ArticleBMC genomics2015
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics.Genomics, proteomics & bioinformatics · 2025Article
- Molecular models of bidirectional promoter regulation.Current opinion in structural biology · 2024Review
- CTCF blocks antisense transcription initiation at divergent promoters.Nature structural & molecular biology · 2022Article
- Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense-Antisense Gene Pair in Human Cancers.Non-coding RNA · 2022Article
- Co-regulation and function ofeLife · 2021Article
- A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization.Molecular cell · 2021Article
- Genome-wide identification of histone methylation (H3K9BMC genomics · 2019Article
- Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.Epigenetics & chromatin · 2018Article
- Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities.Nucleic acids research · 2018Article
- Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.BMC genomics · 2018Article
- Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.Genome biology · 2017Article
- Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.Genome biology · 2017Article
- Histone modifications facilitate the coexpression of bidirectional promoters in rice.BMC genomics · 2016Article
- Functional characterization of open chromatin in bidirectional promoters of rice.Scientific reports · 2016Article
- The Determinants of Directionality in Transcriptional Initiation.Trends in genetics : TIG · 2016Review
- CTCF: making the right connections.Genes & development · 2016Review
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Authors and funding
3 authors.
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Abstract
backgroundSeveral post-translational histone modifications are mainly found in gene promoters and are associated with the promoter activity. It has been hypothesized that histone modifications regulate the transcription, as opposed to the traditional view with transcription factors as the key regulators. Promoters of most active genes do not only initiate transcription of the coding sequence, but also a substantial amount of transcription of the antisense strand upstream of the transcription start site (TSS). This promoter feature has generally not been considered in previous studies of histone modifications and transcription factor binding.
resultsWe annotated protein-coding genes as bi- or unidirectional depending on their mode of transcription and compared histone modifications and transcription factor occurrences between them. We found that H3K4me3, H3K9ac, and H3K27ac were significantly more enriched upstream of the TSS in bidirectional genes compared with the unidirectional ones. In contrast, the downstream histone modification signals were similar, suggesting that the upstream histone modifications might be a consequence of transcription rather than a cause. Notably, we found well-positioned CTCF and RAD21 peaks approximately 60-80 bp upstream of the TSS in the unidirectional genes. The peak heights were related to the amount of antisense transcription and we hypothesized that CTCF and cohesin act as a barrier against antisense transcription.
conclusionsOur results provide insights into the distribution of histone modifications at promoters and suggest a novel role of CTCF and cohesin as regulators of transcriptional direction.
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