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3D structures of individual mammalian genomes reveal principles of nuclear organization

GSE80280 Mus musculus Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other 42 samples Submitted 2017/03/07 Platform GPL17021Platform GPL16417
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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Direct links to NCBI, no account and no request form: the whole study as GSE80280_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 42 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA318485 and SRA study SRP073306. Searching any of these in the dataset finder brings you back here.

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