Differentially Expressed tRNA-Derived Small RNAs Co-Sediment Primarily with Non-Polysomal Fractions in Drosophila

Göktaş, Çağdaş; Yiğit, Hatice; Coşacak, Mehmet İlyas; Akgül, Bünyamin

doi:10.3390/genes8110333

Cited by 20 publications

(23 citation statements)

References 40 publications

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“…5'-tRNA-half-GlyGCC) [13]. Others have identified tRNA halves in murine serum (bound to protein complexes), T cell fragments, yeast and Drosophila [14,15,26,27].…”

Section: Discussionmentioning

confidence: 99%

Maternal circulating syncytiotrophoblast-derived extracellular vesicles contain biologically active 5’-tRNA halves

Cooke

Cribbs

Zhang

et al. 2019

Preprint

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The placenta releases syncytiotrophoblast-derived extracellular vesicles (STB-EV) into the maternal circulation throughout gestation. STB-EV dependent signalling is believed to contribute to the widespread maternal adaptive physiological changes seen in pregnancy.Transfer RNA (tRNA) halves have been identified in vesicles released from other human and murine organ systems, which alter gene expression in target cells. Here, we characterise tRNA-half expression in STB-EV and demonstrate biological activity of a highly abundant tRNA-half. Short RNA from ex-vivo, dual-lobe placental perfusion STB-EV was sequenced,showing that most (>95%) comprised tRNA species. Whole placental tissue contained <50% tRNA species, suggesting selective packaging and export of tRNA into STB-EV. Most tRNA within STB-EV were 5'-tRNA halves cleaved at 30-32 nucleotides. The pattern of tRNA expression differed depending on the size/origin of the STB-EV; this was confirmed by qPCR. Protein synthesis was suppressed in human fibroblasts when they were cultured with a 5'-tRNA half identified from STB-EV sequencing. This study is the first to evaluate tRNA species in STB-EV. The presence of biologically active 5'-tRNA halves, specific to a vesicular origin, suggests a novel mechanism for maternal-fetal signalling in normal pregnancy.

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“…5'-tRNA-half-GlyGCC) [13]. Others have identified tRNA halves in murine serum (bound to protein complexes), T cell fragments, yeast and Drosophila [14,15,26,27].…”

Section: Discussionmentioning

confidence: 99%

Maternal circulating syncytiotrophoblast-derived extracellular vesicles contain biologically active 5’-tRNA halves

Cooke

Cribbs

Zhang

et al. 2019

Preprint

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“…Small RNAs play an important role in the regulation of the MZT to set the stage for post-MZT embryonic events [ 3 , 4 , 10 ]. To gain insight into the expression levels of small RNAs during MZT, we analyzed the small RNA-seq data that was previously deposited to GEO ([ 35 ], GSE35443). This data set includes small RNA-seq of 0–1 h and 7–8 h embryos.…”

Section: Resultsmentioning

confidence: 99%

“…Embryo collection, polysome profiling and small RNA deep-sequencing data have been previously described ([ 35 ], GEO accession number GSE35443). We used the small RNA-seq data to investigate the small RNA dynamics during early development in Drosophila melanogaster .…”

Section: Methodsmentioning

confidence: 99%

Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos

Coşacak

Yiğit

Kızıl

et al. 2018

Genes

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Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate this phenomenon, 0–1 h and 7–8 h Drosophila melanogaster embryos were fractionated on sucrose density gradients into four fractions based on A254 reading (1) translationally inactive messenger ribonucleoprotein (mRNP), (2) 60S, (3) monosome, and (4) polysome. Comparative analysis of deep-sequencing reads from fractionated and un-fractionated 0–1 h and 7–8 h embryos revealed development-specific co-sedimentation pattern of small RNAs with the cellular translation machinery. Although most micro RNAs (miRNAs) did not have a specific preference for any state of the translational machinery, we detected fraction-specific enrichment of a few miRNAs such as dme-miR-1-3p, -184-3p, 5-5p and 263-5p. More interestingly, we observed changes in the subcellular location of a subset of miRNAs in fractionated embryos despite no measurable difference in their amount in unfractionated embryos. Transposon-derived endo small interfering RNAs (siRNAs) were over-expressed in 7–8 h embryos and associated mainly with the mRNP fraction. In contrast, transposon-derived PIWI-interacting RNAs (piRNA), which were more abundant in 0–1 h embryos, co-sedimented primarily with the polysome fractions. These results suggest that there appears to be a complex interplay among the small RNAs with respect to their polysome-cosedimentation pattern during early development in Drosophila melanogaster.

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“…Despite several reports published during the last years describing tRFs in different organisms, a standardized procedure to exhaustively analyze this small RNA populations, in particular using already available small RNA libraries is still lacking. Indeed, each study uses workflows with different parameters, including small RNA preparation, the number of permitted mismatches (0-3 mismatches), the length of analyzed reads, or the way the genome reference has been built (Wang et al, 2013;Goodarzi et al, 2015;Karaiskos et al, 2015aKaraiskos et al, , 2015bKumar et al, 2015;Grigoriev and Karaiskos, 2016;Göktaş et al, 2017;Schorn et al, 2017;Shen et al, 2018;Siira et al, 2018;Kuscu et al, 2018;Liu et al, 2018;Su et al, 2019;Guan et al, 2019). Some studies have modified the genome reference to have pre-tRNAs sequences, but the number of downstream sequences can vary; some have removed introns from the genome reference; some studies have added CCA tag to the genomic reference to recover 3'CCA-tRFs but others have allowed 3 mismatches, then trimmed the CCA tag from reads to match them against the mature tRNA genome reference.…”

Section: Discussionmentioning

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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Differentially Expressed tRNA-Derived Small RNAs Co-Sediment Primarily with Non-Polysomal Fractions in Drosophila

Cited by 20 publications

References 40 publications

Maternal circulating syncytiotrophoblast-derived extracellular vesicles contain biologically active 5’-tRNA halves

Maternal circulating syncytiotrophoblast-derived extracellular vesicles contain biologically active 5’-tRNA halves

Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos

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

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