Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 8 (6), 2015-2030

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. Thaliana

Affiliations

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. Thaliana

Alessandra M Sullivan et al. Cell Rep.

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 ∼ 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.

Similar articles

See all similar articles

Cited by 80 PubMed Central articles

See all "Cited by" articles

Publication types

MeSH terms

Associated data

LinkOut - more resources

Feedback