Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression.
Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression.
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DOI：
10.1186/1471-2164-13-727
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发表时间：
2012-12-26
期刊：
影响因子：
4.4
通讯作者：
Li X
中科院分区：
文献类型：
--
作者：
Luo GZ;Hafner M;Shi Z;Brown M;Feng GH;Tuschl T;Wang XJ;Li X
microRNA（miRNAs）是一类非编码小RNA，在多种生物学过程中调控基因的转录后表达。斑胸草雀（Taeniopygia guttata）是一种具有学习发声行为特征的鸣禽，为生物学家研究发声行为、两性大脑发育和功能以及比较基因组学提供了独特的模型系统。我们对成年雄性和雌性斑胸草雀的大脑、心脏、肝脏和肌肉组织制成的小RNA库进行了深度测序。通过将序列读数映射到斑胸草雀基因组和miRBase中的已知miRNAs，我们总共注释了193个miRNAs。其中，29个（15%）是鸟类特异性的，包括三个新的斑胸草雀特异性miRNAs。许多miRNA表现出序列异质性，包括长度变异、非模板化末端核苷酸添加和GGU基序内尿苷核苷酸处发生的内部取代事件。我们还鉴定了7个Z染色体编码的miRNA。其中，miR-2954是一种鸟类特异性miRNA，在所有检查的组织中，雄性的表达水平显著高于雌性。靶点预测分析表明，miR-2954，而不是其他Z-连锁的miRNA，优先靶向Z染色体编码的基因，包括已知在斑胸草雀大脑中以性二态方式表达的几个基因。我们的成熟序列，基因组位置，进化序列的保守性，和组织表达谱的斑胸草雀miRNA库的全基因组系统分析提供了一个有价值的资源，研究界。我们的分析还揭示了一种可能调节鸟类性别偏见基因表达的miRNA介导的机制。
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. 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. 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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影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
影响因子：
7
作者：
Berezikov, Eugene;Robine, Nicolas;Lai, Eric C.
通讯作者：
Lai, Eric C.
DOI：
10.1126/science.1190809
发表时间：
2010-06-25
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Cifuentes D;Xue H;Taylor DW;Patnode H;Mishima Y;Cheloufi S;Ma E;Mane S;Hannon GJ;Lawson ND;Wolfe SA;Giraldez AJ
通讯作者：
Giraldez AJ
影响因子：
10.5
作者：
Han, JJ;Lee, Y;Kim, VN
通讯作者：
Kim, VN