Atlas of<i>Schistosoma mansoni</i>long non-coding RNAs and their expression correlation to protein-coding genes

Vasconcelos, Elton J R; Mesel, Vinícius C.; DaSilva, Luis; Pires, David S.; Lavezzo, Guilherme M.; Pereira, Adriana S. A.; Amaral, Murilo Sena; Verjovski-Almeida, Sérgio

doi:10.1093/database/bay068

Cited by 14 publications

(13 citation statements)

References 21 publications

(27 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While some of them surely represent assembly artifacts, others might be functionally relevant. According to the recent publications [66][67][68][69][70][71] long non-coding RNAs (ncRNAs) are one of the important regulators of gene expression and indispensable components of genetic networks. Analysis of the diversity and roles of non-coding RNAs in the Psilostomatidae is, therefore, a promising research direction for the future.…”

Section: Discussionmentioning

confidence: 99%

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

et al. 2020

View full text Add to dashboard Cite

Background Parasitic flatworms (Trematoda: Digenea) represent one of the most remarkable examples of drastic morphological diversity among the stages within a life cycle. Which genes are responsible for extreme differences in anatomy, physiology, behavior, and ecology among the stages? Here we report a comparative transcriptomic analysis of parthenogenetic and amphimictic generations in two evolutionary informative species of Digenea belonging to the family Psilostomatidae. Methods In this study the transcriptomes of rediae, cercariae and adult worm stages of Psilotrema simillimum and Sphaeridiotrema pseudoglobulus, were sequenced and analyzed. High-quality transcriptomes were generated, and the reference sets of protein-coding genes were used for differential expression analysis in order to identify stage-specific genes. Comparative analysis of gene sets, their expression dynamics and Gene Ontology enrichment analysis were performed for three life stages within each species and between the two species. Results Reference transcriptomes for P. simillimum and S. pseudoglobulus include 21,433 and 46,424 sequences, respectively. Among 14,051 orthologous groups (OGs), 1354 are common and specific for two analyzed psilostomatid species, whereas 13 and 43 OGs were unique for P. simillimum and S. pseudoglobulus, respectively. In contrast to P. simillimum, where more than 60% of analyzed genes were active in the redia, cercaria and adult worm stages, in S. pseudoglobulus less than 40% of genes had such a ubiquitous expression pattern. In general, 7805 (36.41%) and 30,622 (65.96%) of genes were preferentially expressed in one of the analyzed stages of P. simillimum and S. pseudoglobulus, respectively. In both species 12 clusters of co-expressed genes were identified, and more than a half of the genes belonging to the reference sets were included into these clusters. Functional specialization of the life cycle stages was clearly supported by Gene Ontology enrichment analysis. Conclusions During the life cycles of the two species studied, most of the genes change their expression levels considerably, consequently the molecular signature of a stage is not only a unique set of expressed genes, but also the specific levels of their expression. Our results indicate unexpectedly high level of plasticity in gene regulation between closely related species. Transcriptomes of P. simillimum and S. pseudoglobulus provide high quality reference resource for future evolutionary studies and comparative analyses.

show abstract

Section: Discussionmentioning

confidence: 99%

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The involvement of specific lncR-NAs in hepatic diseases has been described, and hepatic stellate cells trans-differentiation is regulated by different lncRNAs [19][20][21] A previous study employed different tools to study differential gene expression patterns occurring in response to Schistosoma infections [22]. Recently, Schistosoma lncRNAs have also been investigated for their potential functions [23][24][25][26][27][28][29]. However, lncRNAs in Schistosoma japonicum-infected mouse liver and spleen samples have not been investigated by RNA-Seq.…”

Section: Introductionmentioning

confidence: 99%

RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen

et al. 2020

View full text Add to dashboard Cite

Background Schistosomiasis is a chronic, debilitating infectious disease caused by members of the genus Schistosoma. Previous findings have suggested a relationship between infection with Schistosoma spp. and alterations in the liver and spleen of infected animals. Recent reports have shown the regulatory role of noncoding RNAs, such as long noncoding RNAs (lncRNAs), in different biological processes. However, little is known about the role of lncRNAs in the mouse liver and spleen during Schistosoma japonicum infection. Methods In this study, we identified and investigated lncRNAs using standard RNA sequencing (RNA-Seq). The biological functions of the altered expression of lncRNAs and their target genes were predicted using bioinformatics. Ten dysregulated lncRNAs were selected randomly and validated in reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) experiments. Results Our study identified 29,845 and 33,788 lncRNAs from the liver and spleen, respectively, of which 212 were novel lncRNAs. We observed that 759 and 789 of the lncRNAs were differentially expressed in the respective organs. The RT-qPCR results correlated well with the sequencing data. In the liver, 657 differentially expressed lncRNAs were predicted to target 2548 protein-coding genes, whereas in the spleen 660 differentially expressed lncRNAs were predicted to target 2673 protein-coding genes. Moreover, functional annotation showed that the target genes of the differentially expressed lncRNAs were associated with cellular processes, metabolic processes, and binding, and were significantly enriched in metabolic pathways, the cell cycle, ubiquitin-mediated proteolysis, and pathways in cancer. Conclusions Our study showed that numerous lncRNAs were differentially expressed in S. japonicum-infected liver and spleen compared to control liver and spleen; this suggested that lncRNAs may be involved in pathogenesis in the liver and spleen during S. japonicum infection.

show abstract

“…High-throughput next-generation sequencing has brought about the discovery of thousands of noncoding RNA genes (ncRNAs), such as short, long, and circular RNAs, over the last several decades. Also, several studies have been conducted for identification of both miRNAs and lncRNAs in Schistosoma genomes [ 25 – 27 ].…”

Section: Discussionmentioning

confidence: 99%

In Silico Analysis of Common Long Noncoding RNAs in Schistosoma mansoni and Schistosoma haematobium

Sirekbasan

Tan

2021

Journal of Tropical Medicine

View full text Add to dashboard Cite

Background. Schistosomiasis caused by Schistosoma parasites is one of the most common parasitic infections worldwide. Genetic regulation of the genus Schistosoma, which has different developmental stages throughout its life, is quite complex. In these parasites, thousands of long noncoding RNAs (lncRNAs) estimated to be functional were identified. Identifying the transcripts expressed in common and detecting their functions for better understanding of the role of these lncRNAs require a comparative study. Methods. Assembled RNA-seq datasets belonging to S. mansoni and S. haematobium were obtained from the National Center for Biotechnology. A basic local alignment search tool (BLASTN) analysis was conducted against previously constructed lncRNA library to identify the common lncRNAs between two species. LncRNAs target genes and their gene ontology annotation was performed. Results. In S. mansoni and S. haematobium, 5132 and 3589 lncRNA transcripts were detected, respectively. These two species had 694 lncRNAs in common. A significant number of lncRNAs was determined to be transcribed from sex chromosomes. The frequently expressed lncRNAs appear to be involved in metabolic and biological regulation processes. Conclusions. These two species share similar lncRNAs; thus, this finding is a clue that they might have similar functions. In sexual development, they especially might play important roles. Our results will provide important clues to further studies about interactions between human hosts and parasites and the infection mechanisms of Schistosoma parasites.

show abstract

Atlas ofSchistosoma mansonilong non-coding RNAs and their expression correlation to protein-coding genes

Cited by 14 publications

References 21 publications

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen

In Silico Analysis of Common Long Noncoding RNAs in Schistosoma mansoni and Schistosoma haematobium

Contact Info

Product

Resources

About