Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, 27599, USA.
Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.
BMC Genomics. 2018 Feb 21;19(1):157. doi: 10.1186/s12864-018-4510-7.
High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis.
The data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for "enhancer RNAs" (eRNAs) in defining developmental transcription programs.
High-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development.
在黑腹果蝇胚胎和细胞系中的高分辨率转录起始位点 (TSS) 作图揭示了丰富而详细的顺式和反式调控元件和因子图谱。然而，TSS 分析尚未在正交的体内环境中进行研究。在这里，我们提供了一个全面的数据集，将 TSS 动态与核小体占有率和 wandering 第三龄幼虫中的基因表达联系起来，这是一个发育阶段，其特征是为变态做准备的转录程序的大规模转变。
该数据集基于峰宽、启动子近端聚合酶暂停和顺式调控元件密度，再现了 TSS 的主要调控类别。我们证实了黑腹果蝇中发散转录单元的稀少，但也发现了显著的例外。此外，我们还鉴定了数千个在未注释的 TSS 上发生的新的起始事件，这些事件可以根据局部组蛋白修饰密度分类为功能类别。有趣的是，这些未注释的 TSS 中的一个亚类与功能验证的增强子元件重叠，这与“增强子 RNA”（eRNA）在定义发育转录程序中的调节作用一致。
高深度 TSS 作图是识别和表征低丰度和/或低稳定性 RNA 的强大策略。对发育生物体中转录起始模式的全局分析揭示了大量新的起始事件，这些事件可以识别潜在的 eRNA 以及其他对动物发育至关重要的非编码转录本。
