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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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The abundance of each siRNA sequence generated from the two transposons by scanning each siRNA sequence against the two transposons (A. SACI-5 and B. TRE-1). Data represents the percentage of all matched siRNAs identified in adult (red) and schistosomulum (blue) parasites.
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Figure 2: The abundance of each siRNA sequence generated from the two transposons by scanning each siRNA sequence against the two transposons (A. SACI-5 and B. TRE-1). Data represents the percentage of all matched siRNAs identified in adult (red) and schistosomulum (blue) parasites.

Mentions: Of the small sncRNAs transcripts identified in S. japonicum, a large portion was from potential transposable elements (TE) (Additional files 2, 3, 4, 5 and 6). Due to the fact that these sncRNAs showed similar structural signatures to siRNA transcripts reported in Drosophila[10], the small RNA transcript sequences mapped to the transposable elements (TE) and the natural antisense transcripts (NAT) were regarded as endogenous siRNAs[11,12]. Since TEs have not been previously identified in S. japonicum, we conducted TE prediction by scanning the genome sequence using REPET software. Long terminal repeats (LTR), long interspersed nucleotide elements (LINE), short interspersed elements (SINE), large terminal inverted repeats (TIR) and miniature inverted-repeat transposable elements (MITE) were the main classes of transposons identified in the genome. We found that TE-related sequences accounted for 13 percent of the S. japonicum genome (Additional file 7), which is lower than that observed in mammalian DNA that can range between 30 and 50% [13,14]. Further, SiRNAs derived from LTR, TIR and LINE accounted for the majority and transcripts from sense and antisense strands were identified (Fig. 1, Additional files 2, 3, 4, 5 and 6). Sequence scanning of the two transposons SACI-5 (LTR class retrotransposon) [15] and RTE-1 (LINE class) revealed that siRNAs were derived from more concentrated regions in the sequence (Fig. 2a, b), contrast to that found in Drosophila, in which siRNAs were generated uniformly from the whole transposon sequence[10].


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

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

The abundance of each siRNA sequence generated from the two transposons by scanning each siRNA sequence against the two transposons (A. SACI-5 and B. TRE-1). Data represents the percentage of all matched siRNAs identified in adult (red) and schistosomulum (blue) parasites.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The abundance of each siRNA sequence generated from the two transposons by scanning each siRNA sequence against the two transposons (A. SACI-5 and B. TRE-1). Data represents the percentage of all matched siRNAs identified in adult (red) and schistosomulum (blue) parasites.
Mentions: Of the small sncRNAs transcripts identified in S. japonicum, a large portion was from potential transposable elements (TE) (Additional files 2, 3, 4, 5 and 6). Due to the fact that these sncRNAs showed similar structural signatures to siRNA transcripts reported in Drosophila[10], the small RNA transcript sequences mapped to the transposable elements (TE) and the natural antisense transcripts (NAT) were regarded as endogenous siRNAs[11,12]. Since TEs have not been previously identified in S. japonicum, we conducted TE prediction by scanning the genome sequence using REPET software. Long terminal repeats (LTR), long interspersed nucleotide elements (LINE), short interspersed elements (SINE), large terminal inverted repeats (TIR) and miniature inverted-repeat transposable elements (MITE) were the main classes of transposons identified in the genome. We found that TE-related sequences accounted for 13 percent of the S. japonicum genome (Additional file 7), which is lower than that observed in mammalian DNA that can range between 30 and 50% [13,14]. Further, SiRNAs derived from LTR, TIR and LINE accounted for the majority and transcripts from sense and antisense strands were identified (Fig. 1, Additional files 2, 3, 4, 5 and 6). Sequence scanning of the two transposons SACI-5 (LTR class retrotransposon) [15] and RTE-1 (LINE class) revealed that siRNAs were derived from more concentrated regions in the sequence (Fig. 2a, b), contrast to that found in Drosophila, in which siRNAs were generated uniformly from the whole transposon sequence[10].

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