Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
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DOI：
10.1016/j.cell.2011.11.058
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发表时间：
2012-01-20
期刊：
影响因子：
64.5
通讯作者：
Odom DT
中科院分区：
文献类型：
--
作者：
Schmidt D;Schwalie PC;Wilson MD;Ballester B;Gonçalves A;Kutter C;Brown GD;Marshall A;Flicek P;Odom DT
CTCF结合位置代表在进化过程中高度受限的调控序列。为了深入了解这些DNA元件是如何在基因组中保守和传播的，我们定义了CTCF结合位点的全谱，包括33/34聚体基序，并通过比较来自6种哺乳动物的ChIP-seq数据，确定了5000多个高度保守、稳健和组织独立的CTCF结合位点。我们的数据表明，逆转录因子的激活产生了种属特异性的CTCF结合在啮齿动物，狗，负鼠，这往往在功能上作为染色质和转录绝缘子的扩展。我们发现了高度保守的CTCF结合区侧翼的重复序列，表明类似的逆转录转座子扩增发生在数亿年前。CTCF结合的重复驱动分散是哺乳动物谱系中基因组进化的基本、古老且仍然高度活跃的机制。CTCF结合位点在哺乳动物中高度保守CTCF结合的新位点由许多哺乳动物中的SINE重复序列携带古老和新生的CTCF结合事件类似地划分染色质屏障Retroelements可以在整个基因组中重新定位组织元件对六种不同哺乳动物的进化分析揭示了染色质组织者CTCF的高度保守和物种特异性结合位点。这项研究表明，逆转录酶的激活通过重新定位基因组组织元件来驱动基因组进化。
CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages. ► CTCF-binding locations are highly conserved across mammals ► New locations for CTCF binding are carried by SINE repeats in many mammals ► Ancient and newly born CTCF-binding events similarly demarcate chromatin barriers ► Retroelements can reposition organizing elements throughout the genome Evolutionary analysis of six divergent mammals uncovers both highly conserved and species-specific binding locations of the chromatin organizer, CTCF. This study reveals that activation of retroelements drives genome evolution by repositioning genome-organizing elements.
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影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
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作者：
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作者：
Kunarso, Galih;Chia, Na-Yu;Bourque, Guillaume
通讯作者：
Bourque, Guillaume
影响因子：
64.5
作者：
Kim, Tae Hoon;Abdullaev, Ziedulla K.;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
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作者：
Cuddapah, Suresh;Jothi, Raja;Zhao, Keji
通讯作者：
Zhao, Keji