TY - JOUR

T1 - Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana

AU - Cherenkov, Pavel

AU - Novikova, Daria

AU - Omelyanchuk, Nadya

AU - Levitsky, Victor

AU - Grosse, Ivo

AU - Weijers, Dolf

AU - Mironova, Victoria

N1 - © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

PY - 2018/1/4

Y1 - 2018/1/4

N2 - 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.

AB - 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.

KW - ARF

KW - Auxin

KW - AuxRE

KW - bHLH

KW - bioinformatics

KW - bZIP

KW - chromatin states

KW - transcriptional regulation

KW - Datasets as Topic

KW - Chromatin/metabolism

KW - Response Elements

KW - Arabidopsis/genetics

KW - Computational Biology

KW - Indoleacetic Acids/metabolism

KW - Transcription Factors/metabolism

KW - Gene Expression Regulation, Plant

KW - Plant Growth Regulators/metabolism

KW - ACTIVATION

KW - ROOT

KW - FAMILY

KW - BZIP

KW - TRANSCRIPTION FACTORS

KW - IDENTIFICATION

KW - DNA-BINDING SPECIFICITY

KW - PROMOTER

KW - PROTEINS

KW - DIFFERENTIAL EXPRESSION ANALYSIS

UR - http://www.scopus.com/inward/record.url?scp=85040588207&partnerID=8YFLogxK

U2 - 10.1093/jxb/erx254

DO - 10.1093/jxb/erx254

M3 - Article

C2 - 28992117

AN - SCOPUS:85040588207

VL - 69

SP - 329

EP - 339

JO - Journal of Experimental Botany

JF - Journal of Experimental Botany

SN - 0022-0957

IS - 2

ER -