Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.
Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.
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大量表达的一类非编码RNA在分生孢子虫的多细胞进化过程中保持保守。
DOI：
10.1101/gr.272856.120
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发表时间：
2021-03
期刊：
影响因子：
7
通讯作者：
Söderbom F
中科院分区：
文献类型：
--
作者：
Kjellin J;Avesson L;Reimegård J;Liao Z;Eichinger L;Noegel A;Glöckner G;Schaap P;Söderbom F
聚集体多细胞性在不同的真核生物群体中已经进化了多次，例如盘形盘形骨变形虫的发育得到了充分的研究。然而，为什么在这些阿米巴原虫中出现了多细胞，而阿米巴原虫的大多数其他成员是单细胞的，人们仍然知之甚少。此前，一种新型的非编码RNA，即I类RNA，在盘状棘球蚴中被鉴定出来，并被证明对正常的多细胞发育很重要。在这里，我们研究了I类RNA的进化及其与多细胞发育的联系。通过构建协方差模型和基于上游保守序列的评分系统，我们鉴定了大量新的I类RNA基因。在Dictyostelia的每一个主要群体的代表中预测了多个基因，表达分析证实了我们的搜索方法具有较高的准确性和敏感性，并且这些RNA是发育调控的。进一步的研究表明，I类rna在盘形骨菌中普遍存在，并且具有高度保守的结构和序列基序。此外，I类RNA基因似乎是dictyostelid社会性变形虫所特有的，因为它们不能在外群基因组中被识别，包括它们最接近的已知亲属。我们的研究结果表明，I类RNA是一种古老的ncrna，可能存在于至少6亿年前的盘齿柱螈的最后一个共同祖先中。基于先前的功能分析和目前的进化研究，我们假设I类rna参与了盘形钢藻的多细胞进化。
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.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
4.5
作者：
Avesson, Lotta;Reimegard, Johan;Soderbom, Fredrik
通讯作者：
Soderbom, Fredrik
影响因子：
3.3
作者：
Hillmann F;Forbes G;Novohradská S;Ferling I;Riege K;Groth M;Westermann M;Marz M;Spaller T;Winckler T;Schaap P;Glöckner G
通讯作者：
Glöckner G
影响因子：
--
作者：
Blanco, Enrique;Parra, Genis;Guigo, Roderic
通讯作者：
Guigo, Roderic
影响因子：
14.9
作者：
Hinas, Andrea;Reimegard, Johan;Soderbom, Fredrik
通讯作者：
Soderbom, Fredrik