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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 06, 2019 |
| Title |
KLF4 binding during reprogramming is linked to enhancer rewiring and is critical for the architecture and regulation of enhancer hubs [4C-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Purpose: We captured on a genome-wide scale the binding of KLF4 during iPSC formation and its effects on chromatin state, transcriptional activity and chromatin topology around its targets.
Methods: We used a well-characterized reprogramming system to apply genome-wide assays that map KLF4 binding (ChIP-seq), chromatin accessibility (ATAC-seq), enhancer and gene activity (H3K27ac ChIP-seq and RNA-seq), enhancer connectivity (H3K27ac Hi-ChIP) as well as KLF4-centric chromatin looping (KLF4 Hi-ChIP) at different stages during acquisition of pluripotency.
Results: Integrative analysis of our results generated a reference map of stage-specific chromatin changes around KLF4 bound loci and established strong links with enhancer. rewiring and concordant transcriptional changes. Genetic manipulation of KLF4 binding from a PSC enhancer further supported the ability of KLF4 to function both as a transcriptional regulator and a chromatin organizer.
Conclusions: Our study offers novel insights into the intricate roles of a master regulator during cell fate transition.
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| Overall design |
Mouse embryonic fibroblasts (MEFs) (Rosa26-M2rtTA/Col1a1-OKSM) induced with doxycycline (dox) in the presence of ascorbic acid. We collected bulk populations on day 3 after dox treatment, whereas at later stages, on day 6 and day 9, we sorted SSEA1 positive cells to enrich for cells on the trajectory towards induced pluripotency. Finally, we used pluripotent stem cells (PSCs) as a reference point for established pluripotency. Biological replicates were collected to assay for chromatin accessibility (paired-end ATAC-seq), gene activity (single-end RNA-seq), H3K27ac ChIP-seq (single-end) in MEFs, day3, 6, 9 and PSCs. KLF4 binding (single-end ChIP-seq) was assessed in day3, 6, 9 and PSCs. KLF4/H3K27ac centric looping (paired-end Hi-ChIP) was studied in either day3, day6 and PSCs for KLF4 or MEFs and PSCs for H3K27ac. 4C-Seq was conducted for individual viewpoints (Mycn, Ets1, Tbx3) to validate findings from HiChIP/Hi-C assays.
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| Contributor(s) |
Apostolou E, Tsirigos A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 30, 2019 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Effie Apostolou |
| E-mail(s) |
efa2001@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Street address |
1161 York Avenue, Apt 8A
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE113431 |
KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency |
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| Relations |
| BioProject |
PRJNA557475 |
| SRA |
SRP216855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135124_Ets1_promoter_cpm.tsv.gz |
103.8 Kb |
(ftp)(http) |
TSV |
| GSE135124_Mycn_enhancer_cpm.tsv.gz |
89.7 Kb |
(ftp)(http) |
TSV |
| GSE135124_Tbx3_enhancer_cpm.tsv.gz |
19.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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