2009 年4月，北京生命科學(xué)研究所（NIBS）鄧興旺實(shí)驗(yàn)室在The Plant Cell雜志在線發(fā)表題為“Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize”的文章,。該文章報(bào)道了使用高通量測(cè)序技術(shù)(Solexa)對(duì)玉米基因組中四種組蛋白修飾(H3K4me3, H3K9ac, H3K36me3, H3K27me3),，DNA甲基化，mRNA和small RNA轉(zhuǎn)錄活性的分析,。

玉米基因組草圖于2008年初公布,。因此，對(duì)玉米基因組的注釋?zhuān)碛^遺傳修飾,，基因和各種小RNA轉(zhuǎn)錄活性的研究成為玉米功能基因組學(xué)領(lǐng)域的重要課題,。本研究中，作者對(duì)四種組蛋白修飾和DNA甲基化是如何綜合影響基因表達(dá)進(jìn)行了系統(tǒng)的分析：三種組蛋白H3K4me3, H3K9ac, H3K36me3在編碼蛋白的功能基因上豐度很高,，而在轉(zhuǎn)座子相關(guān)基因上很少,，并且對(duì)基因表達(dá)起到正調(diào)控的作用；H3K27me3和DNA methylation對(duì)基因表達(dá)具有負(fù)調(diào)控的作用,，并且是相互排斥的,。小RNA中microRNA和siRNA的組成比例在植物不同的發(fā)育階段是有所不同，這種差異是由mop1基因的組織特異性表達(dá)所控制：高豐度的mop1基因表達(dá)可以使24-nt siRNA比例升高,；相反,，低豐度mop1基因表達(dá)導(dǎo)致24-nt siRNA比例降低，而21-nt miRNA比例升高,。本研究還發(fā)現(xiàn)了兩類(lèi)新的siRNA：一類(lèi)長(zhǎng)度為22-nt的siRNA,，是由基因組中l(wèi)ong hairpin double-stranded RNA產(chǎn)生，作用于基因的編碼區(qū),；另一類(lèi)(20~22-nt)由基因組中的短顛倒重復(fù)序列(Short inverted repeat)產(chǎn)生的類(lèi)似于miRNA的siRNA (miRNA-like small hairpin RNA),，以反式作用的模式與基因的上下游互補(bǔ)鏈結(jié)合。

北京生命科學(xué)研究所王向峰博士和李學(xué)勇博士,，耶魯大學(xué)Axel Elling博士及中國(guó)科學(xué)院李寧博士為文章共同第一作者,。北京生命科學(xué)研究所何光明博士和戚益軍博士，耶魯大學(xué)孫卉參與了ChIP-DNA，mRNA和小RNA庫(kù)的構(gòu)建,。ChIP-Seq與RNA-Seq測(cè)序數(shù)據(jù)是由北京生命科學(xué)研究所產(chǎn)生,，其分析工作是在耶魯大學(xué)和哈佛大學(xué) (X. Shirley Liu)實(shí)驗(yàn)室合作下完成的。北京大學(xué)彭智宇博士參與了玉米基因組功能注釋工作,。鄧興旺教授為該文章的通訊作者,。此項(xiàng)研究為科技部863項(xiàng)目和北京市科委資助課題。（生物谷Bioon.com）

生物谷推薦原始出處：

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.