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| Status |
Public on Apr 08, 2019 |
| Title |
Transcriptional and chromatin profiles of duodenum epithelium upon HNF4 loss in mice by RNA-seq and ChIP-seq |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We find that HNF4G is an intestine-particular HNF4 paralog, and works redundantly with HNF4A for driving intestinal differentiation by controlling chromatin accessibility and regulating thousands of transcripts particular to differentiated cells. Without HNF4s, cells fail to achieve a differentiated state. A positive feedback loop between HNF4 transcriptional regulation and BMP/SMAD signaling stabilizes differentiation, and the two inputs cooperatively activate differentiation gene expression.
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| Overall design |
Transcriptional profiling was employed to identify HNF4-dependent gene expression in the mouse duodenal epithelium. A series of ChIP-seq experiments (Hnf4alpha, Hnf4gamma and H3K27ac-MNase) identified the HNF4 binding regions in mouse duodenal epithelium and discovered and validated extensive co-binding with Smad4 in CaCO2 cells and mouse duodenal epithelium.
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| |
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| Contributor(s) |
Chen L, Ansu PO, Verzi MP |
| Citation(s) |
30988513, 33503426, 36711781 |
| |
| Submission date |
Apr 10, 2018 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Michael P Verzi |
| Organization name |
Rutgers, the State University of New Jersey
|
| Department |
Genetics
|
| Lab |
Verzi
|
| Street address |
145 Bevier Road
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
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| Platforms (4)
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| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL21626 |
NextSeq 550 (Mus musculus) |
|
| Samples (33)
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| Relations |
| BioProject |
PRJNA449547 |
| SRA |
SRP139365 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112946_ATAC_M6_WT_villi_summits_summit_cnt_peaks.bed.gz |
593.8 Kb |
(ftp)(http) |
BED |
| GSE112946_CaCO2_Avi_Smad4_BiotinChIP.bw |
220.0 Mb |
(ftp)(http) |
BW |
| GSE112946_CaCO2_BiotinSmad4ChIP_lib_S12_R1_001_summit_cnt_peaks.bed.gz |
505.0 Kb |
(ftp)(http) |
BED |
| GSE112946_HNF4_gene_exp_Cuffdiff_percondition.diff.gz |
4.6 Mb |
(ftp)(http) |
DIFF |
| GSE112946_Hnf4alphagammaDKO_H3K27ac_MNaseChIP_rep1.bw |
308.0 Mb |
(ftp)(http) |
BW |
| GSE112946_Hnf4alphagammaDKO_H3K27ac_MNaseChIP_rep2.bw |
289.9 Mb |
(ftp)(http) |
BW |
| GSE112946_Merge2_DKO_Mnase_summit_cnt_peaks.bed.gz |
430.9 Kb |
(ftp)(http) |
BED |
| GSE112946_Merge2_WT_Mnase_summit_cnt_peaks.bed.gz |
423.6 Kb |
(ftp)(http) |
BED |
| GSE112946_Merge4_Hnf4Chip_wInp_p03_summit_cnt_peaks.bed.gz |
63.0 Kb |
(ftp)(http) |
BED |
| GSE112946_Merge_WT_Hnf4alphaChIP.bw |
313.8 Mb |
(ftp)(http) |
BW |
| GSE112946_Merge_WT_Hnf4gammaChIP.bw |
327.8 Mb |
(ftp)(http) |
BW |
| GSE112946_Merge_WT_SMAD4ChIP.bed.gz |
206.7 Kb |
(ftp)(http) |
BED |
| GSE112946_RAW.tar |
537.9 Mb |
(http)(custom) |
TAR (of BW, H5) |
| GSE112946_WT_H3K27ac_MNaseChIP_rep1.bw |
302.0 Mb |
(ftp)(http) |
BW |
| GSE112946_WT_H3K27ac_MNaseChIP_rep2.bw |
302.3 Mb |
(ftp)(http) |
BW |
| GSE112946_WT_Villi_ATAC.bw |
185.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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