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Plant Cell. 2018 Jan;30(1):15-36. doi: 10.1105/tpc.17.00581. Epub 2017 Dec 11.

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules.

Author information

1
Department of Biology, Emory University, Atlanta, Georgia 30322.
2
Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322.
3
Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322.
4
Department of Plant Biology and Genome Center, University of California, Davis, California 95616.
5
Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521.
6
Department of Plant Biology, University of California, Davis, California 95616.
7
University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195.
8
Department of Biology, Emory University, Atlanta, Georgia 30322 roger.deal@emory.edu.

Abstract

The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.

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