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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 18, 2017 |
| Title |
Multi-scale 3D genome rewiring during mouse neural development |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We mapped comprehensively 3D chromatin organization during mouse neural differentiation in vitro and in vivo, generating the highest resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating topological domain (TAD) boundaries de novo. Additionally, we discovered long-range contacts between gene bodies of exon-rich, active genes in all cell types. During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact stronger. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between proneural transcription factors appear in vivo. Finally, cell-type specific enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.
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| Overall design |
Hi-C, RNAseq, ChIPseq in mouse cortical development (in vitro and in vivo)
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| Contributor(s) |
Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L, Papadopoulos G, Lubling Y, Xu X, Lv X, Hugnot J, Tanay A, Cavalli G |
| Citation(s) |
29053968 |
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| Submission date |
Mar 11, 2017 |
| Last update date |
Apr 06, 2023 |
| Contact name |
Boyan Bonev |
| E-mail(s) |
boyan.bonev@igh.cnrs.fr
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| Organization name |
Institute of Human Genetics - CNRS
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| Lab |
Giacomo Cavalli
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| Street address |
141 rue de la Cardonille
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| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (92)
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| Relations |
| Reanalyzed by |
GSE229113 |
| BioProject |
PRJNA378980 |
| SRA |
SRP101791 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE96107_CN_CTCF.IDR0.05.filt.narrowPeak.gz |
466.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_CN_CTCF.bw |
501.3 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_H3K27ac.IDR0.05.filt.narrowPeak.gz |
628.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_CN_H3K27ac.bw |
360.3 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_H3K27me3.bw |
329.4 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_H3K36me3.bw |
589.9 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_H3K4me1.bw |
320.5 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_H3K4me3.IDR0.05.filt.narrowPeak.gz |
478.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_CN_H3K4me3.bw |
307.7 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_H3K9me3.bw |
283.0 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_Input.bw |
356.5 Mb |
(ftp)(http) |
BW |
| GSE96107_CN_Ring1B.IDR0.05.filt.narrowPeak.gz |
27.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_CN_Ring1B.bw |
454.6 Mb |
(ftp)(http) |
BW |
| GSE96107_ES_CTCF.IDR0.05.filt.narrowPeak.gz |
2.0 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_ES_CTCF.bw |
328.2 Mb |
(ftp)(http) |
BW |
| GSE96107_ES_Input.bw |
252.7 Mb |
(ftp)(http) |
BW |
| GSE96107_ES_Ring1B.IDR0.05.filt.narrowPeak.gz |
621.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_ES_Ring1B.bw |
441.0 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_CTCF.IDR0.05.filt.narrowPeak.gz |
588.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_NPC_CTCF.bw |
457.5 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_H3K27ac.IDR0.05.filt.narrowPeak.gz |
436.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_NPC_H3K27ac.bw |
527.9 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_H3K27me3.bw |
405.3 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_H3K36me3.bw |
590.8 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_H3K4me1.bw |
577.3 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_H3K4me3.IDR0.05.filt.narrowPeak.gz |
158.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_NPC_H3K4me3.bw |
523.7 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_H3K9me3.bw |
411.0 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_Input.bw |
293.6 Mb |
(ftp)(http) |
BW |
| GSE96107_NPC_Ring1B.IDR0.05.filt.narrowPeak.gz |
66.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE96107_NPC_Ring1B.bw |
405.2 Mb |
(ftp)(http) |
BW |
| GSE96107_RAW.tar |
397.7 Gb |
(http)(custom) |
TAR (of TAR, TXT) |
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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