Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.
Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.
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DOI：
10.1186/s12864-018-4697-7
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发表时间：
2018-05-02
期刊：
影响因子：
4.4
通讯作者：
Galande S
中科院分区：
文献类型：
--
作者：
Jangid RK;Kelkar A;Muley VY;Galande S
与单向启动子相反，单向启动子的反义转录导致短转录本迅速降解，双向启动子在正义和反义方向上都产生成熟转录本。为了了解双向转录调控的分子机制，我们重点描述了双向启动子的染色质特征。我们报告了一个报告系统的产生和效用，该系统可以同时对相反方向的转录活性进行评分。在该系统中测试假定的双向启动子表明没有可测量的偏向于任何一个方向的转录。我们分析了NUP26L-PIH1D3双向基因对在维甲酸介导的胚胎癌细胞分化过程中的作用。在它们的原生环境中，我们观察到，在一对双向基因之间的转录调控区域及其周围的染色质景观与这对基因中每个基因的转录活性一致被调节。然后，我们使用公开的ChIP-Seq和RNA-Seq数据将该分析扩展到两种不同细胞系（H1人胚胎干细胞和CD4阳性T细胞）中的974对双向基因对。双向基因对的分类基于所分析转录本的两个TSS之间的基因间距离以及每个转录本在双向基因对中的相对表达量。我们报道，在整个基因间距离分离双向基因的范围内，这些基因的表达谱（对称或不对称）与主动转录起始和延伸相关标记的组蛋白修饰谱相匹配。我们展示了组蛋白修饰标记的独特分布，这些标记与双向启动子调控的基因的转录状态密切相关。这些发现强烈暗示，这些标记的出现可能表明转录机制驱动双向启动子的反义转录成熟。本文的在线版本（10.1186/s12864-018-4697-7）包含补充材料，授权用户可以使用。
In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is regulated, we focused on delineating the chromatin signature of bidirectional promoters. We report generation and utility of a reporter system that enables simultaneous scoring of transcriptional activity in opposite directions. Testing of putative bidirectional promoters in this system demonstrates no measurable bias towards any one direction of transcription. We analyzed the NUP26L-PIH1D3 bidirectional gene pair during Retinoic acid mediated differentiation of embryonic carcinoma cells. In their native context, we observed that the chromatin landscape at and around the transcription regulatory region between the pair of bidirectional genes is modulated in concordance with transcriptional activity of each gene in the pair. We then extended this analysis to 974 bidirectional gene pairs in two different cell lines, H1 human embryonic stem cells and CD4 positive T cells using publicly available ChIP-Seq and RNA-Seq data. Bidirectional gene pairs were classified based on the intergenic distance separating the two TSS of the transcripts analyzed as well as the relative expression of each transcript in a bidirectional gene pair. We report that for the entire range of intergenic distance separating bidirectional genes, the expression profile of such genes (symmetric or asymmetric) matches the histone modification profile of marks associated with active transcription initiation and elongation. We demonstrate unique distribution of histone modification marks that correlate robustly with the transcription status of genes regulated by bidirectional promoters. These findings strongly imply that occurrence of these marks might signal the transcription machinery to drive maturation of antisense transcription from the bidirectional promoters. The online version of this article (10.1186/s12864-018-4697-7) contains supplementary material, which is available to authorized users.
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影响因子：
2.6
作者：
Lejard, Veronique;Rebours, Emmanuelle;Rocha, Dominique
通讯作者：
Rocha, Dominique
DOI：
10.1126/science.1162253
发表时间：
2008-12-19
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
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3
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Elnitski L
影响因子：
7
作者：
Lin, Jane M.;Collins, Patrick J.;Weng, Zhiping
通讯作者：
Weng, Zhiping
影响因子：
64.5
作者：
Goldberg, Aaron D.;Allis, C. David;Bernstein, Emily
通讯作者：
Bernstein, Emily