|
| Status |
Public on Feb 05, 2011 |
| Title |
[E-MTAB-115] ChIP-seq for FOXA2 HNF4a and NRF2 / GABP in HepG2 |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
In each cell type the expression of genes is regulated by the action of a large number of transcription factors, but so far we have only a rudimentary knowledge of the location of the gene regulatory elements where they bind. This can now be addressed with genome-wide ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. HNF4a and FOXA2 binding was found in at least half of the regions previously identified as bound by USF2 but not USF1, showing that they frequently bind the same regulatory elements. GABP peaks were found at transcription start sites whereas 94 % of FOXA2 and 90 % of HNF4a peaks were located at other positions. We developed a method based on the high resolution achieved by ChIP-seq to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An unexpected interaction between HNF4a and GABP was seen at TSS, with as many as 1/3 of the HNF4a positive promoters being bound also by GABP, and co-immunoprecipitations show that these factors are in the same complex in the nucleus.
ArrayExpress Release Date: 2009-06-10
Publication Title: Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
Publication Author List: Ola Wallerman, Mehdi Motallebipour, Stefan Enroth, Kalicharan Patra, MadhuSudan Reddy Bysani, Jan Komorowski, Claes Wadelius
Person Roles: submitter
Person Last Name: Wallerman
Person First Name: Ola
Person Mid Initials:
Person Email: ola.wallerman@genpat.uu.se
Person Phone:
Person Address: IGP, Rudbecklab
Person Affiliation: Uppsala University
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| |
|
| Overall design |
Experimental Design: high_throughput_sequencing_design
Experimental Design: binding_site_identification_design
Experimental Design: transcription profiling by high throughput sequencing
Experimental Factor Name: IMMUNOPRECIPITATE
Experimental Factor Name: LIBRARY_FRAGMENT_SIZE
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: protocol
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| |
|
| Citation(s) |
19822575 |
| |
| Submission date |
Nov 29, 2010 |
| Last update date |
Feb 21, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
|
| Samples (11)
|
| GSM630942 |
[E-MTAB-115] FOXA2_rep1long_lane_6.um.eland_rep1 |
| GSM630943 |
[E-MTAB-115] FOXA2_rep1long_lane_7.um.eland |
| GSM630944 |
[E-MTAB-115] FOXA2_rep1short_lane_3.um.eland |
| GSM630945 |
[E-MTAB-115] FOXA2_rep1short_lane_4.um.eland |
| GSM630946 |
[E-MTAB-115] FOXA2_rep2b_lane_6.um.eland_rep2b |
| GSM630947 |
[E-MTAB-115] HNF4a_first_lane_FC14065_2.um.eland |
| GSM630948 |
[E-MTAB-115] HNF4a_second_lane_200D9AAXX_7.um.eland |
| GSM630949 |
[E-MTAB-115] lane_6.um.eland_rep2a |
| GSM630950 |
[E-MTAB-115] NRF2_lane1_FC14065_1.nm.eland |
| GSM630951 |
[E-MTAB-115] NRF2_lane1_FC14065_1.um.eland |
| GSM630952 |
[E-MTAB-115] NRF2_lane2_201EKAAXX_6.um.eland |
|
| Relations |
| ArrayExpress |
E-MTAB-115 |
| BioProject |
PRJNA135845 |
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