title: Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes.
abstract: 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.
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: Lisa L
authors.initials: LL
authors.lastname: Hall
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Carone
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: Alvin V
authors.initials: AV
authors.lastname: Gomez
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: Heather J
authors.initials: HJ
authors.lastname: Kolpa
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: Meg
authors.initials: M
authors.lastname: Byron
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
authors.forename: Nitish
authors.initials: N
authors.lastname: Mehta
authors.affiliation: Laboratory of Epigenetics and Chromosome Biology, Department of Biomedical Research, Institute for Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 45110 Ioannina, Greece.
authors.forename: Frank O
authors.initials: FO
authors.lastname: Fackelmayer
authors.affiliation: Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address: jeanne.lawrence@umassmed.edu.
authors.forename: Jeanne B
authors.initials: JB
authors.lastname: Lawrence
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000737:chemistry; D033481:Chromosomes, Mammalian / Q000737:chemistry*; D022041:Euchromatin / Q000737:chemistry*; D006801:Humans; D006822:Hybrid Cells; D007399:Interphase; D020084:Long Interspersed Nucleotide Elements; D051379:Mice; D022661:RNA, Untranslated / Q000032:analysis* / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D022041:Euchromatin; D022661:RNA, Untranslated