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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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miRNA annotation and expression analysis in zebra finch. (A) Mature sequences, expression counts, and precursor sequences with predicted hairpin-like secondary structures of three novel miRNAs identified in the zebra finch. Nucleotides labeled in red and blue in the precursor sequences represent mature miRNAs and their star sequences, respectively. The read numbers are combined from four tissues and two sexes. (B) Relative percentages of small RNA populations among the total sequence reads. Calculations were based on the total reads of the eight libraries combined. (C) The 20 most abundantly expressed miRNAs.
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Figure 1: miRNA annotation and expression analysis in zebra finch. (A) Mature sequences, expression counts, and precursor sequences with predicted hairpin-like secondary structures of three novel miRNAs identified in the zebra finch. Nucleotides labeled in red and blue in the precursor sequences represent mature miRNAs and their star sequences, respectively. The read numbers are combined from four tissues and two sexes. (B) Relative percentages of small RNA populations among the total sequence reads. Calculations were based on the total reads of the eight libraries combined. (C) The 20 most abundantly expressed miRNAs.

Mentions: We prepared eight small RNA libraries from four tissues – brain, heart, liver, and muscle – of adult female and male zebra finches. These libraries were sequenced using the Illumina Genome Analyzer II high throughput sequencing platform. We obtained a total of 23,366,676 raw sequence reads from all libraries combined. After adaptor trimming and removal of low quality reads and orphan sequences (single reads), 19,424,182 high quality sequence reads were retained for subsequent analysis (Additional file1). Of these reads, 60% mapped perfectly to the zebra finch genome assembly (release 1.0). We extracted flanking sequences around mapped reads and used mFold[36] to search for hairpin-like secondary structures. A total of 169 mature miRNAs were identified, which exhibited good hairpin-like precursor structures and matched known miRNAs recorded in miRBase (version 17.0) with high sequence homology (identical or with one mismatch). Considering that the current zebra finch genome assembly is relatively new and may contain gaps[32], we compared the unmapped sequence reads to known miRNA sequences in miRBase, and identified 21 additional miRNAs with high sequence homology (identical or with one mismatch) to known miRNAs in other species. Following the general criteria for miRNA annotation[37], we identified three novel zebra finch specific miRNA candidates, which are supported by good hairpin-like precursor structures, presence of corresponding star sequences, and relatively high expression (Figure1A). Taken together, we identified 193 distinct zebra finch miRNAs. The sequences, genomic locations, and relative expression levels of these miRNAs are summarized in Additional file2.


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)

miRNA annotation and expression analysis in zebra finch. (A) Mature sequences, expression counts, and precursor sequences with predicted hairpin-like secondary structures of three novel miRNAs identified in the zebra finch. Nucleotides labeled in red and blue in the precursor sequences represent mature miRNAs and their star sequences, respectively. The read numbers are combined from four tissues and two sexes. (B) Relative percentages of small RNA populations among the total sequence reads. Calculations were based on the total reads of the eight libraries combined. (C) The 20 most abundantly expressed miRNAs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: miRNA annotation and expression analysis in zebra finch. (A) Mature sequences, expression counts, and precursor sequences with predicted hairpin-like secondary structures of three novel miRNAs identified in the zebra finch. Nucleotides labeled in red and blue in the precursor sequences represent mature miRNAs and their star sequences, respectively. The read numbers are combined from four tissues and two sexes. (B) Relative percentages of small RNA populations among the total sequence reads. Calculations were based on the total reads of the eight libraries combined. (C) The 20 most abundantly expressed miRNAs.
Mentions: We prepared eight small RNA libraries from four tissues – brain, heart, liver, and muscle – of adult female and male zebra finches. These libraries were sequenced using the Illumina Genome Analyzer II high throughput sequencing platform. We obtained a total of 23,366,676 raw sequence reads from all libraries combined. After adaptor trimming and removal of low quality reads and orphan sequences (single reads), 19,424,182 high quality sequence reads were retained for subsequent analysis (Additional file1). Of these reads, 60% mapped perfectly to the zebra finch genome assembly (release 1.0). We extracted flanking sequences around mapped reads and used mFold[36] to search for hairpin-like secondary structures. A total of 169 mature miRNAs were identified, which exhibited good hairpin-like precursor structures and matched known miRNAs recorded in miRBase (version 17.0) with high sequence homology (identical or with one mismatch). Considering that the current zebra finch genome assembly is relatively new and may contain gaps[32], we compared the unmapped sequence reads to known miRNA sequences in miRBase, and identified 21 additional miRNAs with high sequence homology (identical or with one mismatch) to known miRNAs in other species. Following the general criteria for miRNA annotation[37], we identified three novel zebra finch specific miRNA candidates, which are supported by good hairpin-like precursor structures, presence of corresponding star sequences, and relatively high expression (Figure1A). Taken together, we identified 193 distinct zebra finch miRNAs. The sequences, genomic locations, and relative expression levels of these miRNAs are summarized in Additional file2.

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