Characterization of circulating transfer RNA-derived RNA fragments in cattle.
Characterization of circulating transfer RNA-derived RNA fragments in cattle.
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DOI：
10.3389/fgene.2015.00271
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发表时间：
2015
影响因子：
3.7
通讯作者：
Neill JD
中科院分区：
文献类型：
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作者：
Casas E;Cai G;Neill JD
目的是表征牛体内自然发生的循环转移RNA衍生的RNA片段（tRFs） 1。采集8头临床正常成年奶牛的血清，采集后立即提取小片段非编码rna，并用Illumina MiSeq进行测序。序列对准转移RNA （tRNA）基因或其侧翼序列进行了表征。排列在成熟tRNA 5′端开始的序列被归类为tRF5；与成熟tRNA的3′端对齐的被归类为tRF3；排列在3′端侧翼序列开始的部分归类为tRF1。牛基因组中有3190,962个序列映射到转移RNA和小的非编码RNA。其中，2,323,520个被鉴定为trf5, 562个为trf3, 81个为trf1。有866799个序列被鉴定为其他小的非编码rna （microRNA、rRNA、snoRNA等），被排除在研究之外。trf5在28 ~ 40个核苷酸之间；98.7%的基因长度在30 ~ 34个核苷酸之间。序列数最多的trf来源于组氨酸、谷氨酸、赖氨酸、甘氨酸和缬氨酸的tRNA。样品中每个氨基酸的密码子数目与trf数目之间没有相关性。trf5最丰富的原因只有在这些序列与动物体内的功能有关时才能解释。
The objective was to characterize naturally occurring circulating transfer RNA-derived RNA fragments (tRFs) in cattle1. Serum from eight clinically normal adult dairy cows was collected, and small non-coding RNAs were extracted immediately after collection and sequenced by Illumina MiSeq. Sequences aligned to transfer RNA (tRNA) genes or their flanking sequences were characterized. Sequences aligned to the beginning of 5′ end of the mature tRNA were classified as tRF5; those aligned to the 3′ end of mature tRNA were classified as tRF3; and those aligned to the beginning of the 3′ end flanking sequences were classified as tRF1. There were 3,190,962 sequences that mapped to transfer RNA and small non-coding RNAs in the bovine genome. Of these, 2,323,520 were identified as tRF5s, 562 were tRF3s, and 81 were tRF1s. There were 866,799 sequences identified as other small non-coding RNAs (microRNA, rRNA, snoRNA, etc.) and were excluded from the study. The tRF5s ranged from 28 to 40 nucleotides; and 98.7% ranged from 30 to 34 nucleotides in length. The tRFs with the greatest number of sequences were derived from tRNA of histidine, glutamic acid, lysine, glycine, and valine. There was no association between number of codons for each amino acid and number of tRFs in the samples. The reason for tRF5s being the most abundant can only be explained if these sequences are associated with function within the animal.