title: Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.
abstract: The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America.
authors.forename: Mignon A
authors.initials: MA
authors.lastname: Keaton
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Taylor
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Layer
authors.forename: Anindya
authors.initials: A
authors.lastname: Dutta
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D022041:Euchromatin / Q000737:chemistry / Q000378:metabolism; D005786:Gene Expression Regulation; D015894:Genome, Human / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D045170:Matrix Attachment Regions / Q000235:genetics*; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000235:genetics*; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D022041:Euchromatin