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

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


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Chromosomes / genetics*
  • DNA Copy Number Variations
  • Genome, Protozoan / genetics*
  • High-Throughput Nucleotide Sequencing / methods
  • Oxytricha / genetics*
  • Oxytricha / growth & development
  • RNA, Long Noncoding / genetics*
  • RNA, Protozoan / genetics*
  • Telomere / genetics


  • RNA, Long Noncoding
  • RNA, Protozoan