Research output: Contribution to journal › Article › peer-review
Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana. / Cherenkov, Pavel; Novikova, Daria; Omelyanchuk, Nadya et al.
In: Journal of Experimental Botany, Vol. 69, No. 2, 04.01.2018, p. 329-339.Research output: Contribution to journal › Article › peer-review
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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 -
ID: 9444511