Transcriptional Regulators of the 51D Surface Protein Gene of<i>Paramecium tetraurelia</i>

Tanabe, Hiroyuki; Haraguchi, Isao; Yoshioka, Setsuko

doi:10.1271/bbb.66.2567

Cited by 1 publication

(1 citation statement)

References 17 publications

(10 reference statements)

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“…NATs also will not appear in the output of the pipeline as long as they overlap with coding transcripts, although they can be found in the intermediate output of the first two modules by custom scripts. Previously predicted putative lncRNAs such as MS2 (Tanabe and Le 2006;Tanabe and Mori 2003) in P.tetraurelia were found by the pipeline in the first two modules, suggesting that it functions under agreeable parameters. In summary, the pipeline is by no means an alternative for use in model organisms where enough data is available to train machine learning algorithms.…”

Section: Discussionmentioning

confidence: 90%

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

Bechara

Kabbani

Alcala

et al. 2022

RNA

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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.

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Section: Discussionmentioning

confidence: 90%