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Series GSE41583 Query DataSets for GSE41583
Status Public on Oct 30, 2013
Title Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping
Organism Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design generate DamID maps of genome-NL interaction for mouse 3T3 fibroblasts and C2C12 myoblasts with two control samples (*genomic DNA samples).
Contributor(s) Wu F, Yao J
Citation(s) 23987233
Submission date Oct 15, 2012
Last update date Jul 20, 2020
Contact name Jie Yao
Organization name Allen Institute
Street address 615 Westlake Ave N
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (10)
GSM1019691 3T3MEF-Dam rep 1
GSM1019692 3T3MEF-Dam rep 2
GSM1019693 3T3MEF-LmnB1 rep 1
SRA SRP016116
BioProject PRJNA177678

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Supplementary file Size Download File type/resource
GSE41583_RAW.tar 5.8 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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