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Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression.

Luo GZ, Hafner M, Shi Z, Brown M, Feng GH, Tuschl T, Wang XJ, Li X - BMC Genomics (2012)

Bottom Line: Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined.Our genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community.Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

ABSTRACT

Background: MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. The zebra finch (Taeniopygia guttata), an oscine songbird with characteristic learned vocal behavior, provides biologists a unique model system for studying vocal behavior, sexually dimorphic brain development and functions, and comparative genomics.

Results: We deep sequenced small RNA libraries made from the brain, heart, liver, and muscle tissues of adult male and female zebra finches. By mapping the sequence reads to the zebra finch genome and to known miRNAs in miRBase, we annotated a total of 193 miRNAs. Among them, 29 (15%) are avian specific, including three novel zebra finch specific miRNAs. Many of the miRNAs exhibit sequence heterogeneity including length variations, untemplated terminal nucleotide additions, and internal substitution events occurring at the uridine nucleotide within a GGU motif. We also identified seven Z chromosome-encoded miRNAs. Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined. Target prediction analysis reveals that miR-2954, but not other Z-linked miRNAs, preferentially targets Z chromosome-encoded genes, including several genes known to be expressed in a sexually dimorphic manner in the zebra finch brain.

Conclusions: Our genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community. Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.

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Expression analysis of miR-2954. (A) Northern blot analysis shows that miR-2954 was expressed in brain and liver tissues of male zebra finches, but was not detectable in mouse or human tissues. (B) Northern blot shows expression of miR-2954 and miR-9 in the brain tissues of female and male zebra finches. (C) Sex-biased expression of miR-2954 in the brain, heart, liver, muscle, ovary, and testis of male and female zebra finches validated by qRT-PCR. (D) Expression ratios of Z chromosome-encoded miRNAs between male and female zebra finch tissues based on sequence reads. Note, miR-2973, another Z chromosome-encoded miRNA, was not included here because its total combined reads were < 100.
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Figure 5: Expression analysis of miR-2954. (A) Northern blot analysis shows that miR-2954 was expressed in brain and liver tissues of male zebra finches, but was not detectable in mouse or human tissues. (B) Northern blot shows expression of miR-2954 and miR-9 in the brain tissues of female and male zebra finches. (C) Sex-biased expression of miR-2954 in the brain, heart, liver, muscle, ovary, and testis of male and female zebra finches validated by qRT-PCR. (D) Expression ratios of Z chromosome-encoded miRNAs between male and female zebra finch tissues based on sequence reads. Note, miR-2973, another Z chromosome-encoded miRNA, was not included here because its total combined reads were < 100.

Mentions: miR-2954 is a recently identified avian miRNA, which has a single genomic locus on the zebra finch Z chromosome[32,35]. We did not detect it in the chicken genome assembly (version galGal3) or in the genomes of other animal species (Figure2). However, we found the mature miR-2954 sequence among chicken ESTs, and its expression in chicken embryo is detected by Northern blot analysis[50]. Tgu-miR-2954 was expressed in a sex-biased manner in all four examined tissues; and its expression was significantly higher in male tissues than in female tissues (Additional file2). We validated this expression pattern by Northern blot analysis and quantitative real-time PCR (qRT-PCR) (Figure5A, B, and C). Our original sequencing samples did not include ovary and testis; however, using qRT-PCR, we found that the expression of miR-2954 was 3-fold higher in testis than in ovary (Figure5C). In addition to miR-2954, six other miRNAs (miR-23b, miR-24, miR-27b, miR-122, miR-2973, and miR-2992) were encoded solely by the Z chromosome, and most of them showed slightly higher expression in male tissues than in female tissues (Figure5D). The one exception was miR-122, which was expressed at a higher level in heart in females than in males. Several miRNAs (miR-7, miR-9, miR-101, and miR-204) that are encoded by both the Z and the A chromosomes did not exhibit consistent sex-biased expression (Additional file12).


Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression.

