ArticleBMC genomics2016
Histone modifications facilitate the coexpression of bidirectional promoters in rice.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.Nature communications · 2024Article
- Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice.Rice (New York, N.Y.) · 2019Article
- Genome-wide identification of histone methylation (H3K9BMC genomics · 2019Article
- DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.Epigenetics & chromatin · 2018Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However, the underlying mechanisms responsible for the coexpression of BDPs remain understudied, especially in plants.
resultsHere, we characterized chromatin features associated with rice BDPs. Several unique chromatin features were present in rice BDPs but were missing from unidirectional promoters (UDPs), including overrepresented active histone marks, canonical nucleosomes and underrepresented H3K27me3. In particular, overrepresented active marks (H3K4ac, H4K12ac, H4K16ac, H3K4me2 and H3K36me3) were truly overrepresented in type I BDPs but not in the other two BDPs, based on a Kolmogorov-Smirnov test.
conclusionsOur analyses indicate that active marks (H3K4ac, H4K12ac, H4K16ac, H3K4me3, H3K9ac and H3K27ac) may coordinate with repressive marks (H3K27me3 and H3K9me1/3) to build a unique chromatin structure that favors the coregulation of bidirectional gene pairs. Thus, our findings help to enhance the understanding of unique epigenetic mechanisms that regulate bidirectional gene pairs and may improve the manipulation of gene pairs for crop bioengineering.
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