Cell Discov:复旦、浙大团队分别发文报道m6A调控新机制——杨运桂点评

2018-03-16 BioArt BioArt

过去的六七年间,对于真核生物mRNA上最为广泛的修饰m6A来说,围绕该修饰的一系列甲基化转移酶复合物、去甲基化转移酶和识别蛋白以及相关的生物学功能来说已经研究得相对较为透彻,然而这类研究多数还只是停留展示可调控m6A修饰水平变化,并没有回答m6A修饰如何实现位点选择性的分子机制。近日,来自复旦大学、浙江大学以及芝加哥大学等单位相继发表的两篇论文为深入研究以m6A修饰为核心的表观转录组学特征和规律奠

过去的六七年间,对于真核生物mRNA上最为广泛的修饰m6A来说,围绕该修饰的一系列甲基化转移酶复合物、去甲基化转移酶和识别蛋白以及相关的生物学功能来说已经研究得相对较为透彻,然而这类研究多数还只是停留展示可调控m6A修饰水平变化,并没有回答m6A修饰如何实现位点选择性的分子机制。近日,来自复旦大学、浙江大学以及芝加哥大学等单位相继发表的两篇论文为深入研究以m6A修饰为核心的表观转录组学特征和规律奠定了基础。BioArt特别邀请到了中科院基因组研究所杨运桂研究员做点评,以飨读者!

m6A修饰是真核生物mRNA上发生最为广泛的内部化学修饰(m6A/A, 0.3~0.5%),参与调控mRNA稳定性、剪接加工、转运以及翻译等一系列mRNA代谢过程,对mRNA的命运决定发挥重要作用。越来越多的科学证据显示,mRNA化学修饰,尤其是甲基化修饰可调控基因表达,参与细胞分化、生物个体发育及癌症疾病等重要生命过程,该领域被称为RNA表观遗传学或表观转录组学。RNA表观遗传学是由华人科学家芝加哥大学何川教授引领和发展的,值得一提的是2011年他的课题组在Nature Chemical Biology上报道发现第一个mRNA m6A去甲基化酶FTO, 证明了m6A修饰是动态可逆的,掀起了该领域研究的热潮。

哺乳动物细胞内约25%的mRNA有m6A修饰,这些修饰主要集中在成熟的mRNA 3’端非编码区和近终止密码子区,但迄今为止该修饰的特异选择性机理是未知的。上世纪90年代有研究报道预测m6A甲基转移酶复合物大于1000 kDa, 并鉴定出METTL3(当时称为MTA70)这个组分,该蛋白可结合辅助因子SAM,是甲基化所需要的重要因子。之后相继报道了WTAP同源物在酵母、果蝇和拟南芥中和METTL3同源物有相互作用,影响m6A甲基化修饰形成。2014年,何川教授课题组和中科院杨运桂教授课题组等4个国内外课题组独立报道了哺乳动物细胞甲基转移酶复合物的一个重要成分METTL14,体内外实验证明METTL3和METTL14形成异源二聚体,二者协同催化m6A甲基化,而单独成分则活性较低。低等真核生物中只有一个METTL3甲基转移酶同源物,这是高等真核生物不同于低等真核生物的一个重要特征。METTL3/METTL14/WTAP被认为是m6A甲基转移酶复合物的核心组分, VIRMA (KIAA1429/VIRILIZER)、ZFP217、RBM15、RBM15B、HAKAI (CBLL1) 等蛋白也相继被报道与METTL3/METTL14/WTAP有互作关联,并可调节m6A的动态水平。

尽管取得上述进展,但是最上游m6A甲基转移酶调控复合物的组成以及相应的特异性修饰调控机制依然不完全清楚。日前,复旦大学刁建波、施扬、石雨江课题组和浙江大学的刘建钊课题组联合芝加哥大学何川课题组分别在Molecular Cell和Cell Discovery上发表文章 “Zc3h13 regulates nuclear RNA m6A methylation and mouse embryonic stem cell self-renewal ”和“VIRMA mediates preferential m6A mRNA methylation in 3’UTR and near stop codon and associates with alternative polyadenylation”,报道了ZC3H13(~200 KDa)和VIRMA(~200 KDa)对 m6A的选择性调控机制。

浙江大学高分子科学与工程学系刘建钊课题组联合何川教授课题组于2月27日在线发表于Cell Discovery上的工作,从已知METTL3/METTL14/WTAP出发,用蛋白组学的方法对整个甲基转移酶复合物进行表征,找出与三者共同作用的蛋白交集,然后用western blot和siRNA筛选的方法选取出对m6A水平影响明显的蛋白。他们发现METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13是整个甲基转移酶复合物最核心的部分(此外还鉴定了一些其他成分TRIM28和HNRNPH等),而VIRMA是所有表征组分中影响m6A水平最显着的。

