Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.
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DOI：
10.1016/j.molcel.2011.08.027
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发表时间：
2011-11-18
期刊：
影响因子：
16
通讯作者：
Chang HY
中科院分区：
文献类型：
--
作者：
Chu C;Qu K;Zhong FL;Artandi SE;Chang HY
长基因间非编码RNA（lincRNA）是染色质状态的关键调节因子，但RNA-染色质相互作用的性质和位点大多是未知的。在这里，我们介绍通过RNA纯化的染色质分离（ChIRP），其中平铺寡核苷酸检索具有结合的蛋白质和DNA序列的特定lincRNA，其通过深度测序进行计数。三种lincRNA的ChIRP-seq揭示了基因组中的RNA占据位点是局灶性的、序列特异性的和众多的。果蝇roX 2 RNA占据雄性X连锁基因体，向3'端的趋势增加，在CES位点达到峰值。人端粒酶RNA TERC占据端粒和Wnt通路基因。HOTAIR lincRNA优先占据富含GA的DNA基序，以使Polycomb占据和组蛋白H3赖氨酸27三甲基化的广泛结构域成核。HOTAIR占据独立于EZH 2发生，表明Polycomb占据的RNA指导顺序。ChIRP-seq通常适用于以新发现的全基因组精确度阐明RNA和染色质的交叉。
Long intergenic noncoding RNAs (lincRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lincRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lincRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3’ end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lincRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome-wide.
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影响因子：
64.5
作者：
Alekseyenko AA;Peng S;Larschan E;Gorchakov AA;Lee OK;Kharchenko P;McGrath SD;Wang CI;Mardis ER;Park PJ;Kuroda MI
通讯作者：
Kuroda MI
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Park, Jae-Il;Venteicher, Andrew S.;Hong, Ji Yeon;Choi, Jinkuk;Jun, Sohee;Shkreli, Marina;Chang, Woody;Meng, Zhaojing;Cheung, Peggie;Ji, Hong;McLaughlin, Margaret;Veenstra, Timothy D.;Nusse, Roel;McCrea, Pierre D.;Artandi, Steven E.
通讯作者：
Artandi, Steven E.
影响因子：
64.5
作者：
Kelley, RL;Meller, VH;Kuroda, MI
通讯作者：
Kuroda, MI
影响因子：
5.3
作者：
Horard, B;Tatout, C;Pirrotta, V
通讯作者：
Pirrotta, V