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

TitleMapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.
Publication TypeJournal Article
Year of Publication2014
AuthorsSullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB
JournalCell reports
Date Published2014 Sep 25
Keywordsarabidopsis, Arabidopsis Proteins, Protein Binding, Phylogeny, Chromosome Mapping, Codon, Deoxyribonuclease I, Exons, Gene Regulatory Networks, Light, Genome, Plant, Genome-Wide Association Study, Transcription Factors, Plant Development, Regulatory Elements, Transcriptional, Seedling

<p>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 &sim; 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.</p>

Alternate JournalCell Rep