scholarly journals Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells

RNA Biology ◽  
2013 ◽  
Vol 10 (4) ◽  
pp. 553-563 ◽  
Author(s):  
Andrew Sobala ◽  
Gyorgy Hutvagner
Keyword(s):  
Small Rnas ◽  
Protein Translation ◽  
Human Cells ◽  
Inhibit Protein Translation

scholarly journals Effect of RIP Overexpression on Abiotic Stress Tolerance and Development of Rice

2021 ◽  
Vol 22 (3) ◽  
pp. 1434
Author(s):  
Pieter Wytynck ◽  
Jeroen Lambin ◽  
Simin Chen ◽  
Sinem Demirel Asci ◽  
Isabel Verbeke ◽  
...  
Keyword(s):  
Methyl Jasmonate ◽  
Stress Responses ◽  
Abiotic Stress Tolerance ◽  
Protein Translation ◽  
Ribosome Inactivating Proteins ◽  
Close Proximity ◽  
Inhibit Protein Translation ◽  
Plant Ribosomes ◽  
A Cell ◽  
Type 3

Ribosome-inactivating proteins (RIPs) are a class of cytotoxic enzymes that can inhibit protein translation by depurinating rRNA. Most plant RIPs are synthesized with a leader sequence that sequesters the proteins to a cell compartment away from the host ribosomes. However, several rice RIPs lack these signal peptides suggesting they reside in the cytosol in close proximity to the plant ribosomes. This paper aims to elucidate the physiological function of two nucleocytoplasmic RIPs from rice, in particular, the type 1 RIP referred to as OsRIP1 and a presumed type 3 RIP called nuRIP. Transgenic rice lines overexpressing these RIPs were constructed and studied for developmental effects resulting from this overexpression under greenhouse conditions. In addition, the performance of transgenic seedlings in response to drought, salt, abscisic acid and methyl jasmonate treatment was investigated. Results suggest that both RIPs can affect methyl jasmonate mediated stress responses.

scholarly journals An Algorithm for Generating Small RNAs Capable of Epigenetically Modulating Transcriptional Gene Silencing and Activation in Human Cells

2013 ◽  
Vol 2 ◽  
pp. e104 ◽  
Author(s):  
Amanda Ackley ◽  
Alexandra Lenox ◽  
Kenneth Stapleton ◽  
Stuart Knowling ◽  
Tim Lu ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Human Cells ◽  
Transcriptional Gene Silencing

Metabolism of small RNAs in cultured human cells

1989 ◽  
Vol 138 (2) ◽  
pp. 433-438 ◽  
Author(s):  
Kanakendu Choudhury ◽  
Indrani Choudhury ◽  
George L. Eliceiri
Keyword(s):  
Small Rnas ◽  
Human Cells ◽  
Cultured Human Cells

scholarly journals Cohesin Proteins Promote Ribosomal RNA Production and Protein Translation in Yeast and Human Cells

PLoS Genetics ◽  
2012 ◽  
Vol 8 (6) ◽  
pp. e1002749 ◽  
Author(s):  
Tania Bose ◽  
Kenneth K. Lee ◽  
Shuai Lu ◽  
Baoshan Xu ◽  
Bethany Harris ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Protein Translation ◽  
Human Cells

High-efficiency transfection of small RNAs and plasmid DNA in human cells

2007 ◽  
Author(s):  
Graziano Martello ◽  
Michelangelo Cordenonsi ◽  
Stefano Piccolo
Keyword(s):  
Plasmid Dna ◽  
Small Rnas ◽  
High Efficiency ◽  
Human Cells

scholarly journals Adenylation of Small RNAs in Human Cells

1998 ◽  
Vol 273 (12) ◽  
pp. 6853-6859 ◽  
Author(s):  
Krishna M. Sinha ◽  
Jian Gu ◽  
Yahua Chen ◽  
Ram Reddy
Keyword(s):  
Small Rnas ◽  
Human Cells

scholarly journals Transcriptome-based design of antisense inhibitors potentiates carbapenem efficacy in CREEscherichia coli

2020 ◽  
Vol 117 (48) ◽  
pp. 30699-30709
Author(s):  
Thomas R. Aunins ◽  
Keesha E. Erickson ◽  
Anushree Chatterjee
Keyword(s):  
Gene Expression ◽  
Protein Translation ◽  
Resistance Mechanisms ◽  
Transcriptomic Analysis ◽  
Gene Expression Response ◽  
Antibiotic Development ◽  
Resistance Factors ◽  
Inhibit Protein Translation ◽  
Significant Expression ◽  
Expression Response

