ArticleNature communications2018
Determinants of promoter and enhancer transcription directionality in metazoans.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- The molecular basis of transcription initiation by RNA polymerase II.Nature reviews. Molecular cell biology · 2026Review
- Dual promoter-enhancer activities reflect a unified regulatory logic.Nature communications · 2026Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation.Cell genomics · 2025Article
- A single high-zinc activation enhancer can control two genes oriented head-to-head in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2025Article
- Dissecting thebioRxiv : the preprint server for biology · 2024Article
- Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage.iScience · 2024Article
- mRNA initiation and termination are spatially coordinated.bioRxiv : the preprint server for biology · 2024Article
- Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.Cell genomics · 2022Article
- Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads.Molecular biology and evolution · 2021Article
- FAM72, Glioblastoma Multiforme (GBM) and Beyond.Cancers · 2021Review
- Episodes of Rapid Recovery of the Functional Activity of theFrontiers in genetics · 2021Article
- Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.Nature communications · 2020Article
- Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions.Nature communications · 2020Article
- Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs.Transcription · 2020Review
- Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation.Molecular biology and evolution · 2020Article
- A Novel Divergent Gene Transcription Paradigm-the Decisive, Brain-Specific, Neural |-Srgap2-Fam72a-| Master Gene Paradigm.Molecular neurobiology · 2019Article
- Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription.Transcription · 2019Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Divergent transcription from promoters and enhancers is pervasive in many species, but it remains unclear if it is a general feature of all eukaryotic cis regulatory elements. To address this, here we define cis regulatory elements in C. elegans, D. melanogaster and H. sapiens and investigate the determinants of their transcription directionality. In all three species, we find that divergent transcription is initiated from two separate core promoter sequences and promoter regions display competition between histone modifications on the + 1 and -1 nucleosomes. In contrast, promoter directionality, sequence composition surrounding promoters, and positional enrichment of chromatin states, are different across species. Integrative models of H3K4me3 levels and core promoter sequence are highly predictive of promoter and enhancer directionality and support two directional classes, skewed and balanced. The relative importance of features to these models are clearly distinct for promoters and enhancers. Differences in regulatory architecture within and between metazoans are therefore abundant, arguing against a unified eukaryotic model.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.