title: Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping.
abstract: 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 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 NL. Active histone modifications such as H3K4me2/3, H3K9Ac and H3K36me3 are distributed predominantly out of sLADs, consistent with observations from cell imaging that they are localized away from the nuclear periphery. Genomic regions around transcription start sites of expressed sLAD genes display reduced association with the NL; additionally, expressed sLAD genes possess lower levels of active histone modifications than expressed non-sLAD genes.
  
  
  CONCLUSIONS
  Our work has shown that genomic regions associated with the NL are characterized by the paucity of active histone modifications in mammalian cells, and has revealed novel connections between subnuclear gene positioning, histone modifications and gene expression.
authors.affiliation: Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA. yao.j@yale.edu.
authors.forename: Feinan
authors.initials: F
authors.lastname: Wu
authors.forename: Jie
authors.initials: J
authors.lastname: Yao
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics*; D002874:Chromosome Mapping; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D051379:Mice; D032446:Myoblasts / Q000378:metabolism; D041681:NIH 3T3 Cells; D034881:Nuclear Lamina / Q000235:genetics; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site
chemical_list: D006657:Histones