Small RNA sequencing from leaf of Arabidopsis to identify tsRNA
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE95768 | GEO | 2021/03/07
REPOSITORIES: GEO
Similar Datasets
Project description:Emerging evidence indicates that tRNA-derived small RNAs (tsRNAs) with the most abundant RNA modifications play an important role in many complex physiological and pathological processes. However, the biological function and regulation mechanism of modified tsRNA in cancer are still poorly understood. Here, we screened and confirmed a novel m7G modified tsRNA, m7G-3'tiRNA LysTTT (mtiRL) in a variety of chemical carcinogenic models by combined small RNA sequencing with m7G small RNA modified Chip. Moreover, we found that mtiRL catalyzed by tRNA m7G modifying enzyme mettl1 promoted bladder cancer malignancy in vitro and in vivo. Mechanistically, mtiRL specifically bound to oncoprotein Annexin A2 (ANXA2) to promote Tyr24 phosphorylation of ANXA2 by enhancing interactions between ANXA2 and YES1, leading to ANXA2 activation and increased ANXA2 nuclear distribution in bladder cancer cells. Together, these findings define a critical role for mtiRL, targeting this novel m7G modified tsRNA would be an efficient way for the treatment of BC.
2024-05-11 | GSE232579 | GEO
Project description:Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood. Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition. Serum starvation experiments confirm tsRNAs participate in cellular starvation responses by preferential targeting the ribosomal proteins and translational initiation or elongation factors. Knock-down of AGO2 in S2 cells under normal and starved conditions reveals a dependence of the tsRNA-mediated regulation on AGO2. Our study suggests the tsRNA-mediated regulation might be crucial for the energy homeostasis and the metabolic adaptation in the cellular systems.
2018-03-02 | GSE106697 | GEO
Project description:The expression levels of tRNA-derived small RNA, known as tsRNA, were interrogated in the following parental cell lines: MCF10A normal-like mammary epithelial cell, MCF7, MCF10AT1, MCF10CA1a, and MDA-MB-231 breast cancer cells. In addition, tsRNA expression was determined after shRNA-inhibition of RUNX1 in MCF10A cells or RUNX1 induction in MCF10CA1a cells.
2020-01-01 | GSE142382 | GEO
Project description:We sequenced mRNA expression from 3 HeLa and 3 HCT-116 cell lines transfected with LNA (Locked nucleic acid) GL2, LNA CAGMM, or LNA CAGPM respectively. In order to dissect the biological role of 3?tsRNAs (type I tsRNAs) in mammals, we reduced the bioavailable abundance of specific tsRNA species using complementary locked nucleic acid/DNA-mixed antisense oligonucleotides (LNA). The LNA forms a highly stable complex with the target RNA in a sequence specific manner, essentially inhibiting its ability to interact with their biological targets. In our tsRNA-knockdown experiments of HeLa and HCT-116 cell lines, we used three different LNA probes. GL2, is the LNA probe complementary to firefly luciferase gene from pGL2 vector (Promega, WI, USA), which serve as negative control. CAGPM, is the LNA probe perfect complementary to LeuCAG3?tsRNA. CAGMM, is the LNA probe complementary to LeuCAG3?tsRNA with 2 nt mismatches. The sequences for LNA probes are as follows. LNA bases are upper-case letter and DNA bases are lower ?case letter. GL2: GtaCgCgGaaTaCTtC CAGPM: tGTcAGgAgTggGaT CAGMM: tCTcACgAgTggGaT
2017-09-27 | GSE54878 | GEO
Project description:To identify and characterize differentially expressed tsRNA, we collected 3 primary tissues and 3 liver metastasis tissues in pancreatic cancer, and compared the tsRNA expression profiles between primary tissues and liver metastasis tissues in pancreatic cancer using tsRNA sequencing.
2024-01-01 | GSE251943 | GEO
Project description:Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, ROS detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5mo group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18mo group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18mo+curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF.
2024-05-30 | GSE217761 | GEO
Project description:In this study, we analyzed function of the rice RDR701 and various DCLs proteins in small RNA processing. small RNA deep sequencing analyses revealed that RDR701 and OsDCL4 is involved in tasiRNAs and 21- and 24-nt phasiRNAs biogenesis. Further analyses indicate RDR701 coupling with OsDCL4 and OsDCL3b are required for the biogenesis of 21- and 24-nt phasiRNAs, respectively. The triggering miRNAs for intial both size phasiRNAs,are also shown RDR701- and OsDCL4-dependent, suggesting two sequential round activity of RDR701 in associated with different DCLs are essential for rice phasiRNAs biogenesis.
