tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA

Li, Siqi; Xu, Zhengping; Sheng, Jinghao

doi:10.3390/genes9050246

Cited by 225 publications

(222 citation statements)

References 92 publications

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“…17,109,110 To date, the regulatory mechanisms of tRFs mainly involve several strategies as follows. 17,109,110 To date, the regulatory mechanisms of tRFs mainly involve several strategies as follows.…”

Section: Microrna Smentioning

confidence: 99%

“…Recently, tRFs have been found to play an important role in many biological and pathological processes, and they are associated with many diseases, such as virus infection, metabolic disorder, neurodegenerative diseases and cancers. 17,109,110 To date, the regulatory mechanisms of tRFs mainly involve several strategies as follows.…”

Section: Trna-derived Fr Ag Mentsmentioning

confidence: 99%

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Small non‐coding RNA and colorectal cancer

Chen

Liu

2019

J Cellular Molecular Medi

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Colorectal cancer (CRC) is the third most common malignance. Although great efforts have been made to understand the pathogenesis of CRC, the underlying mechanisms are still unclear. It is now clear that more than 90% of the total genome is actively transcribed, but lack of protein‐coding potential. The massive amount of RNA can be classified as housekeeping RNAs (such as ribosomal RNAs, transfer RNAs) and regulatory RNAs (such as microRNAs [miRNAs], PIWI‐interacting RNA [piRNAs], tRNA‐derived stress‐induced RNA, tRNA‐derived small RNA [tRFs] and long non‐coding RNAs [lncRNAs]). Small non‐coding RNAs are a group of ncRNAs with the length no more than 200 nt and they have been found to exert important regulatory functions under many pathological conditions. In this review, we summarize the biogenesis and functions of regulatory sncRNAs, such as miRNAs, piRNA and tRFs, and highlight their involvements in cancers, particularly in CRC.

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Section: Microrna Smentioning

confidence: 99%

Section: Trna-derived Fr Ag Mentsmentioning

confidence: 99%

Small non‐coding RNA and colorectal cancer

Chen

Liu

2019

J Cellular Molecular Medi

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“…These small RNA fragments are not random degradation products, but specific cleavage products, which play important roles in various pathological and physiological conditions [3]. Collectively, there are two types of tsRNAs were produced from tRNAs.…”

Section: Introductionmentioning

confidence: 99%

Emerging role of a novel small non-coding regulatory RNA: tRNA-derived small RNA

Jin

Guo

2019

ExRNA

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The discovery of small non-coding RNAs, such as miRNA and piRNA, has dramatically changed our understanding of the role RNA plays in organisms. Recent studies show that a novel small non-coding RNA generated from cleavage of tRNA or pre-tRNA, called tRNA-derived small RNA (tsRNA), serves as a new regulator of gene expression. tsRNA has been determined participate in regulating some specific physiological and pathological processes. Although knowledge regarding the biological roles of miRNA and piRNA is expanding, whether tsRNAs play similar roles remains poorly understood. Here, we review the current knowledge regarding the mechanisms of action and biological functions of tsRNAs in intracellular, extracellular and intergenerational inheritance, and highlight the potential application of tsRNAs in human diseases, and present the current problems and future research directions.

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“…The impact of tRFs levels in various biological processes is currently under investigation. However, multiple processes impacted by tRFs have already been identified, amongst which stand translation control, transposon silencing, RNA processing, cell proliferation and DNA damage response modulation (Goodarzi et al, 2015;Kuscu et al, 2018;Li et al, 2018;Liu et al, 2018;Schorn and Martienssen, 2018;Shen et al, 2018;Guan et al, 2019;Su et al, 2019) When RNAse P cleaves the 5' trailer of tRNA-precursor the resulting fragment is believed to be degraded by the ribonuclease translin-TRAX complex (C3PO) (Li et al, 2012) (Fig.1A). However, when RNase Z cleaves the 3' trailer it forms Type-II tRFs (Rossmanith, 2012).…”

Section: Introductionmentioning

confidence: 99%

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

Mollà-Herman¹,

Angelova²,

Carré³

et al. 2019

Preprint

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tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline to study tRFs populations and shed light onto tRNA fragments biogenesis. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant Drosophila ovaries affecting two different highly conserved steps of tRNA biogenesis: 5'pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2'-O-methylation (CG7009 and CG5220). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology. MATERIALS AND METHODS Fly stocksFly stocks are described in (Molla-Herman et al., 2015;M. Angelova, 2019). RNA extraction from ovariesRNA was extracted from Drosophila ovaries following standard methods detailed in (Molla-Herman et al., 2015;M. Angelova, 2019). Small RNA sequencingRNA samples of 3-5 µg were used for High-throughput sequencing using Illumina HiSeq, 10% single-reads lane 1×50 bp. (Fasteris). 15-29 nt RNAs sequences excluding rRNA (riboZero) were sequenced. All the analyses were performed with Galaxy tools https://mississippi.snv.jussieu.fr. Data set deposition is described in (Molla-Herman et al., 2015;M. Angelova, 2019). European Nucleotide Archive (ENA) of the EMBL-EBI (http://www.ebi.ac.uk/ena), accession numbers: PRJEB10569 (Rpp30 mutants), PRJEB35301 and PRJEB35713 (Nm mutants). Clipping and concatenationRaw data were used for clipping the adaptors [Clip adapter (Galaxy-Version 2.3.0, owner: artbio)] and FASTQ quality control was performed (FastQC Read Quality reports (Galaxy-Version 0.72)). Since replicates were homogeneous in quality and analysis (replicates for CG7009* heterozygous and homozygous, triplicates for CG7009*-CG5220* double mutants) we merged them [Concatenate multiple datasets tailto-head (Galaxy-Version 1.4.1, owner: artbio) to have single fasta files. CG7009*/Def9487 was used to obtain normalization numbers but is not shown in the figures. Data normalization using DeSeq miRNA countsData were normalized with bank Size Factors (SF) obtained by using [DESeq geometrical normalization (Galaxy-Version 1.0.1, owner: artbio)] with miRNA counts obtained using [miRcounts (Galaxy-Version 1.3.2)], allowing 0 mismatch (MM). Then, 1/SF values were used in Galaxy small RNA maps (Sup. Fig. 5). Data normalization with DeSeq using ...

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tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA

Cited by 225 publications

References 92 publications

Small non‐coding RNA and colorectal cancer

Small non‐coding RNA and colorectal cancer

Emerging role of a novel small non-coding regulatory RNA: tRNA-derived small RNA

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

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