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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.

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


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.


Oxytricha; ciliate; epigenetics; lncRNA; long noncoding RNA

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