Genomics

Dataset Information

219

Multi-scale 3D genome rewiring during mouse neural development


ABSTRACT: 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. Overall design: Hi-C, RNAseq, ChIPseq in mouse cortical development (in vitro and in vivo)

INSTRUMENT(S): Illumina HiSeq 2000 (Mus musculus)

SUBMITTER: Boyan Bonev  

PROVIDER: GSE96107 | GEO | 2017-10-18

SECONDARY ACCESSION(S): PRJNA378980

REPOSITORIES: GEO

altmetric image

Publications


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 comprehensively mapped 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  ...[more]

Similar Datasets

2019-01-01 | S-EPMC6606598 | BioStudies
2020-01-01 | S-EPMC7138649 | BioStudies
1000-01-01 | S-EPMC6309071 | BioStudies
2018-01-01 | S-EPMC5803259 | BioStudies
2019-01-01 | S-EPMC6636040 | BioStudies
2016-01-01 | S-EPMC4889976 | BioStudies
2019-01-01 | S-EPMC6572804 | BioStudies
2016-01-01 | S-EPMC4892410 | BioStudies
2016-01-01 | S-EPMC4691752 | BioStudies
2016-01-01 | S-EPMC4788486 | BioStudies