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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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Expressed kinds of 771 unique miRNAs across ten libraries are summarized.(A) Plot of miRNAs detected in one (1-lib), two (2-lib), … 10-libraries (10-lib). The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in 1-lib, 73/144 means that 73 mammalian-conserved miRNAs and 144 pig-specific are present once in the 10 libraries. The bar graphs are depicted in a similar fashion. (B) Plot of miRNAs detected in each sample. The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in E30d, 168/18 means that 168 mammalian-conserved and 18 pig-specific miRNAs were detected in the E30d library. The bar graphs are depicted in a similar fashion. (C) The Venn diagram displays the distribution of 771 miRNAs through the pre- and postnatal stages (note that the classifications of the miRNAs may be overlapping due to assignment of miRNA to more than one kind of categories). Reading from left to right of the Figure shows the distribution of mammalian-conserved miRNAs, to be 42, 286, and 63 sequences (accounting 100%) for prenatal, co-expression, and postnatal stages, respectively; the distribution for pig-specific miRNAs is 111, 143, and 126 sequences (accounting 100%), respectively. The subclasses of the known, PN(a), PN(b) and PC are explained in Table S5.
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pone-0011541-g003: Expressed kinds of 771 unique miRNAs across ten libraries are summarized.(A) Plot of miRNAs detected in one (1-lib), two (2-lib), … 10-libraries (10-lib). The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in 1-lib, 73/144 means that 73 mammalian-conserved miRNAs and 144 pig-specific are present once in the 10 libraries. The bar graphs are depicted in a similar fashion. (B) Plot of miRNAs detected in each sample. The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in E30d, 168/18 means that 168 mammalian-conserved and 18 pig-specific miRNAs were detected in the E30d library. The bar graphs are depicted in a similar fashion. (C) The Venn diagram displays the distribution of 771 miRNAs through the pre- and postnatal stages (note that the classifications of the miRNAs may be overlapping due to assignment of miRNA to more than one kind of categories). Reading from left to right of the Figure shows the distribution of mammalian-conserved miRNAs, to be 42, 286, and 63 sequences (accounting 100%) for prenatal, co-expression, and postnatal stages, respectively; the distribution for pig-specific miRNAs is 111, 143, and 126 sequences (accounting 100%), respectively. The subclasses of the known, PN(a), PN(b) and PC are explained in Table S5.

Mentions: As shown in Table S14, we classify 493 “PC” (porcine candidate) miRNAs representing 380 unique miRNA sequences derived from genome-mapped sequ-seqs in hairpins and not homologous to any known mammalian miRNAs. These “PC” kinds of miRNAs are likely to be pig-specific. The other 505 miRNAs corresponding to 391 unique miRNA sequences are conserved in mammals. Figures 3 show conserved miRNAs are quite abundant in pig. We examined co-expression of unique miRNAs in ten libraries representing the integrated pre- and postnatal developmental stages. We found that almost all mammalian conserved miRNAs (gray bar-coded in Figure 3A) were ubiquitously expressed in most developmental stages. As shown in Figures 3A, 8- to 10-lib, we can count conserved miRNAs at 49 (out of 54, 90.7%), 63 (out of 64, 98.4%) and 46 (out of 48, 95.8%) unique sequences which were expressed in eight, nine and ten libraries, respectively. Additionally, a larger proportion of the expressed miRNAs (more than 60%) in each library were mammalian conserved miRNAs (gray bar-coded in Figure 3B). Especially during the two early development stages (E30d and E45d), 168 (out of 186, 90.3%) and 76 (out of 86, 88.4%) conserved miRNAs were detected, respectively.


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)

Expressed kinds of 771 unique miRNAs across ten libraries are summarized.(A) Plot of miRNAs detected in one (1-lib), two (2-lib), … 10-libraries (10-lib). The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in 1-lib, 73/144 means that 73 mammalian-conserved miRNAs and 144 pig-specific are present once in the 10 libraries. The bar graphs are depicted in a similar fashion. (B) Plot of miRNAs detected in each sample. The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in E30d, 168/18 means that 168 mammalian-conserved and 18 pig-specific miRNAs were detected in the E30d library. The bar graphs are depicted in a similar fashion. (C) The Venn diagram displays the distribution of 771 miRNAs through the pre- and postnatal stages (note that the classifications of the miRNAs may be overlapping due to assignment of miRNA to more than one kind of categories). Reading from left to right of the Figure shows the distribution of mammalian-conserved miRNAs, to be 42, 286, and 63 sequences (accounting 100%) for prenatal, co-expression, and postnatal stages, respectively; the distribution for pig-specific miRNAs is 111, 143, and 126 sequences (accounting 100%), respectively. The subclasses of the known, PN(a), PN(b) and PC are explained in Table S5.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011541-g003: Expressed kinds of 771 unique miRNAs across ten libraries are summarized.(A) Plot of miRNAs detected in one (1-lib), two (2-lib), … 10-libraries (10-lib). The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in 1-lib, 73/144 means that 73 mammalian-conserved miRNAs and 144 pig-specific are present once in the 10 libraries. The bar graphs are depicted in a similar fashion. (B) Plot of miRNAs detected in each sample. The number marked on top of the bar graph shows the miRNAs of two classifications. For example, in E30d, 168/18 means that 168 mammalian-conserved and 18 pig-specific miRNAs were detected in the E30d library. The bar graphs are depicted in a similar fashion. (C) The Venn diagram displays the distribution of 771 miRNAs through the pre- and postnatal stages (note that the classifications of the miRNAs may be overlapping due to assignment of miRNA to more than one kind of categories). Reading from left to right of the Figure shows the distribution of mammalian-conserved miRNAs, to be 42, 286, and 63 sequences (accounting 100%) for prenatal, co-expression, and postnatal stages, respectively; the distribution for pig-specific miRNAs is 111, 143, and 126 sequences (accounting 100%), respectively. The subclasses of the known, PN(a), PN(b) and PC are explained in Table S5.
Mentions: As shown in Table S14, we classify 493 “PC” (porcine candidate) miRNAs representing 380 unique miRNA sequences derived from genome-mapped sequ-seqs in hairpins and not homologous to any known mammalian miRNAs. These “PC” kinds of miRNAs are likely to be pig-specific. The other 505 miRNAs corresponding to 391 unique miRNA sequences are conserved in mammals. Figures 3 show conserved miRNAs are quite abundant in pig. We examined co-expression of unique miRNAs in ten libraries representing the integrated pre- and postnatal developmental stages. We found that almost all mammalian conserved miRNAs (gray bar-coded in Figure 3A) were ubiquitously expressed in most developmental stages. As shown in Figures 3A, 8- to 10-lib, we can count conserved miRNAs at 49 (out of 54, 90.7%), 63 (out of 64, 98.4%) and 46 (out of 48, 95.8%) unique sequences which were expressed in eight, nine and ten libraries, respectively. Additionally, a larger proportion of the expressed miRNAs (more than 60%) in each library were mammalian conserved miRNAs (gray bar-coded in Figure 3B). Especially during the two early development stages (E30d and E45d), 168 (out of 186, 90.3%) and 76 (out of 86, 88.4%) conserved miRNAs were detected, respectively.

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