伊成器 教授
DNA/RNA修饰与表观遗传研究组
北京大学 生命科学学院教授，博士生导师
电话：
E-mail：chengqi.yi@pku.edu.cn
1、以核酸修饰为机理的表观遗传学
2、新颖RNA修饰对小分子RNA及长链非编码RNA功能的影响及机理
3、碱基切除及核苷酸切除DNA修复通路在防止细胞衰老及癌变过程中的分子机制
RNA表观遗传研究方面：
1、实现了1-甲基腺嘌呤在全转录组水平的谱图鉴定（2016，Nature Chemical Biology）
1-甲基腺嘌呤是已知的一种存在于转运RNA（tRNA）和核糖体RNA（rRNA）上的修饰，这种甲基化修饰对这些非编码RNA的形成过程以及功能发挥有着非常重要的作用。但是，之前并没有关于1-甲基腺嘌呤在信使RNA（mRNA）的相关研究。我们课题组首次证明了1-甲基腺嘌呤在mRNA上广泛存在；同发展了高通量的1-甲基腺嘌呤的全转录组测序技术（m1A-ID-seq），并且利用这个技术，成功地鉴定了1-甲基腺嘌呤在人类细胞系（HEK293T）中的全转录组分布位点。我们通过进一步分析发现，1-甲基腺嘌呤在5’ 非翻译区 (5’ UTR)上高度富集，为后续1-甲基腺嘌呤在mRNA上的功能研究提供了一定的指导。相关工作已发表在Nature Chemical Biology杂志(DOI: 10.1038/nchembio.2040.)。
2、应邀在《Nature Methods》发表“表观转录组分析”综述 (2016, Nature Methods)
表观转录组学（epitranscriptomics，又称“RNA表观遗传学”）是近年来兴起的前沿科研领域。目前已知的转录后修饰已有一百多种，并且这当中许多修饰都能够参与真核生物基因表达的调控。在表观转录组学的研究当中，RNA修饰全转录组水平检测技术的发展至关重要。本论文对于真核生物mRNA上已知的几种主要修饰（包括N6-methyladenosine, N6,2’-O-dimethyladenosine, 5-methylcytidine, 5-hydroxylmethylcytidine, inosine, pseudouridine and N1-methyladenosine）的检测技术进行了综述，并且对目前表观转录组分析技术存在的挑战及未来的发展方向进行了展望。本期 《Nature Methods》 杂志将“表观转录组分析” （Epitranscriptome analysis）评选为2016年的年度方法；我们在该领域发表的两项化学生物学新技术（Nat. Chem. Biol. 11, 592–597 (2015) ；Nat. Chem. Biol. 12, 311–316 (2016) ）也入选了该年度方法（DOI: 10.1038/nmeth.4110）。
3、在全转录组水平检测了假尿嘧啶修饰 （2015，Nature Chemical Biology）
mRNA上的假尿嘧啶修饰及功能研究。假尿嘧啶修饰是RNA上的一种主要修饰，但对于mRNA上的假尿嘧啶修饰的机制和功能的报道非常少。通过定量质谱的方法，我们发现假尿嘧啶广泛存在于哺乳动物的mRNA中。利用化学生物学等手段，我们发展了利用小分子化合物实现特异性标记和富集假尿嘧啶的高通量测序技术 (CeU-seq)，实现了人细胞系以及小鼠（大脑与肝脏组织）全转录组水平的单碱基分辨率假尿嘧啶检测，在数千个mRNA与长非编码RNA (lncRNA)上发现了假尿嘧啶修饰。并进一步确定了多个可作用于mRNA上的假尿嘧啶合酶（其中PUS1、DKC1两种酶之前被发现与线粒体肌病、先天性角化不良等人类疾病相关），并且发现转录组中假尿嘧啶的含量与分布均会受到各种环境刺激的调控，呈现出“刺激条件特异性”的诱导修饰。为这一转录后修饰参与基因表达调控的研究提供了重要工具。相关的研究结果已经发表在Nat. Chem. Biol.上（DOI:10.1038/nchembio.1836）。
DNA表观遗传研究方面：
1、解析了哺乳动物着床前胚胎中的5-醛基胞嘧啶概貌（Cell Stem Cell，2017）
