Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements

RNA. 2022 Aug;28(8):1110-1127. doi: 10.1261/rna.079134.122. Epub 2022 Jun 9.


Noncoding RNAs (ncRNAs) make up to ∼98% percent of the transcriptome of a given organism. In recent years, one relatively new class of ncRNAs, long noncoding RNAs (lncRNAs), were shown to be more than mere by-products of gene expression and regulation. The unicellular eukaryote Paramecium tetraurelia is a member of the ciliate phylum, an extremely heterogeneous group of organisms found in most bodies of water across the globe. A hallmark of ciliate genetics is nuclear dimorphism and programmed elimination of transposons and transposon-derived DNA elements, the latter of which is essential for the maintenance of the somatic genome. Paramecium and ciliates in general harbor a plethora of different ncRNA species, some of which drive the process of large-scale genome rearrangements, including DNA elimination, during sexual development. Here, we identify and validate the first known functional lncRNAs in ciliates to date. Using deep-sequencing and subsequent bioinformatic processing and experimental validation, we show that Paramecium expresses at least 15 lncRNAs. These candidates were predicted by a highly conservative pipeline, and informatic analyses hint at differential expression during development. Depletion of two lncRNAs, lnc1 and lnc15, resulted in clear phenotypes, decreased survival, morphological impairment, and a global effect on DNA elimination.

Keywords: DNA elimination; ciliate; genome rearrangement; lncRNA; sRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus / genetics
  • DNA Transposable Elements / genetics
  • Gene Rearrangement
  • Paramecium tetraurelia* / genetics
  • RNA, Long Noncoding* / genetics
  • RNA, Untranslated / genetics


  • DNA Transposable Elements
  • RNA, Long Noncoding
  • RNA, Untranslated