|
| Status |
Public on Dec 31, 2020 |
| Title |
The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [HiChIP] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Transcriptional and phenotypic robustness during development is believed to require complex regulatory landscapes whereby multiple enhancers redundantly control the expression of major cell identity genes. In contrast, we previously described a limited and genetically distinct set of distal regulatory elements, known as poised enhancers (PEs), that control the induction of genes involved in early brain development in a hierarchical and non-redundant manner. Before becoming activated in neural progenitors, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally identified and subsequently characterized using embryonic stem cells (ESC) as in an in vitro differentiation system, it is currently unknown whether PEs are functionally conserved in vivo. Here, we generate and mine various types of genomic data to conclusively show that the epigenetic and 3D structural features of PEs are conserved among pluripotent cells both in vitro and in vivo. Furthermore, by genetically disrupting evolutionary conserved PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential and non-redundant roles during the induction of major anterior neural genes in vivo.
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| Overall design |
Chromosome confirmation capture for various histone modifications were investigated in mESC (undifferentiated and differentiated), as well as early murine and avian embryonic stages using HiChIP.
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| Contributor(s) |
Crispatzu G, Rehimi R, Rada-Iglesias A |
| Citation(s) |
34272393 |
| |
| Submission date |
Nov 02, 2020 |
| Last update date |
Jul 19, 2021 |
| Contact name |
Giuliano Crispatzu |
| Organization name |
University of Cologne (UoC), Germany
|
| Department |
CECAD
|
| Street address |
Joseph-Stelzmann-Straße 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (13)
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| This SubSeries is part of SuperSeries: |
| GSE160657 |
The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo |
|
| Relations |
| BioProject |
PRJNA673867 |
| SRA |
SRP290827 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE160656_E14_AntNPC_H3K27ac_merged_FitHiChIP.interactions_FitHiC.bed.gz |
480.6 Mb |
(ftp)(http) |
BED |
| GSE160656_E14_AntNPC_H3K27ac_merged_allValidPairs.txt.gz |
907.6 Mb |
(ftp)(http) |
TXT |
| GSE160656_E14_AntNPC_H3K27ac_merged_temporary_control_lambda.ALL.clipped.bedGraph.gz |
479.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE160656_E14_H3K27me3_merged_FitHiChIP_L_COV.interactions_FitHiC.bed.gz |
1.0 Gb |
(ftp)(http) |
BED |
| GSE160656_E14_H3K27me3_merged_allValidPairs.txt.gz |
1.9 Gb |
(ftp)(http) |
TXT |
| GSE160656_E14_H3K27me3_merged_temporary_control_lambda.ALL.clipped.bedGraph.gz |
738.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE160656_E14_H3K4me3_merged_FitHiChIP_L_COV.interactions_FitHiC.bed.gz |
686.4 Mb |
(ftp)(http) |
BED |
| GSE160656_E14_H3K4me3_merged_allValidPairs.txt.gz |
1.7 Gb |
(ftp)(http) |
TXT |
| GSE160656_E14_H3K4me3_merged_temporary_control_lambda.ALL.clipped.bedGraph.gz |
572.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE160656_EED_H3K4me3_merged_FitHiChIP_L_COV.interactions_FitHiC.bed.gz |
221.2 Mb |
(ftp)(http) |
BED |
| GSE160656_EED_H3K4me3_merged_allValidPairs.txt.gz |
925.8 Mb |
(ftp)(http) |
TXT |
| GSE160656_EED_H3K4me3_merged_temporary_control_lambda.ALL.clipped.bedGraph.gz |
393.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE160656_RAW.tar |
16.5 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TXT) |
| GSE160656_RING_H3K4me3_merged_FitHiChIP_L_COV.interactions_FitHiC.bed.gz |
110.4 Mb |
(ftp)(http) |
BED |
| GSE160656_RING_H3K4me3_merged_allValidPairs.txt.gz |
732.1 Mb |
(ftp)(http) |
TXT |
| GSE160656_RING_H3K4me3_merged_temporary_control_lambda.ALL.clipped.bedGraph.gz |
520.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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