title: Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression.
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.
authors.affiliation: State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Guan-Zheng
authors.initials: GZ
authors.lastname: Luo
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
authors.forename: Zhimin
authors.initials: Z
authors.lastname: Shi
authors.forename: Miguel
authors.initials: M
authors.lastname: Brown
authors.forename: Gui-Hai
authors.initials: GH
authors.lastname: Feng
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Wang
authors.forename: XiaoChing
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D001483:Base Sequence; D005260:Female; D046369:Finches / Q000235:genetics*; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000662:veterinary*; D005786:Gene Expression Regulation; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000662:veterinary; D012737:Sex Factors; D014828:Vocalization, Animal
chemical_list: D035683:MicroRNAs