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RNA. 2017 Aug;23(8):1200-1208. doi: 10.1261/rna.058511.116. Epub 2017 Apr 27.

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development.

Author information

1
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.
2
Department of Biology, American University, Washington, DC 20016, USA.
3
Department of Psychiatry, University of California, San Diego, California, La Jolla 92093, USA.
4
Department of Biochemistry and Molecular Biophysics.
5
Department of Biological Sciences, Columbia University, New York, New York 10032, USA.

Abstract

The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, Oxytricha produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which Oxytricha transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that Oxytricha may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.

KEYWORDS:

Oxytricha; ciliate; epigenetics; lncRNA; long noncoding RNA

PMID:
28450531
PMCID:
PMC5513065
DOI:
10.1261/rna.058511.116
[Indexed for MEDLINE]
Free PMC Article

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