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.
Keaton MA, Taylor CM, Layer RM, Dutta A, 2011 Nuclear Scaffold Attachment Sites within ENCODE Regions Associate with Actively Transcribed Genes. PLoS ONE 6(3): e17912. doi:10.1371/journal.pone.0017912