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Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum.

Hao L, Cai P, Jiang N, Wang H, Chen Q - BMC Genomics (2010)

Bottom Line: The endogenous siRNAs were found mainly derived from transposable elements (TE) or transposons and the natural antisense transcripts (NAT).A majority of miRNA transcripts identified in the parasite were species-specific and the expression of certain miRNAs was found developmentally regulated.Both miRNA and siRNAs are potentially important regulators in the development of schistosomal parasites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing 100730, PR China.

ABSTRACT

Background: Small endogenous non-coding RNAs (sncRNAs) such as small interfering RNA (siRNA), microRNA and other small RNA transcripts are derived from distinct loci in the genome and play critical roles in RNA-mediated gene silencing mechanisms in plants and metazoa. They are approximately 22 nucleotides long; regulate mRNA stability through perfect or imperfect match to the targets. The biological activities of sncRNAs have been related to many biological events, from resistance to microbe infections to cellular differentiation. The development of the zoonotic parasite Schistosoma japonicum parasite includes multiple steps of morphological alterations and biological differentiations, which provide a unique model for studies on the functions of small RNAs. Characterization of the genome-wide transcription of the sncRNAs will be a major step in understanding of the parasite biology. The objective of this study is to investigate the transcriptional profile and potential function of the small non-coding RNAs in the development of S. japanicum.

Results: The endogenous siRNAs were found mainly derived from transposable elements (TE) or transposons and the natural antisense transcripts (NAT). In contrast to other organisms, the TE-derived siRNAs in S. japonicum were more predominant than other sncRNAs including microRNAs (miRNAs). Further, there were distinct length and 3'end variations in the sncRNAs, which were associated with the developmental differentiation of the parasite. Among the identified miRNA transcripts, there were 38 unique to S. japonicum and 16 that belonged to 13 miRNA families are common to other metazoan lineages. These miRNAs were either ubiquitously expressed, or they exhibited specific expression patterns related to the developmental stages or sex. Genes that encoded miRNAs are mainly located in clusters within the genome of S. japonicum. However, genes within one cluster could be differentially transcribed, which suggested that individual genes might be regulated by distinct mechanisms during parasite development.

Conclusions: Many miRNA and endogenous siRNA transcripts were identified in S. japonicum and the amount of siRNA was at least 4.4 and 1.6 times more than that of miRNA in both schistosomulum and adult worm stages respectively. SiRNAs are mainly derived from transposable elements (or transposons); while natural antisense transcripts (NAT)-derived siRNAs were much less. A majority of miRNA transcripts identified in the parasite were species-specific and the expression of certain miRNAs was found developmentally regulated. Both miRNA and siRNAs are potentially important regulators in the development of schistosomal parasites.

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Small interfering RNAs and microRNAs identified by high-throughput sequencing in S. japonicum. A and B Length and distribution of siRNAs and miRNAs in adult and schistosomulum stages. C. 3' end variations in TE and NAT-derived siRNAs and miRNAs.
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Figure 3: Small interfering RNAs and microRNAs identified by high-throughput sequencing in S. japonicum. A and B Length and distribution of siRNAs and miRNAs in adult and schistosomulum stages. C. 3' end variations in TE and NAT-derived siRNAs and miRNAs.

Mentions: The variations in the length of sncRNAs in S. japonicum were associated with the developmental stages of the parasite. In adult worms, there was an even distribution of the amount of sncRNAs that were between 20 and 23 nt (Fig 3a,b). The TE-derived siRNAs were predominantly 20 nt in adult worms, whereas they exhibited a wider range in length in schistosomulum between 18 and 28 nt (Fig. 3a,b). The NAT-derived siRNAs were predominantly 20 nt in parasites of both schistosomulum and adult stages. Thus TE-derived siRNAs and NAT-derived siRNAs were generated under different regulatory and processing mechanisms. The size of the miRNAs also differed between the two developmental stages. In adult worms, miRNAs ranging from 19 to 23 nt were found, although the miRNAs of 22 and 23 nt accounted for the majority (Fig. 3a). However, miRNAs of 23 nt were predominant in schistosomulum (Fig. 3b) indicating that several miRNA processing pathways might be functional in different developmental stages of the parasite.


Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum.

