong Wang & Mark T. BedfordDepartment of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, CanadaKaran Joshua Abraham & Karim MekhailLife Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, ChinaSu QinDepartment of Physiology, University of Toronto, Toronto, ON, CanadaJinrong MinAuthorsYanli LiuView author publicationsYou can also search for this author in

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PubMed Google ScholarContributionsY.L. and W.L. purified and crystallized the proteins. A.I. conducted the fragment-based screening under the supervision of P.B.; Y.L., W.L., S.Q., and M.Z. conducted the ITC assays. Z.N., D.Y.Z, K.J.A., and X.G. performed the cellular assay under the supervision of K.M. and J.G.; Y.W. performed the fluorescence analysis and pulldown assay under the supervision of M.T.B.; J.R. synthesized the modified compounds under the supervision of X.J.; P.L. and Y.L. cloned the constructs. H.J., X.Z., and G.X. analyzed the MS data and made the associated figures. Y.L. and J.M. conceived the study and wrote the paper with substantial contributions from all the other authors.Corresponding authorsCorrespondence to

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Reprints and permissionsAbout this articleCite this articleLiu, Y., Iqbal, A., Li, W. et al. A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.

Nat Commun 13, 5453 (2022). https://doi.org/10.1038/s41467-022-33229-5Download citationReceived: 22 June 2022Accepted: 05 September 2022Published: 16 September 2022DOI: https://doi.org/10.1038/s41467-022-33229-5Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard

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