ArticleBMC genomics2018
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 41 citations in OpenAlex.
- Review
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- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
- PARP1 and PARG Are the Draft Horses for Polycomb-Trithorax Chromatin Regulator Machinery.Biomolecules · 2025Article
- A noncanonical role of roX RNAs in autosomal epigenetic repression.Nature communications · 2025Article
- Redesigning the Drosophila histone gene cluster: an improved genetic platform for spatiotemporal manipulation of histone function.Genetics · 2024Article
- DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs.Genome biology and evolution · 2024Article
- Assembling the RNA therapeutics toolbox.Medical review (2021) · 2024Review
- PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development.Life science alliance · 2024Article
- The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes.Nature genetics · 2024Article
- Poly(ADP-ribosyl)ating enzymes coordinate changes in the expression of metabolic genes with developmental progression.Scientific reports · 2023Article
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster.PLoS genetics · 2023Article
- Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster.Nucleic acids research · 2023Article
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.Nucleic acids research · 2023Article
- Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures.Trends in genetics : TIG · 2022Review
- Genomic and functional conservation of lncRNAs: lessons from flies.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster.Genetics · 2022Article
- A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg.PLoS genetics · 2022Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundHigh-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.
resultsThe 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.
conclusionsHigh-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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