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Deep sequencing, profiling and detailed annotation of microRNAs in Takifugu rubripes.

Wongwarangkana C, Fujimori KE, Akiba M, Kinoshita S, Teruya M, Nezuo M, Masatoshi T, Watabe S, Asakawa S - BMC Genomics (2015)

Bottom Line: We elucidated miRNA expression patterns in various organs of T. rubripes.Most miRNA sequences are conserved in vertebrates, indicating that the basic functions of vertebrate miRNAs share a common evolution.Some miRNA species exhibit different distributions of isomiRs between tissues, suggesting that they have a broad range of functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, 113-8657, Tokyo, Japan. tarnjew@gmail.com.

ABSTRACT

Background: microRNAs (miRNAs) in fish have not been as extensively studied as those in mammals. The fish species Takifugu rubripes is an intensively studied model organism whose genome has been sequenced. The T. rubripes genome is approximately eight times smaller than the human genome, but has a similar repertoire of protein-coding genes. Therefore, it is useful for identifying non-coding genes, including miRNA genes. To identify miRNA expression patterns in different organs of T. rubripes and give fundamental information to aid understanding of miRNA populations in this species, we extracted small RNAs from tissues and performed deep sequencing analysis to profile T. rubripes miRNAs. These data will be of assistance in functional studies of miRNAs in T. rubripes.

Results: After analyzing a total of 139 million reads, we found miRNA species in nine tissues (fast and slow muscles, heart, eye, brain, intestine, liver, ovaries, and testes). We identified 1420 known miRNAs, many of which were strongly expressed in certain tissues with expression patterns similar to those described for other animals in previous reports. Most miRNAs were expressed in tissues other than the ovaries or testes. However, some miRNA families were highly abundant in the gonads, but expressed only at low levels in somatic tissue, suggesting specific function in germ cells. The most abundant isomiRs (miRNA variants) of many miRNAs had identical sequences in the 5' region. However, isomiRs of some miRNAs, including fru-miR-462-5p, varied in the 5' region in some tissues, suggesting that they may target different mRNA transcripts. Longer small RNAs (26-31 nt), which were abundant in the gonads, may be putative piRNAs because of their length and their origin from repetitive elements. Additionally, our data include possible novel classes of small RNAs.

Conclusions: We elucidated miRNA expression patterns in various organs of T. rubripes. Most miRNA sequences are conserved in vertebrates, indicating that the basic functions of vertebrate miRNAs share a common evolution. Some miRNA species exhibit different distributions of isomiRs between tissues, suggesting that they have a broad range of functions.

No MeSH data available.


Related in: MedlinePlus

Proportions of small RNA components. Fast muscle (a), slow muscle (b), heart (c), eye (d), brain (e), intestine (f), liver (g), ovaries (h), and testes (i)
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Fig4: Proportions of small RNA components. Fast muscle (a), slow muscle (b), heart (c), eye (d), brain (e), intestine (f), liver (g), ovaries (h), and testes (i)

Mentions: To classify the remaining unidentified small RNAs (18–25 nt unidentified small RNAs and 26–35 nt small RNAs), we performed homology searches against the NCBI database (Fig. 4). In the 1–35 nt population, the majority of small RNAs in the ovaries and testes were derived from repetitive elements. Additionally, 70–75 % of them were identified to be 26–31 nt. The major proportion of small RNAs of each length in the ovaries and testes (except for 21–22 nt in the ovaries) were also derived from repetitive elements (Additional file 7). Finally, in each somatic tissue, only about 1 % of small RNAs were unidentified; while in the ovaries and testes 11.8 and 15.6 % were unidentified, respectively.Fig. 4


Deep sequencing, profiling and detailed annotation of microRNAs in Takifugu rubripes.

Wongwarangkana C, Fujimori KE, Akiba M, Kinoshita S, Teruya M, Nezuo M, Masatoshi T, Watabe S, Asakawa S - BMC Genomics (2015)

Proportions of small RNA components. Fast muscle (a), slow muscle (b), heart (c), eye (d), brain (e), intestine (f), liver (g), ovaries (h), and testes (i)
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4469249&req=5

Fig4: Proportions of small RNA components. Fast muscle (a), slow muscle (b), heart (c), eye (d), brain (e), intestine (f), liver (g), ovaries (h), and testes (i)
Mentions: To classify the remaining unidentified small RNAs (18–25 nt unidentified small RNAs and 26–35 nt small RNAs), we performed homology searches against the NCBI database (Fig. 4). In the 1–35 nt population, the majority of small RNAs in the ovaries and testes were derived from repetitive elements. Additionally, 70–75 % of them were identified to be 26–31 nt. The major proportion of small RNAs of each length in the ovaries and testes (except for 21–22 nt in the ovaries) were also derived from repetitive elements (Additional file 7). Finally, in each somatic tissue, only about 1 % of small RNAs were unidentified; while in the ovaries and testes 11.8 and 15.6 % were unidentified, respectively.Fig. 4

Bottom Line: We elucidated miRNA expression patterns in various organs of T. rubripes.Most miRNA sequences are conserved in vertebrates, indicating that the basic functions of vertebrate miRNAs share a common evolution.Some miRNA species exhibit different distributions of isomiRs between tissues, suggesting that they have a broad range of functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, 113-8657, Tokyo, Japan. tarnjew@gmail.com.

ABSTRACT

Background: microRNAs (miRNAs) in fish have not been as extensively studied as those in mammals. The fish species Takifugu rubripes is an intensively studied model organism whose genome has been sequenced. The T. rubripes genome is approximately eight times smaller than the human genome, but has a similar repertoire of protein-coding genes. Therefore, it is useful for identifying non-coding genes, including miRNA genes. To identify miRNA expression patterns in different organs of T. rubripes and give fundamental information to aid understanding of miRNA populations in this species, we extracted small RNAs from tissues and performed deep sequencing analysis to profile T. rubripes miRNAs. These data will be of assistance in functional studies of miRNAs in T. rubripes.

Results: After analyzing a total of 139 million reads, we found miRNA species in nine tissues (fast and slow muscles, heart, eye, brain, intestine, liver, ovaries, and testes). We identified 1420 known miRNAs, many of which were strongly expressed in certain tissues with expression patterns similar to those described for other animals in previous reports. Most miRNAs were expressed in tissues other than the ovaries or testes. However, some miRNA families were highly abundant in the gonads, but expressed only at low levels in somatic tissue, suggesting specific function in germ cells. The most abundant isomiRs (miRNA variants) of many miRNAs had identical sequences in the 5' region. However, isomiRs of some miRNAs, including fru-miR-462-5p, varied in the 5' region in some tissues, suggesting that they may target different mRNA transcripts. Longer small RNAs (26-31 nt), which were abundant in the gonads, may be putative piRNAs because of their length and their origin from repetitive elements. Additionally, our data include possible novel classes of small RNAs.

Conclusions: We elucidated miRNA expression patterns in various organs of T. rubripes. Most miRNA sequences are conserved in vertebrates, indicating that the basic functions of vertebrate miRNAs share a common evolution. Some miRNA species exhibit different distributions of isomiRs between tissues, suggesting that they have a broad range of functions.

No MeSH data available.


Related in: MedlinePlus