伊成器实验室和汤富酬实验室合作，在国际上首次报道了单细胞、单碱基分辨率的5-醛基胞嘧啶（5fC）谱图。哺乳动物早期胚胎发育过程中会发生剧烈的表观遗传重编程，其中包含了5-甲基胞嘧啶（5mC）的去甲基化以及重新甲基化。在5mC的主动去甲基化过程中会产生一种新颖的表观遗传学修饰5fC。在这项工作中，伊成器实验室与汤富酬实验室密切合作，开发了一种基于特异性化学标记的单细胞、单碱基分辨率的5fC测序技术（CLEVER-seq），并将其应用于小鼠着床前胚胎以及哺乳动物多能干细胞中的5fC检测。研究发现，在小鼠早期胚胎发育过程中，5fC高度动态变化并富集在基因表达调控区域。5fC在不同的胚胎发育阶段以及多能干细胞中具有高度的异质性，同时5fC的异质性在与基因表达密切相关的区域最低。另一方面，启动子区域5fC的产生先于相应基因的表达，说明在哺乳动物早期胚胎发育过程中主动去甲基化可能参与了关键基因的表达调控。这一成果2017年3月发表于Cell Stem Cell杂志（DOI: 10.1016/j.stem）。
2、揭示了抗癌药物顺铂全基因组图谱 ( Angewandte Chemie, 2016)
顺铂是临床上使用最广泛的抗癌药物之一；在实体瘤化疗中占据核心地位。顺铂发挥药效的主要机制是与肿瘤细胞基因组DNA的碱基发生交联，影响DNA转录和复制等重要过程，最终导致细胞死亡。然而，由于技术的缺乏，顺铂与基因组DNA交联的分布规律尚未得知。我们课题组利用了一个能够特异性结合因顺铂交联DNA位点的蛋白，发展了“cisplatin-seq”，对顺铂修饰的DNA进行富集测序（类似于抗体的富集）。同时，利用顺铂交联产物会阻碍DNA合成的特征，该方法实现了碱基分辨率的顺铂结合位置的检测。利用这一技术，该研究成功绘制了人肿瘤细胞全基因组顺铂交联的分布图谱。这项工作发表在Angewandte Chemie上（DOI : 10.1002/anie.201607380），并被编辑选为“Very Important Paper”。
3、解析了碱基切除修复新机制（PNAS, 2016）
DNA的碱基切除修复对于生命体至关重要。NEIL1是一种能识别并修复多重氧化损伤的DNA糖基化酶，而其识别与修复底物的机制并不清楚。为了研究NEIL1蛋白识别与修复DNA损伤的分子机制，伊成器课题组与高毅勤课题组首先通过结构生物学手段获得了NEIL1与不同底物结合的复合物的晶体结构，发现NEIL1具有一个灵活的Loop结构能够通过完全不同的构象来识别不同的底物。该研究继续通过生物化学、分子模拟等手段研究对NEIL1的偏好底物Tg的识别与催化机理进行的深入的研究，发现NEIL1能够促进底物Tg进行异构化。这种酶促进的底物异构化不仅有利于底物的特异性识别，也促进了碱基切除反应的进行。因此，该研究不但从原子水平上揭示了NEIL1特异性识别不同底物的机制，也提出了一种碱基切除修复的新机制。这项工作发表在PNAS上（DOI: 10.1073/pnas.1604591113.）。
4、开发了5-醛基胞嘧啶检测方法（Nature Methods, 2015）
甲基化在基因表达调控中起到非常重要的作用。TET蛋白介导的5mC氧化形成5hmC、5fC及5caC阐明了长期不为所知的哺乳动物基因组主动去甲基化过程的机理，但目前这些新型碱基的生物学功能却知之甚少。缺少相应的检测方法是目前的一个重要研究瓶颈。基于5fC的特殊化学结构，我们发展了一种新型的成环反应标记方法，并发现这一标记对于5fC的单碱基分辨率测序具有非常好的应用。进一步修饰反应化合物，并结合“点击化学”的方法实现了5fC DNA片段的特异性富集。高通量测序结果显示这一方法对于5fC测序非常有效。我们鉴定出至少20000个5fC富集的基因组区域，同时发现单碱基分辨率的5fC分布图与5hmC分布图是不一致的，这一结果显示出5fC碱基的独特生物学地位。相关的研究结果发表在Nat. Methods上（DOI : 10.1038/nmeth.3569.）。
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张美玲,王坤,刘晓,彭金英,伊成器. (2020)新型冠状病毒肺炎防控之表观转录组学分析。中华医学科研管理杂志，33: E002-E002.
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