Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing
Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing
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通过 Solexa 测序鉴定和表征参与钝口鳊（团头鲂）生长的 microRNA
DOI：
10.1186/1471-2164-14-754
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发表时间：
2013-11
期刊：
影响因子：
4.4
通讯作者：
Wei-Min Wang
中科院分区：
文献类型：
--
作者：
Cong Zeng;Wei Luo;Boxiang Chen;Wei-Min Wang
【摘要】 研究背景团头鲂(Megalobrama amblycephala)因其肉质鲜美、经济价值高而成为我国淡水混养系统中重要的经济鱼类。 MicroRNA (miRNA) 在真核生物几乎所有生物过程的调节中发挥着重要作用。尽管之前的研究已经鉴定出来自许多物种的数千种 miRNA，但对于 M 的 miRNA 知之甚少。团头动物。研究与 M 生长相关的 miRNA 的功能。团头菌中，我们采用Solexa测序技术对团头菌四种生长相关组织（脑、垂体、肝脏和肌肉）制备的两个小RNA文库进行了测序。结果在这项研究中，我们鉴定了347个保守的miRNA（属于123个家族）和22个新的miRNA。团头动物。此外，我们观察了 miRNA 的序列变异和种子编辑。在两个文库中观察到的 5,166 个单核苷酸取代中，最丰富的是 G 到 U (15.9%)，其次是 U 到 C (12.1%)、G 到 A (11.2%) 和 A 到 G (11.2%)。随后，我们比较了两个文库中 miRNA 的表达模式（高生长率的大组与低生长率的小组）。结果表明，27 个 miRNA 在两个文库之间表现出显着差异表达（p < 0.05）。其中，与小尺寸组相比，大尺寸组中有 16 个显着上调，11 个显着下调。此外，应用茎环RT-PCR来验证和分析10个组织中差异表达的miRNA的表达，结果表明保守的miRNA的表达水平高于新的miRNA，特别是在脑、肝脏和肌肉中。此外，差异表达miRNA的靶标预测和KEGG通路分析表明差异表达的miRNA参与生长代谢、信号转导、细胞周期、神经发育和功能。结论本研究首次对M中的miRNA进行了大规模表征。团头菌和 miRNA 谱与不同的生长性能相关。本研究发现的 miRNA 资源有望有助于更好地了解 miRNA 在调节鱼类生长生物过程中的作用以及研究 miRNA 功能和表型相关的 miRNA 鉴定。
BackgroundBlunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important roles in regulation of almost all biological processes in eukaryotes. Although previous studies have identified thousands of miRNAs from many species, little information is known for miRNAs ofM. amblycephala. To investigate functions of miRNAs associated with growth ofM. amblycephala, we adopted the Solexa sequencing technology to sequence two small RNA libraries prepared from four growth related tissues (brain, pituitary, liver and muscle) ofM. amblycephalausing individuals with relatively high and low growth rates.ResultsIn this study, we have identified 347 conserved miRNAs (belonging to 123 families) and 22 novel miRNAs inM. amblycephala. Moreover, we observed sequence variants and seed edits of the miRNAs. Of the 5,166 single nucleotide substitutions observed in two libraries, the most abundant were G-to-U (15.9%), followed by U-to-C (12.1%), G-to-A (11.2%), and A to G (11.2%). Subsequently, we compared the expression patterns of miRNAs in the two libraries (big-size group with high growth rate versus small-size group with low growth rate). Results indicated that 27 miRNAs displayed significant differential expressions between the two libraries (p< 0.05). Of these, 16 were significantly up-regulated and 11 were significantly down-regulated in the big-size group compared to the small-size group. Furthermore, stem-loop RT-PCR was applied to validate and profile the expression of the differentially expressed miRNAs in ten tissues, and the result revealed that the conserved miRNAs expressed at higher levels than the novel miRNAs, especially in brain, liver and muscle. Also, targets prediction of differentially expressed miRNAs and KEGG pathway analysis suggested that differentially expressed miRNAs are involved in growth and metabolism, signal transduction, cell cycle, neural development and functions.ConclusionsThe present study provides the first large-scale characterization of miRNAs inM. amblycephalaand miRNA profile related to different growth performances. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes and the study of miRNA function and phenotype-associated miRNA identification in fish.
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影响因子：
14.9
作者：
Ebhardt HA;Tsang HH;Dai DC;Liu Y;Bostan B;Fahlman RP
通讯作者：
Fahlman RP
影响因子：
14.9
作者：
Chen C;Ridzon DA;Broomer AJ;Zhou Z;Lee DH;Nguyen JT;Barbisin M;Xu NL;Mahuvakar VR;Andersen MR;Lao KQ;Livak KJ;Guegler KJ
通讯作者：
Guegler KJ
DOI：
10.1142/9789812776136_0009
发表时间：
2007-12
影响因子：
--
作者：
V. Vacic;Hailing Jin;Jian‐Kang Zhu;S. Lonardi
通讯作者：
V. Vacic;Hailing Jin;Jian‐Kang Zhu;S. Lonardi
影响因子：
3.7
作者：
Fu Y;Shi Z;Wu M;Zhang J;Jia L;Chen X
通讯作者：
Chen X
影响因子：
46.9
作者：
Schuster, S;Fell, DA;Dandekar, T
通讯作者：
Dandekar, T