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Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement

ABSTRACT: Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement

PROVIDER: PRJNA268389 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1662160.fastq.gz	Fastqsanger.gz
	SRR1662161.fastq.gz	Fastqsanger.gz
	SRR1661712.fastq.gz	Fastqsanger.gz
	SRR1661713.fastq.gz	Fastqsanger.gz
	SRR1661714.fastq.gz	Fastqsanger.gz

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Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement.

Project description:Upon exposure to stress, tRNAs are enzymatically cleaved, yielding distinct classes of tRNA-derived fragments (tRFs), yielding distinct classes of tRFs. We identify a novel class of tRFs derived from tRNA(Glu), tRNA(Asp), tRNA(Gly), and tRNA(Tyr) that, upon induction, suppress the stability of multiple oncogenic transcripts in breast cancer cells by displacing their 3' untranslated regions (UTRs) from the RNA-binding protein YBX1. This mode of post-transcriptional silencing is sequence specific, as these fragments all share a common motif that matches the YBX1 recognition sequence. Loss-of-function and gain-of-function studies, using anti-sense locked-nucleic acids (LNAs) and synthetic RNA mimetics, respectively, revealed that these fragments suppress growth under serum-starvation, cancer cell invasion, and metastasis by breast cancer cells. Highly metastatic cells evade this tumor-suppressive pathway by attenuating the induction of these tRFs. Our findings reveal a tumor-suppressive role for specific tRNA-derived fragments and describe a molecular mechanism for their action. This transcript displacement-based mechanism may generalize to other tRNA, ribosomal-RNA, and sno-RNA fragments.

| S-EPMC4457382 | biostudies-literature

YBX1 small-RNA HITS-CLIP

Project description:In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Chi SW, et al. 2009, Nature 460:479)

2015-05-08 | E-GEOD-63597 | biostudies-arrayexpress

YBX1 small-RNA HITS-CLIP

Project description:In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1

2015-05-08 | GSE63597 | GEO

Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-05-07 | GSE63605 | GEO

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

2022-05-20 | GSE86576 | GEO

Chip-chip from HCT116 cells with YBX1

Project description:YBX1 is a multifunctional protein involved in the control of transcription and translation. We identified YBX1 as an target of MEK/ERK signaling in colorectal cancer cell lines. We performed a ChIP-chip analysis of HCT116 cells to identify new potential target genes of YBX1. Comparison of input DNA fragments with fragments coprecipitated with YBX1 in HCT116 cells.

2010-10-09 | E-GEOD-18337 | biostudies-arrayexpress

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

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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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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

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