RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts.
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts.
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DOI：
10.1186/1471-2164-13-118
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发表时间：
2012-03-28
期刊：
影响因子：
4.4
通讯作者：
Khatib H
中科院分区：
文献类型：
--
作者：
Driver AM;Peñagaricano F;Huang W;Ahmad KR;Hackbart KS;Wiltbank MC;Khatib H
体外受精 (IVF) 是一种对研究和工业都很有价值的工具，其应用范围从配子选择、性状保存到克隆。尽管 IVF 已在全球范围内得到应用，仅 2010 年就移植了约 339,685 个牛胚胎，但效率方面仍然存在困难。很少有超过 40% 的体外受精牛卵母细胞在培养第 8 天时达到囊胚阶段，据报道体外产生的胚胎的妊娠率低于 45%。为了研究体外受精 (IVF) 对胚胎发育的潜在影响，本研究比较了处于相似阶段和质量等级（扩展、优质）的体内和体外衍生的牛囊胚，以使用 RNA-Seq 确定形态以外的转录组变异程度。 A total of 26,906,451 and 38,184,547 fragments were sequenced for in vitro and in vivo embryo pools, respectively.我们总共检测到 17,634 个基因的表达，其中 793 个基因在两个胚胎群体之间表现出差异表达，错误发现率 (FDR) < 0.05。 There were also 395 novel transcribed units found, of which 45 were differentially expressed (FDR < 0.05).此外，4,800 个基因显示出选择性剪接的证据，其中 873 个基因在两个池之间显示出差异选择性剪接（FDR < 0.05）。使用GO富集分析，发现差异表达基因（FDR < 0.01）的多个生物途径显着富集，包括胆固醇和甾醇合成、系统发育和细胞分化。因此，我们的结果支持 IVF 可能在转录组水平上产生影响，并且形态学在牛植入前胚胎的全面表征中受到限制。
A valuable tool for both research and industry, in vitro fertilization (IVF) has applications range from gamete selection and preservation of traits to cloning. Although IVF has achieved worldwide use, with approximately 339,685 bovine embryos transferred in 2010 alone, there are still continuing difficulties with efficiency. It is rare to have more than 40% of fertilized in vitro cattle oocytes reach blastocyst stage by day 8 of culture, and pregnancy rates are reported as less than 45% for in vitro produced embryos. To investigate potential influences in-vitro fertilization (IVF) has on embryonic development, this study compares in vivo- and in vitro-derived bovine blastocysts at a similar stage and quality grade (expanded, excellent quality) to determine the degree of transcriptomic variation beyond morphology using RNA-Seq. A total of 26,906,451 and 38,184,547 fragments were sequenced for in vitro and in vivo embryo pools, respectively. We detected expression for a total of 17,634 genes, with 793 genes showing differential expression between the two embryo populations with false discovery rate (FDR) < 0.05. There were also 395 novel transcribed units found, of which 45 were differentially expressed (FDR < 0.05). In addition, 4,800 genes showed evidence of alternative splicing, with 873 genes displaying differential alternative splicing between the two pools (FDR < 0.05). Using GO enrichment analysis, multiple biological pathways were found to be significantly enriched for differentially expressed genes (FDR < 0.01), including cholesterol and sterol synthesis, system development, and cell differentiation. Thus, our results support that IVF may influence at the transcriptomic level and that morphology is limited in full characterization of bovine preimplantation embryos.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
2.8
作者：
Souza, A. H.;Ayres, H.;Wiltbank, M. C.
通讯作者：
Wiltbank, M. C.
DOI：
10.1073/pnas.0805616105
发表时间：
2008-12-16
影响因子：
11.1
作者：
Kues, W. A.;Sudheer, S.;Niemann, H.
通讯作者：
Niemann, H.
DOI：
10.1007/s004290050249
发表时间：
1999-06-01
期刊：
ANATOMY AND EMBRYOLOGY
影响因子：
--
作者：
Abe, H;Otoi, T;Hoshi, H
通讯作者：
Hoshi, H
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y