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MicroRNAome of porcine pre- and postnatal development.

Li M, Xia Y, Gu Y, Zhang K, Lang Q, Chen L, Guan J, Luo Z, Chen H, Li Y, Li Q, Li X, Jiang AA, Shuai S, Wang J, Zhu Q, Zhou X, Gao X, Li X - PLoS ONE (2010)

Bottom Line: Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique.We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data.These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.

View Article: PubMed Central - PubMed

Affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China.

ABSTRACT
The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.

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The temporal profile of the known porcine miRNAs and new miRNA*s.(A) The total pre-miRNAs represented in miRBase (left) and an updated count by this study (right). The pre-miRNAs in four groups: type containing miR-5p (blue), miR-3p (tan), both miR-5p and miR-3p (brown), and miRNAs not detected in this study (white) in the pre-miRNAs. (B) The miRNAs from 16 pre-miRNAs which show patterns of both miR-5p and miR-3p or either miR-5p and miR-3p present in all ten libraries profiled over pre- and postnatal development stages. Data reflect the most abundant isomiRs scaled based on the total counts of the mappable sequences in each library shown in log2-scale. For each miRNA, “New” means miRNA identified in this study; “Diff” means our reported miRNA sequences are different from that of miRBase; “Yes” means our reported miRNA sequences are consistent with those of miRBase. The two miRNAs (miR-1a-3p and miR-122-5p) with the highest expression level (Table S14) are marked by red dots.
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pone-0011541-g002: The temporal profile of the known porcine miRNAs and new miRNA*s.(A) The total pre-miRNAs represented in miRBase (left) and an updated count by this study (right). The pre-miRNAs in four groups: type containing miR-5p (blue), miR-3p (tan), both miR-5p and miR-3p (brown), and miRNAs not detected in this study (white) in the pre-miRNAs. (B) The miRNAs from 16 pre-miRNAs which show patterns of both miR-5p and miR-3p or either miR-5p and miR-3p present in all ten libraries profiled over pre- and postnatal development stages. Data reflect the most abundant isomiRs scaled based on the total counts of the mappable sequences in each library shown in log2-scale. For each miRNA, “New” means miRNA identified in this study; “Diff” means our reported miRNA sequences are different from that of miRBase; “Yes” means our reported miRNA sequences are consistent with those of miRBase. The two miRNAs (miR-1a-3p and miR-122-5p) with the highest expression level (Table S14) are marked by red dots.

Mentions: A closer look at the mapped known porcine miRNAs from ten libraries in this study indicates that 72 of the 77 known porcine miRNAs and one miRNA* (total 92.3%), were detected (Figure 2A). This high detection rate illustrates that our ten small RNA libraries almost encompass the entire repertoire of previously known miRNAs. Additionally, 36 new miRNA*s have been identified (Table S6). When we looked at the distributions and counts of sequences originating from different arms of the pre-miRNAs, we found that in most cases, counts of sequences were heavily skewed toward the RNA hairpin arm containing the known miRNAs (Figure 2B). In many cases, these low abundance miRNA*s cannot be detected by conventional methods possibly due to their rapid turnover and the spatial, temporal, and physiological regulation of miRNA expression. There is only one known porcine pre-miRNA (mir-140) which codes for two miRNAs. In our experiments, the miR-140-5p (annotated as miR-140) has much lower abundance (in total of 23 counts) than miR-140-3p (annotated as miR-140*, in total of 33 K counts) (Table S6). The miRBase database should be updated to reflect these findings.


MicroRNAome of porcine pre- and postnatal development.

Li M, Xia Y, Gu Y, Zhang K, Lang Q, Chen L, Guan J, Luo Z, Chen H, Li Y, Li Q, Li X, Jiang AA, Shuai S, Wang J, Zhu Q, Zhou X, Gao X, Li X - PLoS ONE (2010)

The temporal profile of the known porcine miRNAs and new miRNA*s.(A) The total pre-miRNAs represented in miRBase (left) and an updated count by this study (right). The pre-miRNAs in four groups: type containing miR-5p (blue), miR-3p (tan), both miR-5p and miR-3p (brown), and miRNAs not detected in this study (white) in the pre-miRNAs. (B) The miRNAs from 16 pre-miRNAs which show patterns of both miR-5p and miR-3p or either miR-5p and miR-3p present in all ten libraries profiled over pre- and postnatal development stages. Data reflect the most abundant isomiRs scaled based on the total counts of the mappable sequences in each library shown in log2-scale. For each miRNA, “New” means miRNA identified in this study; “Diff” means our reported miRNA sequences are different from that of miRBase; “Yes” means our reported miRNA sequences are consistent with those of miRBase. The two miRNAs (miR-1a-3p and miR-122-5p) with the highest expression level (Table S14) are marked by red dots.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2902522&req=5

pone-0011541-g002: The temporal profile of the known porcine miRNAs and new miRNA*s.(A) The total pre-miRNAs represented in miRBase (left) and an updated count by this study (right). The pre-miRNAs in four groups: type containing miR-5p (blue), miR-3p (tan), both miR-5p and miR-3p (brown), and miRNAs not detected in this study (white) in the pre-miRNAs. (B) The miRNAs from 16 pre-miRNAs which show patterns of both miR-5p and miR-3p or either miR-5p and miR-3p present in all ten libraries profiled over pre- and postnatal development stages. Data reflect the most abundant isomiRs scaled based on the total counts of the mappable sequences in each library shown in log2-scale. For each miRNA, “New” means miRNA identified in this study; “Diff” means our reported miRNA sequences are different from that of miRBase; “Yes” means our reported miRNA sequences are consistent with those of miRBase. The two miRNAs (miR-1a-3p and miR-122-5p) with the highest expression level (Table S14) are marked by red dots.
Mentions: A closer look at the mapped known porcine miRNAs from ten libraries in this study indicates that 72 of the 77 known porcine miRNAs and one miRNA* (total 92.3%), were detected (Figure 2A). This high detection rate illustrates that our ten small RNA libraries almost encompass the entire repertoire of previously known miRNAs. Additionally, 36 new miRNA*s have been identified (Table S6). When we looked at the distributions and counts of sequences originating from different arms of the pre-miRNAs, we found that in most cases, counts of sequences were heavily skewed toward the RNA hairpin arm containing the known miRNAs (Figure 2B). In many cases, these low abundance miRNA*s cannot be detected by conventional methods possibly due to their rapid turnover and the spatial, temporal, and physiological regulation of miRNA expression. There is only one known porcine pre-miRNA (mir-140) which codes for two miRNAs. In our experiments, the miR-140-5p (annotated as miR-140) has much lower abundance (in total of 23 counts) than miR-140-3p (annotated as miR-140*, in total of 33 K counts) (Table S6). The miRBase database should be updated to reflect these findings.

Bottom Line: Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique.We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data.These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.

View Article: PubMed Central - PubMed

Affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China.

ABSTRACT
The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies.

Show MeSH