Divergent transcription is associated with promoters of transcriptional regulators.
Divergent transcription is associated with promoters of transcriptional regulators.
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DOI：
10.1186/1471-2164-14-914
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发表时间：
2013-12-23
期刊：
影响因子：
4.4
通讯作者：
Spicuglia S
中科院分区：
文献类型：
--
作者：
Lepoivre C;Belhocine M;Bergon A;Griffon A;Yammine M;Vanhille L;Zacarias-Cabeza J;Garibal MA;Koch F;Maqbool MA;Fenouil R;Loriod B;Holota H;Gut M;Gut I;Imbert J;Andrau JC;Puthier D;Spicuglia S
分化转录是哺乳动物中普遍存在的现象。例如，短的双向转录本是活性启动子的标志，而较长的转录本可以在RNA降解机制受到抑制的条件下从活性基因中检测到反义。此外，许多已知的长链非编码rna （lncRNAs）是从编码基因启动子反义转录而来的。然而，不同lncRNA/mRNA基因对转录的一般意义仍然知之甚少。在这里，我们使用高测序深度的链特异性RNA-seq来彻底鉴定编码基因启动子在小鼠原代组织中的反义转录物。我们发现相当一部分编码基因启动子维持长链非编码RNA (lncRNA)/mRNA基因对的发散转录。引人注目的是，上游反义转录与转录调控和发育相关的基因显著相关。它们的启动子与转录发育基因的启动子有几个共同的特点，包括非常大的CpG岛，在ES细胞中高度保守和表观遗传调控。深入分析揭示了这些启动子区域独特的GC偏态，同时发现相关编码基因具有较大的第一外显子，这两个基因组特征可能强制双向转录。最后，与反义转录相关的基因携带特异性H3K79me2表观遗传标记和RNA聚合酶II富集谱，与早期转录延伸率增强有关。我们得出的结论是，一类转录调控因子的启动子具有专门的转录控制机制，该机制直接耦合于宽松的双向转录。
Divergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues. We found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation. We concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription.
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影响因子：
64.8
作者：
Carrieri, Claudia;Cimatti, Laura;Gustincich, Stefano
通讯作者：
Gustincich, Stefano
影响因子：
64.5
作者：
Bhatt DM;Pandya-Jones A;Tong AJ;Barozzi I;Lissner MM;Natoli G;Black DL;Smale ST
通讯作者：
Smale ST
影响因子：
64.5
作者：
Guenther, Matthew G.;Levine, Stuart S.;Young, Richard A.
通讯作者：
Young, Richard A.
DOI：
10.1073/pnas.0910177106
发表时间：
2009-10-27
影响因子：
11.1
作者：
Adelman, Karen;Kennedy, Megan A.;Rogatsky, Inez
通讯作者：
Rogatsky, Inez
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.