Luo GZ, Hafner M, Shi Z, Brown M, Feng GH, Tuschl T, Wang XJ, Li X - BMC Genomics (2012)

Expression analysis of miR-2954. (A) Northern blot analysis shows that miR-2954 was expressed in brain and liver tissues of male zebra finches, but was not detectable in mouse or human tissues. (B) Northern blot shows expression of miR-2954 and miR-9 in the brain tissues of female and male zebra finches. (C) Sex-biased expression of miR-2954 in the brain, heart, liver, muscle, ovary, and testis of male and female zebra finches validated by qRT-PCR. (D) Expression ratios of Z chromosome-encoded miRNAs between male and female zebra finch tissues based on sequence reads. Note, miR-2973, another Z chromosome-encoded miRNA, was not included here because its total combined reads were < 100.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3585881&req=5

Figure 5: Expression analysis of miR-2954. (A) Northern blot analysis shows that miR-2954 was expressed in brain and liver tissues of male zebra finches, but was not detectable in mouse or human tissues. (B) Northern blot shows expression of miR-2954 and miR-9 in the brain tissues of female and male zebra finches. (C) Sex-biased expression of miR-2954 in the brain, heart, liver, muscle, ovary, and testis of male and female zebra finches validated by qRT-PCR. (D) Expression ratios of Z chromosome-encoded miRNAs between male and female zebra finch tissues based on sequence reads. Note, miR-2973, another Z chromosome-encoded miRNA, was not included here because its total combined reads were < 100.
Mentions: miR-2954 is a recently identified avian miRNA, which has a single genomic locus on the zebra finch Z chromosome[32,35]. We did not detect it in the chicken genome assembly (version galGal3) or in the genomes of other animal species (Figure2). However, we found the mature miR-2954 sequence among chicken ESTs, and its expression in chicken embryo is detected by Northern blot analysis[50]. Tgu-miR-2954 was expressed in a sex-biased manner in all four examined tissues; and its expression was significantly higher in male tissues than in female tissues (Additional file2). We validated this expression pattern by Northern blot analysis and quantitative real-time PCR (qRT-PCR) (Figure5A, B, and C). Our original sequencing samples did not include ovary and testis; however, using qRT-PCR, we found that the expression of miR-2954 was 3-fold higher in testis than in ovary (Figure5C). In addition to miR-2954, six other miRNAs (miR-23b, miR-24, miR-27b, miR-122, miR-2973, and miR-2992) were encoded solely by the Z chromosome, and most of them showed slightly higher expression in male tissues than in female tissues (Figure5D). The one exception was miR-122, which was expressed at a higher level in heart in females than in males. Several miRNAs (miR-7, miR-9, miR-101, and miR-204) that are encoded by both the Z and the A chromosomes did not exhibit consistent sex-biased expression (Additional file12).

Bottom Line: Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined.Our genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community.Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

ABSTRACT

Background: MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. The zebra finch (Taeniopygia guttata), an oscine songbird with characteristic learned vocal behavior, provides biologists a unique model system for studying vocal behavior, sexually dimorphic brain development and functions, and comparative genomics.

Results: We deep sequenced small RNA libraries made from the brain, heart, liver, and muscle tissues of adult male and female zebra finches. By mapping the sequence reads to the zebra finch genome and to known miRNAs in miRBase, we annotated a total of 193 miRNAs. Among them, 29 (15%) are avian specific, including three novel zebra finch specific miRNAs. Many of the miRNAs exhibit sequence heterogeneity including length variations, untemplated terminal nucleotide additions, and internal substitution events occurring at the uridine nucleotide within a GGU motif. We also identified seven Z chromosome-encoded miRNAs. Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined. Target prediction analysis reveals that miR-2954, but not other Z-linked miRNAs, preferentially targets Z chromosome-encoded genes, including several genes known to be expressed in a sexually dimorphic manner in the zebra finch brain.

Conclusions: Our genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community. Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.

Show MeSH
Related in: MedlinePlus