In recent years, the prevalence of carbapenem-resistantEnterobacteriaceae(CRE) has risen substantially, and the study of CRE resistance mechanisms has become increasingly important for antibiotic development. Although much research has focused on genomic resistance factors, relatively few studies have examined CRE pathogens through changes in gene expression. In this study, we examined the gene expression profile of a CREEscherichia coliclinical isolate that is sensitive to meropenem but resistant to ertapenem to explore transcriptomic contributions to resistance and to identify gene knockdown targets for carbapenem potentiation. We sequenced total and short RNA to analyze the gene expression response to ertapenem or meropenem treatment and found significant expression changes in genes related to motility, maltodextrin metabolism, the formate hydrogenlyase complex, and the general stress response. To validate these findings, we used our laboratory’s Facile Accelerated Specific Therapeutic (FAST) platform to create antisense peptide nucleic acids (PNAs), gene-specific molecules designed to inhibit protein translation. PNAs were designed to inhibit the pathways identified in our transcriptomic analysis, and each PNA was then tested in combination with each carbapenem to assess its effect on the antibiotics’ minimum inhibitory concentrations. We observed significant PNA–antibiotic interaction with five different PNAs across six combinations. Inhibition of the geneshycA,dsrB, andbolApotentiated carbapenem efficacy in CREE. coli, whereas inhibition of the genesflhCandygaCconferred added resistance. Our results identify resistance factors and demonstrate that transcriptomic analysis is a potent tool for designing antibiotic PNA.

scholarly journals A KLF4-miRNA-206 Autoregulatory Feedback Loop Can Promote or Inhibit Protein Translation Depending upon Cell Context

2011 ◽  
Vol 31 (12) ◽  
pp. 2513-2527 ◽  
Author(s):  
C.-C. Lin ◽  
L.-Z. Liu ◽  
J. B. Addison ◽  
W. F. Wonderlin ◽  
A. V. Ivanov ◽  
...  
Keyword(s):  
Feedback Loop ◽  
Protein Translation ◽  
Inhibit Protein Translation

scholarly journals BRCA1 Mediated Homologous Recombination and S Phase DNA Repair Pathways Restrict LINE-1 Retrotransposition in Human Cells

2019 ◽  
Author(s):  
Xiaoji Sun ◽  
Paolo Mita ◽  
David J. Kahler ◽  
Donghui Li ◽  
Aleksandra Wudzinska ◽  
...  
Keyword(s):  
Dna Repair ◽  
Homologous Recombination ◽  
Potential Role ◽  
Genome Instability ◽  
Protein Translation ◽  
Human Cells ◽  
Host Factors ◽  
Factors Affecting ◽  
A Genome ◽  
Repair Pathways

AbstractLong interspersed element-1 (LINE-1 or L1) is the only autonomous retrotransposon active in human cells. L1s DNA makes about 17% of the human genome and retrotransposition of a few active L1 copies has been detected in various tumors, underscoring the potential role of L1 in mediating or increasing genome instability during tumorigenic development. Different host factors have been shown to influence L1 mobility through several mechanisms. However, systematic analyses of host factors affecting L1 retrotransposition are limited. Here, we developed a high-throughput microscopy-based retrotransposition assay and coupled it to a genome-wide siRNA knockdown screen to study the cellular regulators of L1 retrotransposition in human cells. We showed that L1 insertion frequency was stimulated by knockdown of Double-Stranded Break (DSB) repair factors that are active in the S/G2 phase of the cell cycle including Homologous Recombination (HR), Fanconi Anemia (FA) and, to a less extent, microhomology-mediated end-joining (MMEJ) factors. In particular, we show that BRCA1, an E3 ubiquitin ligase with a key role in several DNA repair pathways, plays multiple roles in regulating L1; BRCA1 knockdown directly affects L1 retrotransposition frequency and structure and also plays a role in controlling L1 ORF2 protein translation through L1 mRNA binding. These results suggest the existence of a “battle” between HR factors and L1 retrotransposons, revealing a potential role for L1 in development of tumors characterized by BRCA1 and HR repair deficiencies.

scholarly journals Dynamic expression of tRNA-derived small RNAs define cellular states

2017 ◽  
Author(s):  
Daniel GR Yim ◽  
Srikar Krishna ◽  
Vairavan Lakshmanan ◽  
Judice LY Koh ◽  
Jung Eun Park ◽  
...  
Keyword(s):  
Small Rnas ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Functional Characterization ◽  
Embryonic Stem ◽  
Protein Translation ◽  
State Transitions ◽  
Cell State ◽  
Normal States ◽  
Factor C

AbstractTransfer RNA (tRNA)-derived small RNAs (tsRNAs) have recently emerged as important regulators of protein translation and shown to have diverse biological functions. However, the underlying cellular and molecular mechanisms of tsRNA function in the context of dynamic cell-state transitions remain unclear. Here we report the identification of a set of tsRNAs upregulated in differentiating mouse embryonic stem cells (mESCs). Mechanistic analyses revealed primary functions of tsRNAs in regulating polysome assembly and translation. Notably, interactome studies with differentially-enriched tsRNAs revealed a switch in associations with ‘effector’ RNPs and ‘target’ mRNAs in different cell-states. We also demonstrate that a specific pool of tsRNAs can interact with Igf2bp1, an RNA-binding protein, to influence the expression of the pluripotency-promoting factor-c-Myc, thereby providing evidence for tsRNAs in modulating stem cell-states in mESCs. Finally, tsRNA expression analyses in distinct, heterologous cell and tissue models of stem/transformed versus differentiated/normal states reveal that tsRNA-mediated regulation of protein translation may represent a global biological phenomenon associated with cell-state transitions.One Sentence SummaryIdentification and functional characterization of tRNA-derived small RNAs (tsRNAs) in cell state switches.

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