Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements
Open Access
- 9 June 2022
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 28 (8), 1110-1127
- https://doi.org/10.1261/rna.079134.122
Abstract
Non-coding RNAs (ncRNAs) make up to ~98% percent of the transcriptome of a given organism. In recent years one relatively new class of ncRNAs, long non-coding 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 harbour 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
Funding Information
- European Research Council grants (260358)
- “EPIGENOME” (681178)
- “G-EDIT,”
- Swiss National Science Foundation Grants (31003A_146257, 31003A_166407)
- National Center of Competence in Research (NCCR) RNA and Disease
This publication has 75 references indexed in Scilit:
- An integrated encyclopedia of DNA elements in the human genomeNature, 2012
- Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genesNucleic Acids Research, 2011
- Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodellingNucleic Acids Research, 2011
- RNA-mediated epigenetic regulation of DNA copy numberProceedings of the National Academy of Sciences of the United States of America, 2010
- The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor PhosphorylationMolecular Cell, 2010
- PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraureliaGenes & Development, 2009
- Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraureliaNucleic Acids Research, 2008
- RNA-mediated epigenetic programming of a genome-rearrangement pathwayNature, 2007
- Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAsCell, 2007
- Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraureliaNature, 2006