Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 533100
Title Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Author(s) Cherenkov, Pavel; Novikova, Daria; Omelyanchuk, Nadya; Levitsky, Victor; Grosse, Ivo; Weijers, Dolf; Mironova, Victoria
Source Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 329 - 339.
DOI http://dx.doi.org/10.1093/jxb/erx254
Department(s) EPS
Biochemistry
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) ARF - Auxin - AuxRE - bHLH - bioinformatics - bZIP - chromatin states - transcriptional regulation
Abstract 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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