Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

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Title:	Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements
Authors:	Mason, C.E.a, Shu, F.-J.b, Wang, C.b, Session, R.M.b, Kallen, R.G.c, Sidell, N.b, Yu, T.d, Liu, M.H.e, Cheung, E.e, Kallen, C.B.
Contributors:	Department of Foreign Languages and Literature, Tunghai University
Keywords:	article;cell strain MCF 7;chromatin immunoprecipitation;consensus sequence;controlled study;DNA sequence;estrogen responsive element;gel mobility shift assay;gene location;gene locus;gene targeting;human;human cell;nucleotide binding site;polymerase chain reaction;priority journal;protein DNA binding;receptor binding;regulatory sequence;binding site;chemistry;DNA responsive element;genetic transcription;metabolism;nucleotide repeat;tumor cell line
Date:	2010
Issue Date:	2013-06-04T08:20:23Z (UTC)
Abstract:	Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10-20% nucleotide deviation from the canonical ERE sequence. We demonstrate that ~50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptorbound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogendependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers. ?The Author(s) 2010. Published by Oxford University Press.
Relation:	Nucleic Acids Research 38 (7) , art. no. gkp1188 , pp. 2355-2368
Appears in Collections:	[Department of Foreign Languages and Literature] Periodical Articles

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