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Integrative analysis of chromatin states in A rabidopsis identified potential regulatory mechanisms for natural antisense transcript production
Author(s) -
Luo Chongyuan,
Sidote David J.,
Zhang Yi,
Kerstetter Randall A.,
Michael Todd P.,
Lam Eric
Publication year - 2013
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12017
Subject(s) - chromatin , biology , epigenome , epigenetics , context (archaeology) , genetics , epigenomics , computational biology , histone , nat , dna methylation , chromatin immunoprecipitation , gene , gene expression , promoter , computer science , paleontology , computer network
Summary Genome‐wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the construction of functionally relevant hypotheses from correlative patterns and the rigorous testing of these hypotheses may be challenging. We combined bioinformatics‐driven hypothesis building with mutant analyses to identify potential epigenetic mechanisms using the model plant A rabidopsis thaliana . Genome‐wide maps of nine histone modifications produced by Ch IP ‐seq were used together with a strand‐specific RNA ‐seq dataset to profile the epigenome and transcriptome of A rabidopsis. Combinatorial chromatin patterns were described by 42 major chromatin states with selected states validated using the re‐ChIP assay. The functional relevance of chromatin modifications was analyzed using the AN chored COR relative P attern ( ANCORP ) method and a newly developed state‐specific effects analysis ( SSEA ) method, which interrogates individual chromatin marks in the context of combinatorial chromatin states. Based on results from these approaches, we propose the hypothesis that cytosine methylation (5m C ) and histone methylation H 3 K 36me may synergistically repress production of natural antisense transcripts ( NAT s) in the context of actively expressed genes. Mutant analyses supported this proposed model at a significant proportion of the tested loci. We further identified polymerase‐associated factor as a potential repressor for NAT abundance. Although the majority of tested NAT s were found to localize to the nucleus, we also found evidence for cytoplasmically partitioned NAT s. The significance of the subcellular localization of NAT s and their biological functions remain to be defined.