Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes

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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 C 0T-1 (highly repeated) DNA probes detects surprisingly abundant euchromatin-associated RNA comprised predominantly of repeat sequences (C 0T-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. © 2014 Elsevier Inc.




Hall, L. L., Carone, D. M., Gomez, A. V., Kolpa, H. J., Byron, M., Mehta, N., … Lawrence, J. B. (2014). Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. Cell, 156(5), 907–919.

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