Journal
JOURNAL OF EXPERIMENTAL BOTANY
Volume 69, Issue 2, Pages 329-339Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jxb/erx254
Keywords
Auxin; AuxRE; ARF; bZIP; bHLH; transcriptional regulation; chromatin states; bioinformatics
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Funding
- Russian Ministry of Science and Education under 5-100 Excellence Programme
- Russian State Budget [0324-2016-0008]
- Wageningen Graduate School
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The phytohormone auxin regulates virtually every developmental process in land plants. This regulation is mediated via de-repression of DNA-binding auxin response factors (ARFs). ARFs bind TGTC-containing auxin response cis-elements (AuxREs), but there is growing evidence that additional cis-elements occur in auxin-responsive regulatory regions. The repertoire of auxin-related cis-elements and their involvement in different modes of auxin response are not yet known. Here we analyze the enrichment of nucleotide hexamers in upstream regions of auxin-responsive genes associated with auxin up-or down-regulation, with early or late response, ARF-binding domains, and with different chromatin states. Intriguingly, hexamers potentially bound by basic helix-loop-helix (bHLH) and basic leucine zipper (bZIP) factors as well as a family of A/T-rich hexamers are more highly enriched in auxin-responsive regions than canonical TGTC-containing AuxREs. We classify and annotate the whole spectrum of enriched hexamers and discuss their patterns of enrichment related to different modes of auxin response.
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