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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

miRNA proportions as percentages of 18–25 nt small RNAs. The dark blue color indicates reads that exactly matched the reference sequences, 1–2 nt extended or shortened at the 5′ end, or 1–4 nt extended or shortened at the 3′ end of known miRNAs. The red color indicates the complete match of continuous sequences of 16 nt or more. The green color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score equal to or more than 70. The purple color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score less than 70. The light blue color indicates 18–25 nt unidentified small RNAs. 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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Fig2: miRNA proportions as percentages of 18–25 nt small RNAs. The dark blue color indicates reads that exactly matched the reference sequences, 1–2 nt extended or shortened at the 5′ end, or 1–4 nt extended or shortened at the 3′ end of known miRNAs. The red color indicates the complete match of continuous sequences of 16 nt or more. The green color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score equal to or more than 70. The purple color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score less than 70. The light blue color indicates 18–25 nt unidentified small RNAs. Fast muscle (a), slow muscle (b), heart (c), eye (d), brain (e), intestine (f), liver (g), ovaries (h), and testes (i)

Mentions: Because miRNA sequences are conserved in vertebrates, we identified miRNAs by conducting a homology search against the miRNA database. After investigating the length distributions of known miRNAs deposited in miRBase 19.0 [10], we found that almost every miRNA was 18–25 nt in length. Therefore, small RNA sequences (18–25 nucleotides in length) were subjected to a BLAST search against mature miRNAs deposited in miRBase 19.0 [10]. The criteria for miRNA annotation were as follows (Additional file 1): 1. Query reads exactly match the reference sequences; 2. Reads with 1–2 nt extended or shortened at the 5′ end, and/or reads with 1–4 nt extended or shortened at the 3′ end of known miRNAs. Using these criteria, among the small RNA sequence reads approximately 32.1 % in fast muscle, 34.5 % in slow muscle, 32.2 % in heart, 30.3 % in eye, 32.2 % in brain, 34.2 % in intestine, and 33.5 % in liver were identified as miRNAs. However, the proportion of small RNA sequence reads that were miRNAs in the ovaries and testes was only 10.8 and 2.5 %, respectively (Fig. 2, Additional file 3).Fig. 2


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)

miRNA proportions as percentages of 18–25 nt small RNAs. The dark blue color indicates reads that exactly matched the reference sequences, 1–2 nt extended or shortened at the 5′ end, or 1–4 nt extended or shortened at the 3′ end of known miRNAs. The red color indicates the complete match of continuous sequences of 16 nt or more. The green color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score equal to or more than 70. The purple color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score less than 70. The light blue color indicates 18–25 nt unidentified small RNAs. 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

Fig2: miRNA proportions as percentages of 18–25 nt small RNAs. The dark blue color indicates reads that exactly matched the reference sequences, 1–2 nt extended or shortened at the 5′ end, or 1–4 nt extended or shortened at the 3′ end of known miRNAs. The red color indicates the complete match of continuous sequences of 16 nt or more. The green color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score equal to or more than 70. The purple color indicates the matching of continuous sequences of less than 16 nt with a Smith-Waterman score less than 70. The light blue color indicates 18–25 nt unidentified small RNAs. Fast muscle (a), slow muscle (b), heart (c), eye (d), brain (e), intestine (f), liver (g), ovaries (h), and testes (i)
Mentions: Because miRNA sequences are conserved in vertebrates, we identified miRNAs by conducting a homology search against the miRNA database. After investigating the length distributions of known miRNAs deposited in miRBase 19.0 [10], we found that almost every miRNA was 18–25 nt in length. Therefore, small RNA sequences (18–25 nucleotides in length) were subjected to a BLAST search against mature miRNAs deposited in miRBase 19.0 [10]. The criteria for miRNA annotation were as follows (Additional file 1): 1. Query reads exactly match the reference sequences; 2. Reads with 1–2 nt extended or shortened at the 5′ end, and/or reads with 1–4 nt extended or shortened at the 3′ end of known miRNAs. Using these criteria, among the small RNA sequence reads approximately 32.1 % in fast muscle, 34.5 % in slow muscle, 32.2 % in heart, 30.3 % in eye, 32.2 % in brain, 34.2 % in intestine, and 33.5 % in liver were identified as miRNAs. However, the proportion of small RNA sequence reads that were miRNAs in the ovaries and testes was only 10.8 and 2.5 %, respectively (Fig. 2, Additional file 3).Fig. 2

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