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Binding sites for m...
Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
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- Rada-Iglesias, Alvaro (author)
- Uppsala universitet,Institutionen för genetik och patologi,Systems genomics
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- Wallerman, Ola (author)
- Uppsala universitet,Institutionen för genetik och patologi,Systems genomics
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Koch, Christoph (author)
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- Ameur, Adam (author)
- Uppsala universitet,Centrum för bioinformatik
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- Enroth, Stefan (author)
- Uppsala universitet,Centrum för bioinformatik
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Clelland, Gayle (author)
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- Wester, Kenneth (author)
- Uppsala universitet,Institutionen för genetik och patologi
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Wilcox, Sarah (author)
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Dovey, Oliver M (author)
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Ellis, Peter D (author)
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Wraight, Vicki L (author)
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James, Keith (author)
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Andrews, Rob (author)
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Langford, Cordelia (author)
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Dhami, Pawandeep (author)
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Carter, Nigel (author)
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Vetrie, David (author)
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- Pontén, Fredrik (author)
- Uppsala universitet,Institutionen för genetik och patologi
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- Komorowski, Jan (author)
- Uppsala universitet,Centrum för bioinformatik
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Dunham, Ian (author)
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- Wadelius, Claes (author)
- Uppsala universitet,Institutionen för genetik och patologi,Systems genomics
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(creator_code:org_t)
- 2005-10-13
- 2005
- English.
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 14:22, s. 3435-3447
- Related links:
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http://hmg.oxfordjou...
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
Close
- We present a detailed in vivo characterization of hepatocyte transcriptional regulation in HepG2 cells, using chromatin immunoprecipitation and detection on PCR fragment-based genomic tiling path arrays covering the encyclopedia of DNA element (ENCODE) regions. Our data suggest that HNF-4α and HNF-3β, which were commonly bound to distal regulatory elements, may cooperate in the regulation of a large fraction of the liver transcriptome and that both HNF-4α and USF1 may promote H3 acetylation to many of their targets. Importantly, bioinformatic analysis of the sequences bound by each transcription factor (TF) shows an over-representation of motifs highly similar to the in vitro established consensus sequences. On the basis of these data, we have inferred tentative binding sites at base pair resolution. Some of these sites have been previously found by in vitro analysis and some were verified in vitro in this study. Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome.
Keyword
- Base Pairing/*genetics
- Binding Sites/genetics
- Cell Line; Tumor
- Chromatin/*metabolism
- Chromatin Immunoprecipitation/methods
- Consensus Sequence
- Genome; Human
- Hepatocyte Nuclear Factor 3-beta/physiology
- Hepatocyte Nuclear Factor 4/physiology
- Hepatocytes/metabolism
- Histones/metabolism
- Humans
- Metabolic Diseases/*metabolism
- Oligonucleotide Array Sequence Analysis/methods
- Promoter Regions (Genetics)
- Research Support; N.I.H.; Extramural
- Research Support; Non-U.S. Gov't
- Sequence Analysis; DNA
- Transcription Factors/genetics/*metabolism
- Upstream Stimulatory Factors/metabolism
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
To the university's database
- By the author/editor
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Rada-Iglesias, A ...
-
Wallerman, Ola
-
Koch, Christoph
-
Ameur, Adam
-
Enroth, Stefan
-
Clelland, Gayle
-
show more...
-
Wester, Kenneth
-
Wilcox, Sarah
-
Dovey, Oliver M
-
Ellis, Peter D
-
Wraight, Vicki L
-
James, Keith
-
Andrews, Rob
-
Langford, Cordel ...
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Dhami, Pawandeep
-
Carter, Nigel
-
Vetrie, David
-
Pontén, Fredrik
-
Komorowski, Jan
-
Dunham, Ian
-
Wadelius, Claes
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show less...
- Articles in the publication
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Human Molecular ...
- By the university
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Uppsala University