Comment[ArrayExpressAccession] E-GEOD-41583 MAGE-TAB Version 1.1 Public Release Date 2013-10-30 Investigation Title Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping Comment[Submitted Name] Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping Experiment Description 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 Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Wu Wu Yao Person First Name Feinan Feinan Jie Person Email geo@ncbi.nlm.nih.gov Person Affiliation Yale School of Medicine Person Address Cell Biology, Yale School of Medicine, 333 Cedar St., New Haven, CT, USA Person Roles submitter Protocol Name P-GSE41583-3 P-GSE41583-2 P-GSE41583-1 Protocol Description Basecalls performed using CASAVA version 1.8. Reads were aligned to mm9 by Bowtie2-2.0.0-beta5 using the following command: bowtie2 -phred3 -x mm9 -U -S . Genome build: mm9. Supplementary_files_format_and_content: Alignment of the reads to mm9 in BED format. Genomic DNA was isolated using Dneasy blood and tissue kit (Qiagen). PCR-enriched methylated DNA fragments from the DamID assay were fragmented by NEBNext® dsDNA Fragmentase, then subject to end repair, addition of "A" bases, ligation of Illumina adaptors, size selection of libary and PCR enrichment of adaptor-modified DNA fragments according to the protocol provided by Yale Center for Genome Analysis (http://ycga.yale.edu/sequencing/Illumina/protocols.aspx) Lamin B1 cDNA was cloned into the pLGW-dam-V5 vectors. Lentivirus with Dam-V5 and Dam-V5-Lmnb1 vectors was generated by the Virapower Lentivirus Expression system (Invitrogen) and was stored at -80 °C before use. The lentivirus was diluted with the growth medium and incubated with the cells for two days before changing to the growth media. Protocol Type normalization data transformation protocol nucleic acid library construction protocol growth protocol Experimental Factor Name CELL LINE EXPRESSING PROTEIN Experimental Factor Type cell line expressing protein Publication Title Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping. Publication Author List Wu F, Yao J PubMed ID 23987233 Publication DOI 10.1186/1471-2164-14-591 Comment[SecondaryAccession] GSE41583 Comment[GEOReleaseDate] 2013-10-30 Comment[ArrayExpressSubmissionDate] 2012-10-15 Comment[GEOLastUpdateDate] 2013-11-15 Comment[AEExperimentType] other Comment[AEExperimentType] ChIP-seq Comment[SecondaryAccession] SRP016116 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR592261-SRR592571 SDRF File E-GEOD-41583.sdrf.txt