2009 年4月，北京生命科学研究所（NIBS）邓兴旺实验室在The Plant Cell杂志在线发表题为“Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize”的文章。该文章报道了使用高通量测序技术(Solexa)对玉米基因组中四种组蛋白修饰(H3K4me3, H3K9ac, H3K36me3, H3K27me3)，DNA甲基化，mRNA和small RNA转录活性的分析。
玉米基因组草图于2008年初公布。因此，对玉米基因组的注释，表观遗传修饰，基因和各种小RNA转录活性的研究成为玉米功能基因组学领域的重要课题。本研究中，作者对四种组蛋白修饰和DNA甲基化是如何综合影响基因表达进行了系统的分析：三种组蛋白H3K4me3, H3K9ac, H3K36me3在编码蛋白的功能基因上丰度很高，而在转座子相关基因上很少，并且对基因表达起到正调控的作用；H3K27me3和DNA methylation对基因表达具有负调控的作用，并且是相互排斥的。小RNA中microRNA和siRNA的组成比例在植物不同的发育阶段是有所不同，这种差异是由mop1基因的组织特异性表达所控制：高丰度的mop1基因表达可以使24-nt siRNA比例升高；相反，低丰度mop1基因表达导致24-nt siRNA比例降低，而21-nt miRNA比例升高。本研究还发现了两类新的siRNA：一类长度为22-nt的siRNA，是由基因组中long hairpin double-stranded RNA产生，作用于基因的编码区；另一类(20~22-nt)由基因组中的短颠倒重复序列(Short inverted repeat)产生的类似于miRNA的siRNA (miRNA-like small hairpin RNA)，以反式作用的模式与基因的上下游互补链结合。
北京生命科学研究所王向峰博士和李学勇博士，耶鲁大学Axel Elling博士及中国科学院李宁博士为文章共同第一作者。北京生命科学研究所何光明博士和戚益军博士，耶鲁大学孙卉参与了ChIP-DNA，mRNA和小RNA库的构建。ChIP-Seq与RNA-Seq测序数据是由北京生命科学研究所产生，其分析工作是在耶鲁大学和哈佛大学 (X. Shirley Liu)实验室合作下完成的。北京大学彭智宇博士参与了玉米基因组功能注释工作。邓兴旺教授为该文章的通讯作者。此项研究为科技部863项目和北京市科委资助课题。（生物谷Bioon.com）
生物谷推荐原始出处：
The Plant Cell April 17, 2009; 10.1105/tpc.109.065714
Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize
Xiangfeng Wang 1, Axel A. Elling 2, Xueyong Li 3, Ning Li 4, Zhiyu Peng 5, Guangming He 6, Hui Sun 2, Yijun Qi 6, X. Shirley Liu 7, and Xing Wang Deng 8*
1 Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China; National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115
2 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
3 National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
4 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
5 Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China; Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
6 National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
7 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115
8 Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China; National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
* To whom correspondence should be addressed.
Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.
