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Differential bindin...
Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq
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- Motallebipour, Mehdi (author)
- Uppsala universitet,Institutionen för genetik och patologi
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- Ameur, Adam (author)
- Uppsala universitet,Centrum för bioinformatik,Institutionen för genetik och patologi
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- Bysani, Madhusudhan Reddy (author)
- Uppsala universitet,Medicinsk genetik
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- Patra, Kalicharan (author)
- Uppsala universitet,Institutionen för genetik och patologi,Zoologisk utvecklingsbiologi
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- Wallerman, Ola (author)
- Uppsala universitet,Medicinsk genetik
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Mangion, Jonathan (author)
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Barker, Melissa (author)
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McKernan, Kevin (author)
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- Komorowski, Jan (author)
- Uppsala universitet,Centrum för bioinformatik
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- Wadelius, Claes (author)
- Uppsala universitet,Medicinsk genetik
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(creator_code:org_t)
- Springer Science and Business Media LLC, 2009
- 2009
- English.
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 10:11, s. R129-
- Related links:
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https://genomebiolog...
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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
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- BACKGROUND: The forkhead box/winged helix family members FOXA1, FOXA2, and FOXA3 are of high importance in development and specification of the hepatic linage and the continued expression of liver-specific genes. RESULTS: Here, we present a genome-wide location analysis of FOXA1 and FOXA3 binding sites in HepG2 cells through chromatin immunoprecipitation with detection by sequencing (ChIP-seq) studies and compare these with our previous results on FOXA2. We found that these factors often bind close to each other in different combinations and consecutive immunoprecipitation of chromatin for one and then a second factor (ChIP-reChIP) shows that this occurs in the same cell and on the same DNA molecule, suggestive of molecular interactions. Using co-immunoprecipitation, we further show that FOXA2 interacts with both FOXA1 and FOXA3 in vivo, while FOXA1 and FOXA3 do not appear to interact. Additionally, we detected diverse patterns of trimethylation of lysine 4 on histone H3 (H3K4me3) at transcriptional start sites and directionality of this modification at FOXA binding sites. Using the sequence reads at polymorphic positions, we were able to predict allele specific binding for FOXA1, FOXA3, and H3K4me3. Finally, several SNPs associated with diseases and quantitative traits were located in the enriched regions. CONCLUSIONS: We find that ChIP-seq can be used not only to create gene regulatory maps but also to predict molecular interactions and to inform on the mechanisms for common quantitative variation.
Subject headings
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Keyword
- MEDICINE
- MEDICIN
- Biology
- Biologi
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Motallebipour, M ...
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Ameur, Adam
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Bysani, Madhusud ...
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Patra, Kalichara ...
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Wallerman, Ola
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Mangion, Jonatha ...
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show more...
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Barker, Melissa
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McKernan, Kevin
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Komorowski, Jan
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Wadelius, Claes
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
- Articles in the publication
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Genome Biology
- By the university
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Uppsala University