Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster

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  • Meers, Michael P
    • Affiliation: School of Medicine, Department of Genetics
  • Adelman, Karen
    • Other Affiliation: Harvard Medical School
  • Duronio, Robert
    • Affiliation: School of Medicine, Department of Genetics
  • Strahl, Brian
    • Affiliation: School of Medicine, Curriculum in Genetics and Molecular Biology
  • McKay, Daniel
    • Affiliation: School of Medicine, Department of Genetics
  • Matera, Gregory
    • Affiliation: School of Medicine, Department of Genetics
Abstract
  • Background 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. Results 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. Conclusions 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.
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  • Article
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  • In Copyright
Rights holder
  • The Author(s).
Journal title
  • BMC Genomics
Journal volume
  • 19
Journal issue
  • 1
Language
  • English
Bibliographic citation
  • BMC Genomics. 2018 Feb 21;19(1):157
Publisher
  • BioMed Central

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