Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics.
Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics.
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DOI：
10.1099/mgen.0.000821
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发表时间：
2022-05
影响因子：
3.9
通讯作者：
Kissinger, Jessica C.
中科院分区：
文献类型：
--
作者：
Li, Yiran;Baptista, Rodrigo P.;Mei, Xiaohan;Kissinger, Jessica C.
中小型非编码rna （sRNAs和is-ncRNAs）已被证明在几种真核生物的发育中发挥重要的调节作用。然而，它们尚未在隐孢子虫小隐孢子虫中进行彻底的探索，隐孢子虫小隐孢子虫是一种专性人畜共患原生寄生虫，负责腹泻病隐孢子虫病。利用Illumina对小RNA文库进行测序，系统地鉴定了新的小RNA和is-ncRNAs。共鉴定出79个新的候选is-ncRNA，包括反义、基因间和内含子的is-ncRNA，其中包括7个新的小核仁rna （small nucleolar rna, snorna）。通过RT-PCR证实了选择的新型is- ncrna的表达。利用协方差模型（CMs）分析隐孢子虫和顶复合体相关基因组序列的系统发育保守性。从tRNA片段中衍生出一种潜在的新型小ncRNA。总体而言，对小虫卵及其相关物种中新型is-ncRNAs的深入分析揭示了这些新型is-ncRNAs的结构特征和保守性。协方差模型可用于检测其他密切相关寄生虫中的is-ncRNA基因。这些发现为原病原体小孢子虫中新型is- ncrna的额外功能表征提供了重要的新序列。
Small and intermediate-size noncoding RNAs (sRNAs and is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Cryptosporidium parvum, an obligate zoonotic protist parasite responsible for the diarrhoeal disease cryptosporidiosis. Using Illumina sequencing of a small RNA library, a systematic identification of novel small and is-ncRNAs was performed in C. parvum excysted sporozoites. A total of 79 novel is-ncRNA candidates, including antisense, intergenic and intronic is-ncRNAs, were identified, including 7 new small nucleolar RNAs (snoRNAs). Expression of select novel is-ncRNAs was confirmed by RT-PCR. Phylogenetic conservation was analysed using covariance models (CMs) in related Cryptosporidium and apicomplexan parasite genome sequences. A potential new type of small ncRNA derived from tRNA fragments was observed. Overall, a deep profiling analysis of novel is-ncRNAs in C. parvum and related species revealed structural features and conservation of these novel is-ncRNAs. Covariance models can be used to detect is-ncRNA genes in other closely related parasites. These findings provide important new sequences for additional functional characterization of novel is-ncRNAs in the protist pathogen C. parvum.
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影响因子：
--
作者：
Kalvari I;Nawrocki EP;Argasinska J;Quinones-Olvera N;Finn RD;Bateman A;Petrov AI
通讯作者：
Petrov AI
影响因子：
--
作者：
Langmead, Ben
通讯作者：
Langmead, Ben
DOI：
10.1093/bioinformatics/btp250
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Darty K;Denise A;Ponty Y
通讯作者：
Ponty Y
影响因子：
3.7
作者：
Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
通讯作者：
Ribeca P
影响因子：
16.6
作者：
Fricker, Roger;Brogli, Rebecca;Polacek, Norbert
通讯作者：
Polacek, Norbert