title: Histone modifications facilitate the coexpression of bidirectional promoters in rice.
abstract: Bidirectional 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.
  
  
  
  Here, 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.
  
  
  
  Our 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.
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Fang
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Ximeng
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, CBS, China Agricultural University, Beijing, 100193, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: You
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Xiucai
authors.initials: X
authors.lastname: Pan
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Xiao
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Xiu-E
authors.initials: XE
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, CBS, China Agricultural University, Beijing, 100193, China. zhensu@cau.edu.cn.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Su
authors.affiliation: State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China. wzhang25@njau.edu.cn.|JiangSu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China. wzhang25@njau.edu.cn.
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
mesh_terms: D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D006657:Histones / Q000378:metabolism*; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism; D059372:Nucleotide Motifs; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D013312:Stress, Physiological
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes
keywords: Bidirectional promoters,regulation of gene expression; Coexpression; Nucleosome positioning; Oryza sativa; histone marks