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The genetic code - thawing the 'frozen accident'.遗传密码——解冻“冻结的偶然”。
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2
Tissue-specific differences in human transfer RNA expression.人类转运RNA表达的组织特异性差异。
PLoS Genet. 2006 Dec;2(12):e221. doi: 10.1371/journal.pgen.0020221. Epub 2006 Nov 13.
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Diversity of tRNA genes in eukaryotes.真核生物中转运RNA基因的多样性。
Nucleic Acids Res. 2006;34(21):6137-46. doi: 10.1093/nar/gkl725. Epub 2006 Nov 6.
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Microarray analysis of RNA processing and modification.RNA加工与修饰的微阵列分析
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The distal sequence element of the selenocysteine tRNA gene is a tissue-dependent enhancer essential for mouse embryogenesis.硒代半胱氨酸tRNA基因的远端序列元件是小鼠胚胎发育所必需的组织依赖性增强子。
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Compilation of tRNA sequences and sequences of tRNA genes.tRNA序列及tRNA基因序列的汇编。
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Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation.一种人类核酸内切酶复合物的鉴定揭示了tRNA剪接与前体mRNA 3'端形成之间的联系。
Cell. 2004 Apr 30;117(3):311-21. doi: 10.1016/s0092-8674(04)00342-3.
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ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.ARAGORN，一个用于在核苷酸序列中检测tRNA基因和tmRNA基因的程序。
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Multiple sequence alignment with the Clustal series of programs.使用Clustal系列程序进行多序列比对。
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Mfold web server for nucleic acid folding and hybridization prediction.用于核酸折叠和杂交预测的Mfold网络服务器。
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预测和验证小鼠 tRNA 基因家族。

Prediction and verification of mouse tRNA gene families.

机构信息

Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.

出版信息

RNA Biol. 2009 Apr-Jun;6(2):195-202. doi: 10.4161/rna.6.2.8050. Epub 2009 May 1.

DOI:10.4161/rna.6.2.8050
PMID:19246989
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2783191/
Abstract

BACKGROUND

Transfer RNA (tRNA) gene predictions are complicated by challenges such as structural variation, limited sequence conservation and the presence of highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units. Annotation of "tRNA genes" in sequenced genomes generally have not been accompanied by experimental verification of the expression status of predicted sequences.

RESULTS

To address this for mouse tRNA genes, we have employed two programs, tRNAScan-SE and ARAGORN, to predict the tRNA genes in the nuclear genome, resulting in diverse but overlapping predicted gene sets. From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes. In particular, four families of intron-containing tRNA genes were predicted for the first time in mouse, with introns in positions and structures similar to the well characterized intron-containing tRNA genes in yeast. We verified the expression of the predicted tRNA genes by microarray analysis. We then confirmed the expression of appropriately sized RNA for the four intron-containing tRNA gene families, as well as the other 30 tRNA gene families creating an index of expression-verified mouse tRNAs.

CONCLUSIONS

These confirmed tRNA genes represent all anticodons and all known mammalian tRNA structural groups, as well as a variety of predicted "rogue" tRNA genes within families with altered anticodon identities.

摘要

背景

转移 RNA(tRNA)基因预测受到结构变异、有限的序列保守性以及高度重复的短散在序列(SINEs)的存在等挑战的影响，这些 SINEs最初来自 tRNA 基因或 tRNA 样转录单元。在测序基因组中，“tRNA 基因”的注释通常没有伴随对预测序列表达状态的实验验证。

结果

为了解决小鼠 tRNA 基因的这个问题，我们使用了两个程序 tRNAScan-SE 和 ARAGORN 来预测核基因组中的 tRNA 基因，从而产生了不同但重叠的预测基因集。从中，我们去除了已知的 SINE 重复，并将基因分类为预测的家族和单拷贝基因。特别是，在小鼠中首次预测了四个包含内含子的 tRNA 基因家族，内含子的位置和结构与酵母中特征明确的内含子 tRNA 基因相似。我们通过微阵列分析验证了预测的 tRNA 基因的表达。然后，我们确认了四个内含子 tRNA 基因家族以及其他 30 个 tRNA 基因家族的适当大小的 RNA 的表达，从而创建了一个表达验证的小鼠 tRNA 索引。

结论

这些经过验证的 tRNA 基因代表了所有反密码子和所有已知的哺乳动物 tRNA 结构群，以及在具有改变的反密码子身份的家族内的各种预测的“流氓”tRNA 基因。