论文的并列第一作者为博士后岳亚男、刘君、崔晓龙和博士研究生曹婕,浙江大学刘建钊研究员和芝加哥大学何川教授为论文共同通讯作者

敲低VIRMA导致的mRNA上3’端非编码区和近终止密码子区m6A水平降低最显着,同时WTAP蛋白水平降低,但恢复WTAP蛋白水平并不能消除上述影响。报告基因系统实验表明, VIRMA的N端具有招募甲基转移酶催化核心METTL3/METTL14/WTAP实现mRNA上定点m6A水平调控的能力。同时作者发现VIRMA可与mRNA末端poly(A)加工因子CPSF5有依赖于RNA的相互作用,敲低CPSF5后HeLa细胞内有2800多种mRNA的3’端非编码区变短, 并且这些mRNA中高达84%含有m6A修饰。VIRMA和METTL3部分敲除的细胞中有数百个共同靶基因mRNA的3’端非编码区变长。这些现象显示了mRNA上m6A的修饰与其选择性添加poly(A)尾巴(Alternative polyadenylation)间存在调控的联系,相关机理正在研究之中。

此前, Andrew Emili实验室的研究表明ZC3H13-WTAP-VIRILIZER-HAKAI是一个进化上保守的复合物。然而尽管WTAP、VIRILIZER和HAKAI都有报道表明和m6A的水平相关,但是关于ZC3H13的作用以及ZC3H13-WTAP-VIRILIZER-HAKAI复合物成分如何协同调控mRNA上m6A修饰的过程并不清楚。

3月16日,复旦大学生物医学研究院刁建波、施扬、石雨江团队和何川教授的合作发表在Molecular Cell杂志上的研究揭示ZC3H13可以直接调控 RNA m6A修饰。

论文的并列第一作者为博士研究生温菁、吕瑞途和博士后马红辉,复旦大学刁建波副研究员、施扬教授、石雨江教授和芝加哥大学何川教授为论文并列通讯作者。

他们的工作显示在小鼠胚胎干细胞中抑制Zc3h13能够降低60-70%的mRNA m6A水平,这些m6A的下降主要发生在mRNA的3’端非编码区域。在探讨Zc3h13对m6A调控的分子机制研究中,作者发现敲低Zc3h13对m6A的调节是通过控制WTAP/Virilizer/Hakai的细胞定位而发生作用的。敲低Zc3h13导致复合物成员WTAP、Virilizer及Hakai蛋白发生由细胞核向细胞质的转移,同时伴随甲基转移酶Mettl3和Mettl14核内组分的减少,从而抑制m6A的形成。与该复合物中其他组分WTAP、Virilizer、Hakai不同的是,Zc3h13的核内定位不受这些组分的调节,这提示了Zc3h13在该复合物的细胞定位中具有独特作用。此外,作者还发现敲低Zc3h13会损害小鼠胚胎干细胞的自我更新潜能并促进细胞的分化,这为m6A途径调节小鼠胚胎干细胞的多潜能性提供了进一步的证据和线索。

专家点评杨运桂(中科院基因组所研究员,国家杰青)

日前以m6A修饰为引擎的表观转录组学引领了表观遗传学发展的新浪潮。何川/刘建钊和施扬/刁建波/石雨江合作团队近期报道了VIRMA和ZC3H13作为m6A甲基转移酶复合物新组分,调控mRNA 上m6A位点修饰的选择性,为揭示m6A发生调控机制提供了新的线索。回顾发展势头迅猛的m6A领域,何川教授2011年发现FTO作为第一个mRNA m6A去甲基化酶的研究成果无疑最具有开创性,首次证明了m6A修饰类似于DNA修饰,具有动态可逆性,奠定了表观转录组学基础。而m6A甲基转移酶复合物核心成分的鉴定,对于揭示RNA甲基化特征和调控规律至关重要。2014年包括何川团队和我的团队在内的四个实验室独立报道了m6A甲基转移酶复合物核心催化成分METTL3/METTL14/WTAP,后续多个实验室相继报道VIRMA(KIAA1429/VIRILIZER)、ZFP217、RBM15、RBM15B、HAKAI (CBLL1)等蛋白与METTL3/METTL14/WTAP相互作用,但这类研究多数展示可调控m6A修饰水平变化,没有回答m6A修饰如何实现位点选择性机制。在刚刚发表这两篇研究中,作者发现VIRMA招募甲基转移酶催化核心METTL3/METTL14/WTAP,从而实现mRNA上m6A修饰的位点选择发生及调控mRNA末端非编码区长度(alternative polyadenylation)新现象;而Zc3h13能够调控Wtap/Virilizer/Hakai/Mettl3/Mettl14复合物在细胞内的定位及小鼠胚胎干细胞的自我更新和分化能力。这两项成果为深入研究以RNA甲基化修饰为核心的表观转录组学特征和规律奠定了基础。

