title: Global epigenomic analysis indicates that epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice.
abstract: BACKGROUND
  For heterozygous genes, alleles on the chromatin from two different parents exhibit histone modification variations known as allele-specific histone modifications (ASHMs). The regulation of allele-specific gene expression (ASE) by ASHMs has been reported in animals. However, to date, the regulation of ASE by ASHM genes remains poorly understood in higher plants.
  
  
  RESULTS
  We used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL × 93-11 and GL × TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study.
  
  
  CONCLUSIONS
  Our results demonstrate that epialleles from parents can be inherited by the F1 to produce ASHMs in the F1 hybrid. Our findings indicate that ASHM-H3K36me3, rather than H3K27me3, mainly regulates ASE in hybrid rice.
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. zhibin.guo@whu.edu.cn.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. sgy0097@126.com.
authors.forename: Gaoyuan
authors.initials: G
authors.lastname: Song
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. whuliu06@163.com.
authors.forename: Zhenwei
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. chuxiefong1111@163.com.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Qu
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. chenrong891111@126.com.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. jdmay1986@126.com.
authors.forename: Daiming
authors.initials: D
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. jennifelsun@163.com.
authors.forename: Yunfang
authors.initials: Y
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. whuliuchuan@163.com.
authors.forename: Chuan
authors.initials: C
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. zhuyg@public.wh.hb.cn.
authors.forename: Yingguo
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, , Hubei Province, China. dyang@whu.edu.cn.
authors.forename: Daichang
authors.initials: D
authors.lastname: Yang
mesh_terms: D000483:Alleles; D002678:Chimera / Q000235:genetics; D057890:Epigenomics; D018506:Gene Expression Regulation, Plant; D006657:Histones / Q000378:metabolism*; D012275:Oryza / Q000145:classification / Q000235:genetics*; D011499:Protein Processing, Post-Translational
chemical_list: D006657:Histones