典型的tRNA共表达多个5 ' tRNA半部分,其序列和丰度取决于同位解码器和同位受体,并随组织类型、细胞类型和疾病而变化

IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Non-Coding RNA Pub Date : 2023-11-06 DOI:10.3390/ncrna9060069
Robert Brian Akins, Kayleigh Ostberg, Tess Cherlin, Nikolas J. Tsiouplis, Phillipe Loher, Isidore Rigoutsos
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引用次数: 0

摘要

转移rna衍生片段(tRFs)是由成熟的转移rna (trna)或其前体产生的非编码rna。trf的一个重要类别包括tRNA的一半,它们是通过反密码子的切割产生的。一个给定的tRNA通常会产生几个共同表达的5 ' -tRNA一半(5 ' -tRHs),它们的3 '端位置不同。这些5 ' - trh,即使是不同的,由于它们几乎相同的序列和长度,传统上被认为是无法区分的。我们专注于由相同tRNA产生的共表达5 ' - trh,并系统地检查了它们在10种不同人体组织中的确切序列和丰度。为此,我们手工整理和分析了来自NCBI序列运行档案(SRA)的数百个人类RNA-seq数据集。我们将来自同一组织的数据集分组到各自的集合中,并分别检查每组。我们发现,给定的tRNA在不同的组织、不同的细胞系和不同的疾病中产生不同组的共表达5 ' - trh。重要的是,共表达的5 ' - trh在序列、绝对丰度和相对丰度上存在差异,即使在来自同一同位解码器或同位受体组的具有几乎相同序列的trna之间也是如此。研究结果表明,由相同tRNA或密切相关的tRNA产生的共表达5 ' - trh具有不同的上下文依赖作用。此外,我们的分析表明,当涉及到tRFs实验时,模拟相同组织类型和疾病的细胞系可能无法互换。
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The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease
Transfer RNA-derived fragments (tRFs) are noncoding RNAs that arise from either mature transfer RNAs (tRNAs) or their precursors. One important category of tRFs comprises the tRNA halves, which are generated through cleavage at the anticodon. A given tRNA typically gives rise to several co-expressed 5’-tRNA halves (5′-tRHs) that differ in the location of their 3′ ends. These 5′-tRHs, even though distinct, have traditionally been treated as indistinguishable from one another due to their near-identical sequences and lengths. We focused on co-expressed 5′-tRHs that arise from the same tRNA and systematically examined their exact sequences and abundances across 10 different human tissues. To this end, we manually curated and analyzed several hundred human RNA-seq datasets from NCBI’s Sequence Run Archive (SRA). We grouped datasets from the same tissue into their own collection and examined each group separately. We found that a given tRNA produces different groups of co-expressed 5′-tRHs in different tissues, different cell lines, and different diseases. Importantly, the co-expressed 5′-tRHs differ in their sequences, absolute abundances, and relative abundances, even among tRNAs with near-identical sequences from the same isodecoder or isoacceptor group. The findings suggest that co-expressed 5′-tRHs that are produced from the same tRNA or closely related tRNAs have distinct, context-dependent roles. Moreover, our analyses show that cell lines modeling the same tissue type and disease may not be interchangeable when it comes to experimenting with tRFs.
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来源期刊
Non-Coding RNA
Non-Coding RNA Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
6.70
自引率
4.70%
发文量
74
审稿时长
10 weeks
期刊介绍: Functional studies dealing with identification, structure-function relationships or biological activity of: small regulatory RNAs (miRNAs, siRNAs and piRNAs) associated with the RNA interference pathway small nuclear RNAs, small nucleolar and tRNAs derived small RNAs other types of small RNAs, such as those associated with splice junctions and transcription start sites long non-coding RNAs, including antisense RNAs, long ''intergenic'' RNAs, intronic RNAs and ''enhancer'' RNAs other classes of RNAs such as vault RNAs, scaRNAs, circular RNAs, 7SL RNAs, telomeric and centromeric RNAs regulatory functions of mRNAs and UTR-derived RNAs catalytic and allosteric (riboswitch) RNAs viral, transposon and repeat-derived RNAs bacterial regulatory RNAs, including CRISPR RNAS Analysis of RNA processing, RNA binding proteins, RNA signaling and RNA interaction pathways: DICER AGO, PIWI and PIWI-like proteins other classes of RNA binding and RNA transport proteins RNA interactions with chromatin-modifying complexes RNA interactions with DNA and other RNAs the role of RNA in the formation and function of specialized subnuclear organelles and other aspects of cell biology intercellular and intergenerational RNA signaling RNA processing structure-function relationships in RNA complexes RNA analyses, informatics, tools and technologies: transcriptomic analyses and technologies development of tools and technologies for RNA biology and therapeutics Translational studies involving long and short non-coding RNAs: identification of biomarkers development of new therapies involving microRNAs and other ncRNAs clinical studies involving microRNAs and other ncRNAs.
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