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Differential Expression Spectrum of tRNA fragments in Alzheimer's Disease

ABSTRACT: Differential Expression Spectrum of tRNA fragments in Alzheimer's Disease

PROVIDER: PRJNA1260545 | ENA |

REPOSITORIES: ENA

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Differential Expression Spectrum of tRNA fragments in Alzheimer's Disease

Project description:We report the profiling of tRNA fragments from the temporal cortex of controls and late-stage Alzheimer's disease subjects. We show tRNA fragments expression changes between the two groups. Four upregulatedtRNA fragments in the results of Real Time-qPCR were consistent with the small RNA microarray:5'tRF_GluCTC, 5'tRF_GluTTC, 5'tRF_GlyGCC, 5'tRF_GlyCCC

2025-05-08 | GSE296695 | GEO

Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

Project description:The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons); but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to non-canonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include: PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate non-canonical tRNA functions performed by tRFs.

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Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

Project description:Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

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Endogenous tRNA fragments are expressed in a phosphaturic mesenchymal tumor and Paget's associated osteosarcoma

Project description:We profiled the differential expression of microRNAs and tRNA fragments between a case of a patient harbouring an FGF23-producing tumor and malignant osteosarcoma.

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tRNAArg-derived fragments mediate protein arginylation [tRNA]

Project description:tRNAArg-derived fragments mediate protein arginylation [tRNA]

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Human ANGIOGENIN is sufficient but not required for tRNA cleavage to generate tRNA fragments

Project description:To identify tRNA fragments regulated by angiogenin (ANG, Rnase 5), we sequenced 15-50nt small RNAs upon ANG overexpression and ANG knockout.

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Endogenous tRNA fragments suppress hypoxia-driven bone cancer progression

Project description:We report a modulated expression of tRNA fragments and microRNAs linked to chondrosarcoma progression and demonstrate a method for re-modulating this pathway

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Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

Project description:Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5â?? fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during posttesticular maturation in the epididymis. We find that epididymosomes â?? extracellular vesicles which fuse with sperm during epididymal transit â?? exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo. E14 mESCs were transfected with LNA-containing oligos antisense to tRF-GG or GFP-esiRNA as control, then either total RNA was isolated or 80S ribosomes were isolated from Rnase-digested whole cell lysate, and footprints between 26-32nt were collected for ribosome profiling library construction using a kit-free protocol based on Heyer et al. 2015 NAR.

2016-01-04 | E-GEOD-74537 | biostudies-arrayexpress

Differential Expression Spectrum of tRNA-Derived small RNAs in Idiopathic Pulmonary Arterial Hypertension

Project description:Differential Expression Spectrum of tRNA-Derived small RNAs in Idiopathic Pulmonary Arterial Hypertension

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Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (smallRNA-seq)

Project description:Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5â fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during post-testicular maturation in the epididymis. We find that epididymosomes â extracellular vesicles which fuse with sperm during epididymal transit â exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo. Small RNA (<40nt) profile of various tissues and cells was examined by deep sequencing

2015-12-31 | E-GEOD-75613 | biostudies-arrayexpress

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