原始出处:
[1]Yue Y, Liu J, Cui X,et al.VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation.Cell Discov. 2018 Feb 27;4:10. doi: 10.1038/s41421-018-0019-0. eCollection 2018.
[2]Jing Wen, Ruitu Lv, Honghui Ma, et al.Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic Stem Cell Self-Renewal.Molecular Cell.Volume 69, Issue 6, p1028–1038.e6, 15 March 2018

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    2018-08-19 kcb077
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    2018-03-18 saikp
  6. [GetPortalCommentsPageByObjectIdResponse(id=2012610, encodeId=7a4e201261009, content=<a href='/topic/show?id=7d69598468' target=_blank style='color:#2F92EE;'>#Dis#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=30, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=5984, encryptionId=7d69598468, topicName=Dis)], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=c689267, createdName=cmj8wellington, createdTime=Sun Sep 09 06:17:00 CST 2018, time=2018-09-09, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1647766, encodeId=174f164e766e0, content=<a href='/topic/show?id=ac501119586' target=_blank style='color:#2F92EE;'>#m6A#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=37, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=11195, encryptionId=ac501119586, topicName=m6A)], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=e88323484130, createdName=kcb077, createdTime=Sun Aug 19 00:17:00 CST 2018, time=2018-08-19, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1870509, encodeId=a6be18e05099b, content=<a href='/topic/show?id=fd764459a8' target=_blank style='color:#2F92EE;'>#Cell#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=27, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=4459, encryptionId=fd764459a8, topicName=Cell)], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=524d95, createdName=zhaozhouchifen, createdTime=Fri Jun 01 05:17:00 CST 2018, time=2018-06-01, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1536000, encodeId=753315360001a, content=<a href='/topic/show?id=67446550602' target=_blank style='color:#2F92EE;'>#浙大#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=30, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=65506, encryptionId=67446550602, topicName=浙大)], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=42f112649926, createdName=pandamao2014, createdTime=Sun Mar 18 05:17:00 CST 2018, time=2018-03-18, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1538533, encodeId=33b1153853388, content=<a href='/topic/show?id=751e42660f1' target=_blank style='color:#2F92EE;'>#复旦#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=30, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=42660, encryptionId=751e42660f1, topicName=复旦)], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=e6c312994908, createdName=saikp, createdTime=Sun Mar 18 05:17:00 CST 2018, time=2018-03-18, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1587841, encodeId=2eb0158e84119, content=<a href='/topic/show?id=cb1e1006ebd' target=_blank style='color:#2F92EE;'>#ISC#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=27, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=10067, encryptionId=cb1e1006ebd, topicName=ISC)], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=173417575755, createdName=yankaienglish, createdTime=Sun Mar 18 05:17:00 CST 2018, time=2018-03-18, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1960777, encodeId=83f31960e777f, content=<a href='/topic/show?id=dbe6445416' target=_blank style='color:#2F92EE;'>#CEL#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=25, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=4454, encryptionId=dbe6445416, topicName=CEL)], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=c3ff68, createdName=维他命, createdTime=Sun Apr 29 01:17:00 CST 2018, time=2018-04-29, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=296822, encodeId=2518296822cf, content=谢谢分享学习, beContent=null, objectType=article, channel=null, level=null, likeNumber=63, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/Q3auHgzwzM4o2XVpJ6449yqDsjibydI5HnJ8MibGxNn4HZiaZib0bdfibbwoz3KQrIyN9AGxq36ZlZRNicYlPfOOWMtwgsajY6mGNFiaPclFdowjD0/0, createdBy=97bd1338592, createdName=清风拂面, createdTime=Fri Mar 16 15:42:25 CST 2018, time=2018-03-16, status=1, ipAttribution=)]
    2018-03-18 yankaienglish
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    2018-04-29 维他命
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    2018-03-16 清风拂面

    谢谢分享学习

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