Genome-wide Identification and Quantitative Analysis of Cleaved tRNA Fragments Induced by Cellular Stress

Case Western Reserve University, United States
Journal of Biological Chemistry (Impact Factor: 4.57). 10/2012; 287(51). DOI: 10.1074/jbc.M112.371799
Source: PubMed


Certain stress conditions can induce cleavage of tRNAs around the anticodon loop via the use of the ribonuclease angiogenin. The cellular factors that regulate tRNA cleavage are not well known. In this study we used normal and eIF2α phosphorylation-deficient mouse embryonic fibroblasts (MEFs) and applied a microarray based methodology to identify and compare tRNA cleavage patterns in response to hypertonic stress, oxidative stress (arsenite) and treatment with recombinant angiogenin. In all three scenarios MEFs deficient in eIF2α phosphorylation showed a higher accumulation of tRNA fragments including those derived from initiator-tRNA(Met). We have shown that tRNA cleavage is regulated by the availability of angiogenin, its substrate (tRNA), the levels of the angiogenin inhibitor RNH1 and the rates of protein synthesis. These conclusions are supported by the following findings: (i) exogenous treatment with angiogenin or knockdown of RNH1 increased tRNA cleavage, (ii) tRNA fragment accumulation was higher during oxidative stress than hypertonic stress, in agreement with a dramatic decrease of RNH1 levels during oxidative stress and (iii) a positive correlation was observed between angiogenin-mediated tRNA cleavage and global protein synthesis rates. Identification of the stress-specific tRNA cleavage mechanisms and patterns will provide insights into the role of tRNA fragments in signaling pathways and stress related disorders.

Download full-text


Available from: Bo-Jhih Guan, Jul 16, 2015
1 Follower
43 Reads
  • Source
    • "They were later observed in unstressed human cells (Kawaji et al., 2008; Fu et al., 2009). However, their levels in resting cells are very low and often increase significantly only during stress conditions (Saikia et al., 2012). Our group and others detected tRNAderived small RNAs circulating in mouse and human bloodstream (Meiri et al., 2010; Dhahbi et al., 2013a,b, 2014; Dhahbi, 2014a). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent evidence demonstrates that serum levels of specific miRNAs significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 21 miRNAs during aging [genotype-by-age interaction (GbA)]. Genotype-by-age miRNAs showed four distinct expression patterns and significant overtargeting of transcripts involved in age-related processes. Functional enrichment analysis of putative and validated miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs modulated by age in the long-lived Ames mouse. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.
    Aging cell 07/2015; DOI:10.1111/acel.12373 · 6.34 Impact Factor
  • Source
    • "Angiogenin - induced fragmentation of tRNAs to inhibit translation is a common response to various stress conditions ( Gold et al , 1963 ; Thompson et al , 2008 ; Fu et al , 2009 ; Yamasaki et al , 2009 ; Ivanov et al , 2011 ; Abbasi - Moheb et al , 2012 ; Saikia et al , 2012 ) . Although cellular factors regulating tRNA cleavage are largely unknown , "
    [Show abstract] [Hide abstract]
    ABSTRACT: Mutations in the cytosine-5 RNA methyltransferase NSun2 cause microcephaly and other neurological abnormalities in mice and human. How post-transcriptional methylation contributes to the human disease is currently unknown. By comparing gene expression data with global cytosine-5 RNA methylomes in patient fibroblasts and NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the angiogenin-mediated endonucleolytic cleavage of transfer RNAs (tRNA) leading to an accumulation of 5′ tRNA-derived small RNA fragments. Accumulation of 5′ tRNA fragments in the absence of NSun2 reduces protein translation rates and activates stress pathways leading to reduced cell size and increased apoptosis of cortical, hippocampal and striatal neurons. Mechanistically, we demonstrate that angiogenin binds with higher affinity to tRNAs lacking site-specific NSun2-mediated methylation and that the presence of 5′ tRNA fragments is sufficient and required to trigger cellular stress responses. Furthermore, the enhanced sensitivity of NSun2-deficient brains to oxidative stress can be rescued through inhibition of angiogenin during embryogenesis. In conclusion, failure in NSun2-mediated tRNA methylation contributes to human diseases via stress-induced RNA cleavage.
    The EMBO Journal 07/2014; 33(18). DOI:10.15252/embj.201489282 · 10.43 Impact Factor
  • Source
    • "However, the mode of translational regulation by tRNA cleavage is not simple. It has been shown previously that during stress conditions, formation of tRNA cleavage products does not change the pool of full-length tRNA significantly, rather these fragments represent only a small portion of the tRNA pool (Saikia et al., 2012). Ivanov et al. (2011) showed a more intricate role for tRNA halves in translational control. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Transfer RNAs (tRNA) are best known for their role as adaptors during translation of the genetic code. Beyond their canonical role during protein biosynthesis, tRNAs also perform additional functions in both prokaryotes and eukaryotes for example in regulating gene expression. Aminoacylated tRNAs have also been implicated as substrates for non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosyntheses. Most recently tRNA fragments, or tRFs, have also been recognized to play regulatory roles. Here, we examine in more detail some of the new functions emerging for tRNA in a variety of cellular processes outside of protein synthesis.
    Frontiers in Genetics 06/2014; 5:171. DOI:10.3389/fgene.2014.00171
Show more