Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.
Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.
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DOI：
10.1186/s12864-018-4504-5
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发表时间：
2018-02-26
期刊：
影响因子：
4.4
通讯作者：
Thompson EM
中科院分区：
文献类型：
--
作者：
Danks GB;Navratilova P;Lenhard B;Thompson EM
发育在很大程度上是由转录程序之间的转换驱动的。在基因组中的适当位点开始转录是这一过程的关键组成部分，但很少有人知道管理选择的规则。在这里，我们使用帽分析基因表达（CAGE）生成bp分辨率地图的转录起始位点（TSS）在基因组的Oikopleura dioica，一个成员的最近的生活亲属脊椎动物。我们的TSS图谱揭示了与脊椎动物共同的启动子特征，以及显著的差异，并揭示了核心启动子元件在发育调控中的关键作用。在精子发生过程中，转录起始模式发生了全基因组范围的转变，其特征在于新的核心启动子元件。该元件与> 70%的雄性特异性转录相关，包括操纵子内隐藏的内部启动子的使用。在许多情况下，这导致了反式剪接位点的排除，揭示了一种新的机制来调节哪些mRNA接受剪接的前导序列。结合的细胞周期调节剂，E2 F1，是丰富的内循环护士核中的母源基因的TSS。此外，母体启动子缺乏斑马鱼中发现的TATA样元件，并且具有广泛的而不是尖锐的有序核小体结构。核糖体蛋白基因的启动子缺乏高度保守的TCT起始子。我们还报告了转录基因体上的DNA甲基化与TATA盒之间的关联。我们的研究结果表明，不同的功能启动子类别和重叠的启动子代码存在于原脊索动物一样，在脊椎动物，但显示出非凡的谱系特异性创新。此外，我们发现了一个全基因组的，特定的发展阶段的TSS选择模式的转变。我们的研究结果为后生动物启动子结构和进化的研究提供了丰富的资源。本文的在线版本（10.1186/s12864-018-4504-5）包含补充材料，可供授权用户使用。
Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa. The online version of this article (10.1186/s12864-018-4504-5) contains supplementary material, which is available to authorized users.
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