Transcriptomics,Genomics

Dataset Information

300

Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping


ABSTRACT: How gene positioning to the nuclear periphery regulates transcription remains largely unclear. We have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we have integrated high throughput DNA sequencing into the DNA adenine methyltransferase identification (DamID) assay, and have identified ~15, 000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts. These genomic regions range from a few kb to over 1 Mb and cover ~30% of the genome, and are spatially proximal to the nuclear lamina (NL). Active histone modifications such as H3K4me2, H3K9Ac, H3K36me3 and H3K79me2 are all localized away from the nuclear periphery microscopically, and distributed predominantly out of sLADs genome-wide. Therefore, the spatial compartmentalization of active histone modifications likely characterizes a major portion of chromatin at the nuclear periphery in mammalian cells. Genomic regions around transcription start sites of expressed sLAD genes display reduced associations with the NL and possess active histone modifications; in contrast, gene bodies of expressed sLAD genes possess very low levels of active histone modifications. Our genome-wide analyses of NL-associated chromatin have enabled functional and mechanistic dissections of gene positioning on transcription regulation. generate DamID maps of genome-NL interaction for mouse 3T3 fibroblasts and C2C12 myoblasts

ORGANISM(S): Mus musculus  

SUBMITTER: Feinan Wu   Jie Yao 

PROVIDER: E-GEOD-41583 | ArrayExpress | 2013-10-30

SECONDARY ACCESSION(S): GSE41583SRP016116PRJNA177678

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping.

Wu Feinan F   Yao Jie J  

BMC genomics 20130830


BACKGROUND: How gene positioning to the nuclear periphery regulates transcription remains largely unclear. By cell imaging, we have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we aim to identify DNA sequences associated with the nuclear lamina (NL) and examine this compartmentalization at the genome-wide level. RESULTS: We have integrated high throughput DNA sequencing into t  ...[more]

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