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| Status |
Public on Mar 15, 2022 |
| Title |
Three-dimensional geome study of procine livers during development and metabolic adaptation |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Liver development and metabolic adaptation are well-orchestrated by a series of signaling pathways and genes. Chromatin architecture is known to influence gene expression, yet its role in controlling liver development and metabolism remains unclear. We performed high-throughput chromatin conformation capture sequencing (HiC-seq) and integrated RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) on liver tissue that were collected from six key developmental stages (embryonic day 38 [E38] – 2 years [2y]) and a high fat diet (HFD) feeding group. Our data revealed global three-dimensional (3D) reorganization during liver development from the scales of compartment, topologically associated domain (TAD) and promoter-enhancer interaction (PEI), which consistently affects the expression level of genes known to be important for liver development and function. Comparison of 3D genome and gene expression profiles between pig liver development and human hepatocellular carcinoma (HCC) revealed similarities between fatal liver and HCC and provided potential explanation for the aberrant expression in HCC from the perspective of chromatin architecture. Moreover, the similar genome architecture and expression of genes related to lipid metabolism between nomally and HFD feeding pigs, along with the thicker back fat in HFD feeding pigs compared to normally feeding pigs, supported that pigs are resistant to nonalcoholic fatty liver disease (NAFLD). Together, our results provide a global view of dynamic chromatin interactions during liver development and metabolic adaptation induced by HFD feeding, which may open new avenues for liver research and HCC therapeutic interventions.
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| Overall design |
We generated high-throughput chromatin conformation capture (Hi-C) sequencing data, integrated RNA sequencing data and chromatin immunoprecipitation (ChIP) sequencing data of pig liver tissues at embryonic day 38 (E38), embryonic day 80 (E80), birth day (0d), postnatal day 28 (28d), postnatal day 110 (110d) and 2 years (2y) as well as high fat diet (HFD) treatment with 1-6 replicates.
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| Contributor(s) |
Chen L, Li M |
| Citation(s) |
35701393 |
| BioProject |
PRJNA721459 |
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| Submission date |
Jun 08, 2021 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Jing Li |
| E-mail(s) |
lijing-jane@foxmail.com
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| Phone |
+8615882474902
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| Organization name |
Sichuan Agricultural University
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| Department |
College of Animal Science and Technology
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| Street address |
No. 211 Huimin Road, Wenjiang District
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| City |
Chengdu |
| State/province |
China |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platforms (3) |
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| Samples (129)
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| Relations |
| SRA |
SRP314566 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE176387_0d.merged.replicates.tad.txt.gz |
19.9 Kb |
(ftp)(http) |
TXT |
| GSE176387_110d.merged.replicates.tad.txt.gz |
20.9 Kb |
(ftp)(http) |
TXT |
| GSE176387_28d.merged.replicates.tad.txt.gz |
20.3 Kb |
(ftp)(http) |
TXT |
| GSE176387_2y.merged.replicates.tad.txt.gz |
21.2 Kb |
(ftp)(http) |
TXT |
| GSE176387_2y_HFD.Dscore.txt.gz |
235.1 Kb |
(ftp)(http) |
TXT |
| GSE176387_2y_HFD.consensus.TAD.txt.gz |
20.0 Kb |
(ftp)(http) |
TXT |
| GSE176387_E38.merged.replicates.tad.txt.gz |
18.5 Kb |
(ftp)(http) |
TXT |
| GSE176387_E80.merged.replicates.tad.txt.gz |
20.8 Kb |
(ftp)(http) |
TXT |
| GSE176387_HFD.merged.replicates.tad.txt.gz |
21.5 Kb |
(ftp)(http) |
TXT |
| GSE176387_RAW.tar |
31.4 Gb |
(http)(custom) |
TAR (of HIC, NARROWPEAK, TXT) |
| GSE176387_all.samples.abindex.txt.gz |
26.1 Mb |
(ftp)(http) |
TXT |
| GSE176387_all_samples_quant_mRNA.tpm.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE176387_developmental.Dscore.txt.gz |
612.4 Kb |
(ftp)(http) |
TXT |
| GSE176387_developmental.consensus.TAD.txt.gz |
22.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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