Identification of long noncoding RNAs in Schistosoma mansoni and Schistosoma japonicum

Liao, Qi; Zhang, Yuwei; Zhu, Yuchao; Chen, Jia; Chen, Dong; Yang, Tao; He, Anbang; Liu, Jianfa; Wu, Zhongdao

doi:10.1016/j.exppara.2018.07.001

Cited by 24 publications

(43 citation statements)

References 52 publications

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Section: Thousands Of Lncrnas Are Expressed In S Japonicummentioning

confidence: 99%

“…Liao et al [10] previously identified 3247 and 3033 potential lncRNAs in S. mansoni and S. japonicum, respectively. These authors used only two RNA-Seq libraries from S. japonicum, one from males and one from females [10]. Here we used a much higher number of RNA-Seq libraries from cercariae, sporocysts, schistosomula, and early-development or adult males and females, including the two libraries used by Liao et al [10], along with the newest version of the genome and transcriptome of S. japonicum, which were recently released with significant improvement in assembly contiguity [13].…”

Section: Thousands Of Lncrnas Are Expressed In S Japonicummentioning

confidence: 99%

“…These authors used only two RNA-Seq libraries from S. japonicum, one from males and one from females [10]. Here we used a much higher number of RNA-Seq libraries from cercariae, sporocysts, schistosomula, and early-development or adult males and females, including the two libraries used by Liao et al [10], along with the newest version of the genome and transcriptome of S. japonicum, which were recently released with significant improvement in assembly contiguity [13]. Our group has recently developed an improved pipeline for identification of lncRNAs [12] and we showed that a large set of the S. mansoni transcripts that we previously annotated as lncRNAs with a different pipeline [14] and also that by Liao et al [10], now seem to represent partially processed pre-mRNAs arising from novel protein-coding genes annotated in the newest version of the S. mansoni genome and transcriptome [12].…”

Section: Thousands Of Lncrnas Are Expressed In S Japonicummentioning

confidence: 99%

“…LncRNAs are defined as transcripts longer than 200 nucleotides, without any apparent protein-coding potential [9]. They were more recently annotated for the first time in S. japonicum by Liao et al [10], using only two RNA-Seq libraries, one from males and one from females. In mammals, lncRNAs were already identified as important regulators of vital processes, including sexual maturation and reproduction [11].…”

Section: Introductionmentioning

confidence: 99%

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Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

Maciel

Morales-Vicente

Verjovski-Almeida

2020

ncRNA

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Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification of protein-coding genes and pathways, whose expression levels were related to sexual development. However, this work did not include an analysis of long non-coding RNAs (lncRNAs). Here, we applied a pipeline to identify and annotate lncRNAs in 66 S. japonicum RNA-Seq publicly available libraries, from different life-cycle stages. We also performed co-expression analyses to find stage-specific lncRNAs possibly related to sexual maturation. We identified 12,291 S. japonicum expressed lncRNAs. Sequence similarity search and synteny conservation indicated that some 14% of S. japonicum intergenic lncRNAs have synteny conservation with S. mansoni intergenic lncRNAs. Co-expression analyses showed that lncRNAs and protein-coding genes in S. japonicum males and females have a dynamic co-expression throughout sexual maturation, showing differential expression between the sexes; the protein-coding genes were related to the nervous system development, lipid and drug metabolism, and overall parasite survival. Co-expression pattern suggests that lncRNAs possibly regulate these processes or are regulated by the same activation program as that of protein-coding genes.

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Section: Thousands Of Lncrnas Are Expressed In S Japonicummentioning

confidence: 99%

Section: Thousands Of Lncrnas Are Expressed In S Japonicummentioning

confidence: 99%

Section: Thousands Of Lncrnas Are Expressed In S Japonicummentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

Maciel

Morales-Vicente

Verjovski-Almeida

2020

ncRNA

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“…As sporocysts develop, they integrate into the snail host hepatopancreas resulting in challenges to RNA sequencing analysis to distinguish snail transcripts from mature sporocyst transcripts. Thus, while lncRNA identification has been performed in S. mansoni [22][23][24][25], there has not been a lncRNA analysis in in vivo sporocysts.…”

Section: Introductionmentioning

confidence: 99%

LncRNAs in molluscan and mammalian stages of parasitic schistosomes are developmentally-regulated and coordinately expressed with protein-coding genes

2020

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Despite the low level expression of some long noncoding RNAs (lncRNAs), the differential expression of specific lncRNAs plays important roles during the development of many organisms. Schistosomes, parasitic flatworms that are responsible for schistosomiasis, infects over 200 million people resulting in chronic disease and hundreds of thousands of deaths. Schistosomes have a complex life cycle that transitions between molluscan and mammalian hosts. In a molluscan snail host, the sporocyst stage develops over 5 weeks undergoing asexual reproduction to give rise to free-swimming and infectious cercariae that penetrate human skin and eventually mature into egg producing worms in mammals. The tight integration of the sporocyst to the snail host hepatopancreas hinders the-omics study in the molluscan stage, so the sporocyst transcriptome has only been examined for lncRNAs in immature in vitro samples. Here we analyzed the in vivo mature sporocyst transcriptome to identify 4,930 total lncRNAs between the molluscan and mammalian stages of the parasite. We further demonstrate that the lncRNAs are differentially expressed in a development-dependent manner. In addition, we constructed a co-expression correlation network between lncRNAs and protein-coding (PC) genes that was used to identify clusters of lncRNA transcripts with potential functional relevance. We also describe lncRNA-lncRNA and lncRNA-kinome correlations that identify lncRNAs with prospective roles in gene regulation. Finally, our results show clear differential expression patterns of lncRNAs in host-dependent development stages of S. mansoni and ascribe potential functional roles in development based on predicted intracellular interaction.

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Step-by-Step Bioinformatics Analysis of Schistosoma mansoni Long Non-coding RNA Sequences

Maciel

Verjovski-Almeida

2020

Methods in Molecular Biology

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Identification of long noncoding RNAs in Schistosoma mansoni and Schistosoma japonicum

Cited by 24 publications

References 52 publications

Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

LncRNAs in molluscan and mammalian stages of parasitic schistosomes are developmentally-regulated and coordinately expressed with protein-coding genes

Step-by-Step Bioinformatics Analysis of Schistosoma mansoni Long Non-coding RNA Sequences

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