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| Status |
Public on Jan 01, 2022 |
| Title |
Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells [CUT&RUN, ChIP-Seq] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Transcription factors (TFs) play crucial roles in kidney development and disease by recognizing specific DNA sequences to control gene expression programs. The kidney’s cellular heterogeneity poses substantial challenges to identifying the genomic binding sites and direct target genes of TFs in vivo. We apply the CUT&RUN (cleavage under targets and release using nuclease) technique, together with transcriptomic analysis, to identify cAMP-response element-binding protein (CREB) target genes in cystic epithelial cells of autosomal dominant polycystic kidney disease (ADPKD). Our results reveal that CREB binds to and activates ribosomal biogenesis genes, and that inhibition of CREB retards cyst growth in ADPKD mouse models. Our findings demonstrate that CUT&RUN is a powerful method for genome-scale profiling and identifying direct targets of TFs from small numbers of specific kidney cells.
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| Overall design |
CUT&RUN of p-CREB, H3K4me3 and H3K27ac were performed in freshly isolated Dolichos biflorus lectin (DBA) positive cells from WT or ADPKD mice kidneys. CUT&RUN were compared with ChIP-seq in WT 9-12 cells.
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| Contributor(s) |
Chen Y, Liu Z |
| Citation(s) |
34162733, 39323486 |
| |
| Submission date |
Jan 25, 2021 |
| Last update date |
Oct 10, 2024 |
| Contact name |
Zhiheng Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Tianjin Medical University
|
| Department |
Tianjin Research Center for Basic Medical Science
|
| Lab |
Gene Expression Laboratory
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| Street address |
No.22 Qixiangtai Road
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
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| Platforms (3) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE165418 |
Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells |
|
| Relations |
| BioProject |
PRJNA694566 |
| SRA |
SRP303121 |
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