Hao L, Cai P, Jiang N, Wang H, Chen Q - BMC Genomics (2010)

Small interfering RNAs and microRNAs identified by high-throughput sequencing in S. japonicum. A and B Length and distribution of siRNAs and miRNAs in adult and schistosomulum stages. C. 3' end variations in TE and NAT-derived siRNAs and miRNAs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2820009&req=5

Figure 3: Small interfering RNAs and microRNAs identified by high-throughput sequencing in S. japonicum. A and B Length and distribution of siRNAs and miRNAs in adult and schistosomulum stages. C. 3' end variations in TE and NAT-derived siRNAs and miRNAs.
Mentions: The variations in the length of sncRNAs in S. japonicum were associated with the developmental stages of the parasite. In adult worms, there was an even distribution of the amount of sncRNAs that were between 20 and 23 nt (Fig 3a,b). The TE-derived siRNAs were predominantly 20 nt in adult worms, whereas they exhibited a wider range in length in schistosomulum between 18 and 28 nt (Fig. 3a,b). The NAT-derived siRNAs were predominantly 20 nt in parasites of both schistosomulum and adult stages. Thus TE-derived siRNAs and NAT-derived siRNAs were generated under different regulatory and processing mechanisms. The size of the miRNAs also differed between the two developmental stages. In adult worms, miRNAs ranging from 19 to 23 nt were found, although the miRNAs of 22 and 23 nt accounted for the majority (Fig. 3a). However, miRNAs of 23 nt were predominant in schistosomulum (Fig. 3b) indicating that several miRNA processing pathways might be functional in different developmental stages of the parasite.

Bottom Line: The endogenous siRNAs were found mainly derived from transposable elements (TE) or transposons and the natural antisense transcripts (NAT).A majority of miRNA transcripts identified in the parasite were species-specific and the expression of certain miRNAs was found developmentally regulated.Both miRNA and siRNAs are potentially important regulators in the development of schistosomal parasites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Parasitology, Institute of Pathogen Biology/Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing 100730, PR China.

ABSTRACT

Background: Small endogenous non-coding RNAs (sncRNAs) such as small interfering RNA (siRNA), microRNA and other small RNA transcripts are derived from distinct loci in the genome and play critical roles in RNA-mediated gene silencing mechanisms in plants and metazoa. They are approximately 22 nucleotides long; regulate mRNA stability through perfect or imperfect match to the targets. The biological activities of sncRNAs have been related to many biological events, from resistance to microbe infections to cellular differentiation. The development of the zoonotic parasite Schistosoma japonicum parasite includes multiple steps of morphological alterations and biological differentiations, which provide a unique model for studies on the functions of small RNAs. Characterization of the genome-wide transcription of the sncRNAs will be a major step in understanding of the parasite biology. The objective of this study is to investigate the transcriptional profile and potential function of the small non-coding RNAs in the development of S. japanicum.

Results: The endogenous siRNAs were found mainly derived from transposable elements (TE) or transposons and the natural antisense transcripts (NAT). In contrast to other organisms, the TE-derived siRNAs in S. japonicum were more predominant than other sncRNAs including microRNAs (miRNAs). Further, there were distinct length and 3'end variations in the sncRNAs, which were associated with the developmental differentiation of the parasite. Among the identified miRNA transcripts, there were 38 unique to S. japonicum and 16 that belonged to 13 miRNA families are common to other metazoan lineages. These miRNAs were either ubiquitously expressed, or they exhibited specific expression patterns related to the developmental stages or sex. Genes that encoded miRNAs are mainly located in clusters within the genome of S. japonicum. However, genes within one cluster could be differentially transcribed, which suggested that individual genes might be regulated by distinct mechanisms during parasite development.

Conclusions: Many miRNA and endogenous siRNA transcripts were identified in S. japonicum and the amount of siRNA was at least 4.4 and 1.6 times more than that of miRNA in both schistosomulum and adult worm stages respectively. SiRNAs are mainly derived from transposable elements (or transposons); while natural antisense transcripts (NAT)-derived siRNAs were much less. A majority of miRNA transcripts identified in the parasite were species-specific and the expression of certain miRNAs was found developmentally regulated. Both miRNA and siRNAs are potentially important regulators in the development of schistosomal parasites.

Show MeSH
Related in: MedlinePlus