Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Spatial organisation of the X inactivation center

ABSTRACT: We report the application of Chromosome Conformation Capture Carbon-copy (5C) to a 4.5 Mb stretch of the mouse X chromosome encompassing the X inactivation center locus. We uncover a series of discrete 200kb-1Mb topologically associating domains (TADs). These align with several domain-wide epigenomic features as well as co-regulated gene clusters. 5C analysis in EED and G9A mutants reveal that this segmental organisation in TADs does not relie on the underlying H3K27me3 or H3K9me2 blocks. Deletion of a boundary between two TADs leads to ectopic chromosomal contacts between them. Analysis of mESCs, mNPCs and MEFs suggest that the positioning of TADs on the chromosome is stable during cell differentiation though their internal organisation changes. Comparison of male (XY) and female (XX) differentiated cells highlights that the long-range chromosomal contacts within TADs are dampened on the inactive X compared to the active X. 5C oligonucleotides were designed around HindIII restriction site following an alternative scheme

ORGANISM(S): Mus musculus

SUBMITTER: Elphege Nora

PROVIDER: E-GEOD-35721 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Nora Elphège P EP Lajoie Bryan R BR Schulz Edda G EG Giorgetti Luca L Okamoto Ikuhiro I Servant Nicolas N Piolot Tristan T van Berkum Nynke L NL Meisig Johannes J Sedat John J Gribnau Joost J Barillot Emmanuel E Blüthgen Nils N Dekker Job J Heard Edith E

Nature 20120411 7398

In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the non-protein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C) and su ...[more]

PMID: 22495304

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Dataset Information

Spatial organisation of the X inactivation center

Publications

Spatial partitioning of the regulatory landscape of the X-inactivation centre.

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