Starvation-induced Cleavage of the tRNA Anticodon Loop in Tetrahymena thermophila

Lee, Suzanne R.; Collins, Kathleen

doi:10.1074/jbc.m510356200

Cited by 204 publications

(238 citation statements)

References 43 publications

(29 reference statements)

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“…tRNA fragments of 30-35 nt have been identified in bacteria, fungi, plants, and animals (Lee and Collins 2005;Haiser et al 2008;Jochl et al 2008;Kawaji et al 2008;Li et al 2008;Thompson et al 2008;Zhang et al 2009). These tRNA fragments are different from the ones reported here in that they are derived from a cleavage at or around the anti-codon loop by Rny1p in yeast (Thompson and Parker 2009) or angiogenin in humans (Yamasaki et al 2009).…”

Section: Discussionmentioning

confidence: 99%

“…Below the mature tRNA bands, there are additional bands of intermediate size (35-60 nt long) that could correspond to the tRNA cleavage products that were reported recently (Lee and Collins 2005;Haiser et al 2008;Jochl et al 2008;Kawaji et al 2008;Li et al 2008;Thompson et al 2008;Zhang et al 2009). tRF-1001 was also measured by splinted ligation assays (Supplemental Fig.…”

Section: Expression Of Trfs Validated By Other Techniquesmentioning

confidence: 99%

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A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

Lee¹,

Shibata²,

Malhotra³

et al. 2009

Genes Dev.

937

1,248

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New types of small RNAs distinct from microRNAs (miRNAs) are progressively being discovered in various organisms. In order to discover such novel small RNAs, a library of 17-to 26-base-long RNAs was created from prostate cancer cell lines and sequenced by ultra-high-throughput sequencing. A significant number of the sequences are derived from precise processing at the 59 or 39 end of mature or precursor tRNAs to form three series of tRFs (tRNA-derived RNA fragments): the tRF-5, tRF-3, and tRF-1 series. These sequences constitute a class of short RNAs that are second most abundant to miRNAs. Northern hybridization, quantitative RT-PCR, and splinted ligation assays independently measured the levels of at least 17 tRFs. To demonstrate the biological importance of tRFs, we further investigated tRF-1001, derived from the 39 end of a Ser-TGA tRNA precursor transcript that is not retained in the mature tRNA. tRF-1001 is expressed highly in a wide range of cancer cell lines but much less in tissues, and its expression in cell lines was tightly correlated with cell proliferation. siRNAmediated knockdown of tRF-1001 impaired cell proliferation with the specific accumulation of cells in G2, phenotypes that were reversed specifically by cointroducing a synthetic 29-O-methyl tRF-1001 oligoribonucleotide resistant to the siRNA. tRF-1001 is generated in the cytoplasm by tRNA 39-endonuclease ELAC2, a prostate cancer susceptibility gene. Our data suggest that tRFs are not random by-products of tRNA degradation or biogenesis, but an abundant and novel class of short RNAs with precise sequence structure that have specific expression patterns and specific biological roles.[Keywords: Small RNA; tRNA; deep sequencing; cancer cell proliferation] Supplemental material is available at http://www.genesdev.org.

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Section: Discussionmentioning

confidence: 99%

Section: Expression Of Trfs Validated By Other Techniquesmentioning

confidence: 99%

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

Lee¹,

Shibata²,

Malhotra³

et al. 2009

Genes Dev.

937

1,248

View full text Add to dashboard Cite

show abstract

“…tRNA endonucleolytic cleavage tRNA endonucleolytic cleavage generating 59 and 39 approximately half-size molecules occurs in numerous organisms, as first demonstrated in C. elegans (Lee and Collins 2005; reviewed in Thompson and Parker 2009a;Parker 2012). Generally the half-size tRNA pieces accumulate when cells are nutrient deprived or otherwise stressed.…”

Section: To 39 Exonucleolyic Degradation By the Rtd Pathwaymentioning

confidence: 99%

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

2013

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Transfer RNAs (tRNAs) are essential for protein synthesis. In eukaryotes, tRNA biosynthesis employs a specialized RNA polymerase that generates initial transcripts that must be subsequently altered via a multitude of post-transcriptional steps before the tRNAs beome mature molecules that function in protein synthesis. Genetic, genomic, biochemical, and cell biological approaches possible in the powerful Saccharomyces cerevisiae system have led to exciting advances in our understandings of tRNA post-transcriptional processing as well as to novel insights into tRNA turnover and tRNA subcellular dynamics. tRNA processing steps include removal of transcribed leader and trailer sequences, addition of CCA to the 39 mature sequence and, for tRNA His , addition of a 59 G. About 20% of yeast tRNAs are encoded by intron-containing genes. The three-step splicing process to remove the introns surprisingly occurs in the cytoplasm in yeast and each of the splicing enzymes appears to moonlight in functions in addition to tRNA splicing. There are 25 different nucleoside modifications that are added post-transcriptionally, creating tRNAs in which 15% of the residues are nucleosides other than A, G, U, or C. These modified nucleosides serve numerous important functions including tRNA discrimination, translation fidelity, and tRNA quality control. Mature tRNAs are very stable, but nevertheless yeast cells possess multiple pathways to degrade inappropriately processed or folded tRNAs. Mature tRNAs are also dynamic in cells, moving from the cytoplasm to the nucleus and back again to the cytoplasm; the mechanism and function of this retrograde process is poorly understood. Here, the state of knowledge for tRNA post-transcriptional processing, turnover, and subcellular dynamics is addressed, highlighting the questions that remain. TABLE OF CONTENTS Abstract 43Introduction 44

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“…40 Conspicuously, two different kinds of cleavage phenomena have been observed. While global tRNA cleavage correlated with codon usage in organisms like Streptomyces coelicolor, 41,42 other groups reported on isoacceptor-specific preferences. Here no correlation between targeted tRNAs and their number of genes, their cellular copy number, or the codon usage, has been found.…”

Section: Trna In Piecesmentioning

confidence: 99%