Piecing together cis-regulatory networks

Insights from epigenomics studies in plants

Shao-Shan Huang, Joseph Ecker

Research output: Contribution to journalArticle

Abstract

5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits.

Original languageEnglish (US)
JournalWiley Interdisciplinary Reviews: Systems Biology and Medicine
DOIs
StateAccepted/In press - Jan 1 2017

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Methylation
DNA Methylation
Epigenomics
DNA Transposable Elements
Genes
Arabidopsis
Plant Gene Expression Regulation
Transcription Factors
Histone Code
Transcriptional Silencer Elements
5-Methylcytosine
Plant Genome
Nucleic Acid Repetitive Sequences
Chemical modification
Gene Silencing
Transcription
Transcriptome
Gene expression
Histones
Machinery

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Cite this

Piecing together cis-regulatory networks : Insights from epigenomics studies in plants. / Huang, Shao-Shan; Ecker, Joseph.

In: Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 01.01.2017.

Research output: Contribution to journalArticle

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