Journal
CELL
Volume 156, Issue 5, Pages 907-919Publisher
CELL PRESS
DOI: 10.1016/j.cell.2014.01.042
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Funding
- NIH [GM053234, GM107604, S10RR027897]
- NIH/NCI NRSA [1F32CA154086]
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Recent studies recognize a vast diversity of noncoding RNAs with largely unknown functions, but few have examined interspersed repeat sequences, which constitute almost half our genome. RNA hybridization in situ using C0T-1 (highly repeated) DNA probes detects surprisingly abundant euchromatin-associated RNA comprised predominantly of repeat sequences (C0T-1 RNA), including LINE-1. C0T-1-hybridizing RNA strictly localizes to the interphase chromosome territory in cis and remains stably associated with the chromosome territory following prolonged transcriptional inhibition. The C0T-1 RNA territory resists mechanical disruption and fractionates with the nonchromatin scaffold but can be experimentally released. Loss of repeat-rich, stable nuclear RNAs from euchromatin corresponds to aberrant chromatin distribution and condensation. C0T-1 RNA has several properties similar to XIST chromosomal RNA but is excluded from chromatin condensed by XIST. These findings impact two black boxes of genome science: the poorly understood diversity of noncoding RNA and the unexplained abundance of repetitive elements.
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