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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| Overall design |
generate DamID maps of genome-NL interaction for mouse 3T3 fibroblasts and C2C12 myoblasts with two control samples (*genomic DNA samples).
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| Contributor(s) |
Wu F, Yao J |
| Citation(s) |
23987233 |
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| Submission date |
Oct 15, 2012 |
| Last update date |
Jul 20, 2020 |
| Contact name |
Jie Yao |
| E-mail(s) |
[email protected]
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| Organization name |
Allen Institute
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| Street address |
615 Westlake Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (10)
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| Relations |
| SRA |
SRP016116 |
| BioProject |
PRJNA177678 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41583_RAW.tar |
5.8 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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