2012-07-03 | GSE26405 | GEO
Project description:DICER-like 3 (DCL3) is a major player in heterochromatic 24-nucleotide siRNA and long miRNA biogenesis and mutants have been characterized from Arabidopsis and rice. Here, a tomato DCL3 mutant was generated through the use of trans-activated artificial microRNA and characterized. Global tomato DCL3 (SlDCL3) silencing was induced by crossing the generated responder line (OP:amiRDCL3) with constitutive driver line. Constitutive trans-activation knocked down SlDCL3 levels by ~77%, resulting in dramatically decreased 24-nucleotide small RNA levels, but a significant increase in 21- and 22- nucleotide small RNAs, which was correlated with specific upregulation of SlDCL4 and SlDCL2b. Moreover, in the majority of small RNA-generating loci an almost complete overlap between the control and 35S>>amiRSlDCL3 siRNA signatures, was observed, strongly suggesting that the reduction in 24-nucleotide siRNAs was compensated by increased biogenesis of 21-22 nt siRNAs from the same genomic sequences. Collectively, these results suggest the requirement of SlDCL3 for the biogenesis of 23-24 nt sRNAs and its substitution by SlDCL4 and SlDCL2b, which function in the biogenesis of 21- and 22-nt small RNAs. In addition, differential expression between control and SlDCL3-silenced small RNAs indicated a significant reduction in the abundance of 24-nt putative long miRNAs, which was validated by northern blots, implicating SlDCL3 in their biogenesis. Examination of small RNA populations in control (35S:LhG4) and SlDCL3 silenced seedlings (35S>>amiRSlDCL3) 2 biological replicates each
2014-03-31 | E-GEOD-52265 | biostudies-arrayexpress
Project description:In this study, we analyzed function of the rice RDR701 and various DCLs proteins in small RNA processing. small RNA deep sequencing analyses revealed that RDR701 and OsDCL4 is involved in tasiRNAs and 21- and 24-nt phasiRNAs biogenesis. Further analyses indicate RDR701 coupling with OsDCL4 and OsDCL3b are required for the biogenesis of 21- and 24-nt phasiRNAs, respectively. The triggering miRNAs for intial both size phasiRNAs,are also shown RDR701- and OsDCL4-dependent, suggesting two sequential round activity of RDR701 in associated with different DCLs are essential for rice phasiRNAs biogenesis. Four small RNA libraries were constructed from panicles of zhonghua11 (a wild-type Japonica rice variety) and rdr701-1 at high temperature (Day average temperature 32M-bM-^DM-^C) and low temperature (Day average temperature 28M-bM-^DM-^C).
2012-07-02 | E-GEOD-26405 | biostudies-arrayexpress
Project description:DICER-like 3 (DCL3) is a major player in heterochromatic 24-nucleotide siRNA and long miRNA biogenesis and mutants have been characterized from Arabidopsis and rice. Here, a tomato DCL3 mutant was generated through the use of trans-activated artificial microRNA and characterized. Global tomato DCL3 (SlDCL3) silencing was induced by crossing the generated responder line (OP:amiRDCL3) with constitutive driver line. Constitutive trans-activation knocked down SlDCL3 levels by ~77%, resulting in dramatically decreased 24-nucleotide small RNA levels, but a significant increase in 21- and 22- nucleotide small RNAs, which was correlated with specific upregulation of SlDCL4 and SlDCL2b. Moreover, in the majority of small RNA-generating loci an almost complete overlap between the control and 35S>>amiRSlDCL3 siRNA signatures, was observed, strongly suggesting that the reduction in 24-nucleotide siRNAs was compensated by increased biogenesis of 21-22 nt siRNAs from the same genomic sequences. Collectively, these results suggest the requirement of SlDCL3 for the biogenesis of 23-24 nt sRNAs and its substitution by SlDCL4 and SlDCL2b, which function in the biogenesis of 21- and 22-nt small RNAs. In addition, differential expression between control and SlDCL3-silenced small RNAs indicated a significant reduction in the abundance of 24-nt putative long miRNAs, which was validated by northern blots, implicating SlDCL3 in their biogenesis.
2014-03-31 | GSE52265 | GEO