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| Status |
Public on Mar 07, 2017 |
| Title |
3D structures of individual mammalian genomes reveal principles of nuclear organization |
| 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 |
The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is thought to be critically linked to nuclear processes, but it is unclear to what degree it is a cause or consequence of function. We have calculated the first 3D structural models of entire mammalian genomes using data from a new chromosome conformation capture protocol that allows us to first image and then process single cells. This has allowed us to study the folding of chromosomes down to a sub-100 kb scale. We show that the structures of individual topological-associated domains, chromosomes, and the way they pack together, varies very substantially from cell-to-cell. However, in all cells we find a consistent large-scale organization of compartments, with active enhancers and promoters clustering near inter-chromosomal interfaces, suggesting that nuclear processes such as transcription may drive chromosome and genome folding.
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| Overall design |
ChIP-seq, RNA-seq and nuclear RNA-seq in haploid and diploid mouse embryonic stem cells
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| Contributor(s) |
Laue ED |
| Citation(s) |
28289288 |
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| Submission date |
Apr 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andre J Faure |
| E-mail(s) |
andre.faure@crg.eu
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| Organization name |
Centre for Genomic Regulation (CRG)
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| Department |
EMBL-CRG Systems Biology Unit
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| Street address |
Dr. Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platforms (2) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (42)
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| Relations |
| BioProject |
PRJNA318485 |
| SRA |
SRP073306 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE80280_Chd4_ESC_peaks.bed.gz |
837.8 Kb |
(ftp)(http) |
BED |
| GSE80280_Mbd3_ESC_peaks.bed.gz |
496.8 Kb |
(ftp)(http) |
BED |
| GSE80280_RAW.tar |
19.7 Gb |
(http)(custom) |
TAR (of BED, HDF5, PDB, TSV, TXT, XYZ) |
| GSE80280_corr_Expression_Chd4.txt.gz |
2.1 Mb |
(ftp)(http) |
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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