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Cell Rep. 2014 Sep 25;8(6):2015-2030. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15.

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
2
Department of Biology, University of Washington, Seattle, WA 98195, USA.
3
Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, CincinnatiĀ Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
4
Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada.
5
Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada; Canadian Institute for Advanced Research (CIFAR) Program in Genetic Networks, Toronto ON M5G 1Z8, Canada.
6
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address: queitsch@uw.edu.
7
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address: jstam@uw.edu.

Abstract

Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. We mapped DNase I hypersensitive sites (DHSs) in A. thaliana seedlings and used genomic footprinting to delineate āˆ¼ 700,000 sites of in vivo transcription factor (TF) occupancy at nucleotide resolution. We show that variation associated with 72 diverse quantitative phenotypes localizes within DHSs. TF footprints encode an extensive cis-regulatory lexicon subject to recent evolutionary pressures, and widespread TF binding within exons may have shaped codon usage patterns. The architecture of A. thaliana TF regulatory networks is strikingly similar to that of animals in spite of diverged regulatory repertoires. We analyzed regulatory landscape dynamics during heat shock and photomorphogenesis, disclosing thousands of environmentally sensitive elements and enabling mapping of key TF regulatory circuits underlying these fundamental responses. Our results provide an extensive resource for the study of A. thaliana gene regulation and functional biology.

PMID:
25220462
DOI:
10.1016/j.celrep.2014.08.019
[Indexed for MEDLINE]
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