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Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas

Kjellin, Jonas and Avesson, Lotta and Reimegard, Johan and Liao, Zhen and Eichinger, Ludwig and Noegel, Angelika and Glockner, Gernot and Schaap, Pauline and Soderbom, Fredrik (2021). Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas. Genome Research. 31 , 436-447
[Research article]

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Abstract

Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum. However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.

Authors/Creators:Kjellin, Jonas and Avesson, Lotta and Reimegard, Johan and Liao, Zhen and Eichinger, Ludwig and Noegel, Angelika and Glockner, Gernot and Schaap, Pauline and Soderbom, Fredrik
Title:Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas
Series Name/Journal:Genome Research
Year of publishing :2021
Volume:31
Page range:436-447
Number of Pages:12
Publisher:COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
ISSN:1088-9051
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
URN:NBN:urn:nbn:se:slu:epsilon-p-111359
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-111359
Additional ID:
Type of IDID
DOI10.1101/gr.272856.120
Web of Science (WoS)000625081500001
ID Code:23261
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Molecular Biology (until 131231)
Deposited By: SLUpub Connector
Deposited On:13 Apr 2021 19:03
Metadata Last Modified:14 Apr 2021 05:01

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