ArticleScientific reports2016
Functional characterization of open chromatin in bidirectional promoters of rice.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- H3K4me1 directs H3K36me2 and H3K36me3 deposition in land plants.Nature communications · 2026Article
- Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin.Scientific reports · 2023Article
- Article
- Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice.Nucleic acids research · 2022Article
- Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription.Plant physiology · 2022Article
- Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions.The Plant cell · 2021Article
- The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice.Frontiers in plant science · 2021Article
- 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
- H3K4me2 functions as a repressive epigenetic mark in plants.Epigenetics & chromatin · 2019Article
- Global Quantitative Mapping of Enhancers in Rice by STARR-seq.Genomics, proteomics & bioinformatics · 2019Article
- Histone modifications facilitate the coexpression of bidirectional promoters in rice.BMC genomics · 2016Article
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Authors and funding
8 authors.
Funding
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Abstract
Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.
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