RT Journal Article
SR Electronic
T1 Regulatory DNA in A. thaliana can tolerate high levels of sequence divergence
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 104323
DO 10.1101/104323
A1 C.M. Alexandre
A1 J.R. Urton
A1 K. Jean-Baptiste
A1 M.W. Dorrity
A1 J.C. Cuperus
A1 A.M. Sullivan
A1 F. Bemm
A1 D. Jolic
A1 A.A. Arsovski
A1 A. Thompson
A1 J.L. Nemhauser
A1 S. Fields
A1 D. Weigel
A1 K.L. Bubb
A1 C. Queitsch
YR 2017
UL http://biorxiv.org/content/early/2017/01/30/104323.abstract
AB Variation in regulatory DNA is thought to drive evolution. Cross-species comparisons of regulatory DNA have provided evidence for both weak purifying selection and substantial turnover in regulatory regions. However, disruption of transcription factor binding sites can affect the expression of neighboring genes. Thus, the base-pair level functional annotation of regulatory DNA has proven challenging. Here, we explore regulatory DNA variation and its functional consequences in genetically diverse strains of the plant Arabidopsis thaliana, which largely maintain the positional homology of regulatory DNA. Using chromatin accessibility to delineate regulatory DNA genome-wide, we find that 15% of approximately 50,000 regulatory sites varied in accessibility among strains. Some of these accessibility differences are associated with extensive underlying sequence variation, encompassing many deletions and dramatically hypervariable sequence. For the majority of such regulatory sites, nearby gene expression was similar, despite this large genetic variation. However, among all regulatory sites, those with both high levels of sequence variation and differential chromatin accessibility are the most likely to reside near genes with differential expression among strains. Unexpectedly, the vast majority of regulatory sites that differed in chromatin accessibility among strains show little variation in the underlying DNA sequence, implicating variation in upstream regulators.