Characterization of bovine miRNAs by sequencing and bioinformatics analysis.
Characterization of bovine miRNAs by sequencing and bioinformatics analysis.
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DOI：
10.1186/1471-2199-10-90
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发表时间：
2009-09-16
影响因子：
--
通讯作者：
Guan LL
中科院分区：
文献类型：
--
作者：
Jin W;Grant JR;Stothard P;Moore SS;Guan LL
MicroRNA (miRNA) 是一个约 22 个核苷酸的小 RNA 分子家族，通过完全或部分结合 mRNA 或启动子中的互补序列来调节基因表达。大量 miRNA 及其表达模式已在人类、小鼠和大鼠中得到报道。然而，miRNA 及其在肉牛等家畜物种中的表达模式尚未得到充分研究。我们构建了小 RNA 文库并对其进行了测序，从 11 个牛组织（包括脑、皮下脂肪、肌肉、肝脏、肾脏、脾脏和胸腺）中获得了总共 13,541 个小 RNA 序列。总共鉴定了 228 个 miRNA，其中包括 29 个新的 miRNA 候选者。在 199 种 miRNA 中，101 种先前已被报道为牛 miRNA，另外 98 种是已知 miRNA 的牛直向同源物，这些 miRNA 已在至少一种其他哺乳动物物种中得到鉴定。在 29 个新的 miRNA 候选者中，有 17 个此时出现为牛特异性，而其余 12 个有其他哺乳动物物种进化保守的证据。 5 个 miRNA（miR-23a、-23b、-99a、-125b 和 -126-5p）在 11 个组织中非常丰富，占所有小 RNA 序列的 44.3%。使用 qRT-PCR 对所选 miRNA 的表达分析还表明，miR-26a 和 -99a 在所有组织中均高表达，而 miR-122 和 miR-133a 分别主要在肝脏和肌肉中表达。肉牛 11 个组织中 miRNA 的表达模式表明，大多数 miRNA 在所有组织中普遍表达，而只有少数 miRNA 具有组织特异性。本研究中仅 60% 的 miRNA 被发现表现出链偏倚，这表明除了内部稳定性之外，成熟 miRNA 选择还有一些关键因素。大多数牛 miRNA 在其他三种哺乳动物物种中高度保守，表明这些 miRNA 可能在不同物种中发挥作用，是进化的潜在分子标记。
MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules which regulate gene expression by fully or partially binding to their complementary sequences in mRNAs or promoters. A large number of miRNAs and their expression patterns have been reported in human, mouse and rat. However, miRNAs and their expression patterns in live stock species such as beef cattle are not well studied. We constructed and sequenced small-RNA libraries to yield a total of 13,541 small-RNA sequences from 11 bovine tissues including brain, subcutaneous fat, muscle, liver, kidney, spleen and thymus. In total, 228 miRNAs including 29 novel miRNA candidates were identified. Of the 199 miRNAs, 101 have been previously reported as bovine miRNAs and the other 98 are bovine orthologs of known miRNAs that have been identified in at least one other mammalian species. Of the 29 novel miRNA candidates, 17 appeared at this point in time to be bovine specific, while the remaining 12 had evidence of evolutionary conservation in other mammalian species. Five miRNAs (miR-23a, -23b, -99a, -125b and -126-5p) were very abundant across the 11 tissues, accounting for 44.3% of all small RNA sequences. The expression analysis of selected miRNAs using qRT-PCR also showed that miR-26a and -99a were highly expressed in all tissues, while miR-122 and miR-133a were predominantly expressed in liver and muscle, respectively. The miRNA expression patterns among 11 tissues from beef cattle revealed that most miRNAs were ubiquitously expressed in all tissues, while only a few miRNAs were tissue specific. Only 60% miRNAs in this study were found to display strand bias, suggesting that there are some key factors for mature miRNA selection other than internal stability. Most bovine miRNAs are highly conserved in other three mammalian species, indicating that these miRNAs may have a role in different species that are potential molecular markers for evolution.
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影响因子：
56.9
作者：
Lagos-Quintana, M;Rauhut, R;Tuschl, T
通讯作者：
Tuschl, T
影响因子：
10.5
作者：
Chen, PY;Manninga, H;Tuschl, T
通讯作者：
Tuschl, T
影响因子：
30.8
作者：
Bentwich, I;Avniel, A;Bentwich, Z
通讯作者：
Bentwich, Z
影响因子：
4.6
作者：
Coutinho, Luiz L.;Matukumalli, Lakshmi K.;Smith, Timothy P. L.
通讯作者：
Smith, Timothy P. L.
影响因子：
12.3
作者：
Blow MJ;Grocock RJ;van Dongen S;Enright AJ;Dicks E;Futreal PA;Wooster R;Stratton MR
通讯作者：
Stratton MR