Publications by authors named "Boris Slobodin"

14 Publications

  • Page 1 of 1

SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis.

Nature 2021 06 12;594(7862):240-245. Epub 2021 May 12.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

The coronavirus SARS-CoV-2 is the cause of the ongoing pandemic of COVID-19. Coronaviruses have developed a variety of mechanisms to repress host mRNA translation to allow the translation of viral mRNA, and concomitantly block the cellular innate immune response. Although several different proteins of SARS-CoV-2 have previously been implicated in shutting off host expression, a comprehensive picture of the effects of SARS-CoV-2 infection on cellular gene expression is lacking. Here we combine RNA sequencing, ribosome profiling and metabolic labelling of newly synthesized RNA to comprehensively define the mechanisms that are used by SARS-CoV-2 to shut off cellular protein synthesis. We show that infection leads to a global reduction in translation, but that viral transcripts are not preferentially translated. Instead, we find that infection leads to the accelerated degradation of cytosolic cellular mRNAs, which facilitates viral takeover of the mRNA pool in infected cells. We reveal that the translation of transcripts that are induced in response to infection (including innate immune genes) is impaired. We demonstrate this impairment is probably mediated by inhibition of nuclear mRNA export, which prevents newly transcribed cellular mRNA from accessing ribosomes. Overall, our results uncover a multipronged strategy that is used by SARS-CoV-2 to take over the translation machinery and to suppress host defences.
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http://dx.doi.org/10.1038/s41586-021-03610-3DOI Listing
June 2021

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.

EMBO Rep 2020 09 16;21(9):e50799. Epub 2020 Aug 16.

Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.

Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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http://dx.doi.org/10.15252/embr.202050799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7507372PMC
September 2020

Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels.

Mol Cell 2020 05 14;78(3):434-444.e5. Epub 2020 Apr 14.

Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show that reduced transcription dynamics of specific genes leads to enhanced mA deposition, preferential activity of the CCR4-Not complex, shortened poly(A) tails, and reduced stability of the respective mRNAs. These effects are also exerted by internal ribosome entry site (IRES) elements, which we found to be transcriptional pause sites. However, when transcription dynamics, and subsequently poly(A) tails, are globally altered, cells buffer mRNA levels by adjusting the expression of mRNA degradation machinery. Stress-provoked global impediment of transcription elongation leads to a dramatic inhibition of the mRNA degradation machinery and massive mRNA stabilization. Accordingly, globally enhanced transcription, such as following B cell activation or glucose stimulation, has the opposite effects. This study uncovers two molecular pathways that maintain balanced gene expression in mammalian cells by linking transcription to mRNA stability.
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http://dx.doi.org/10.1016/j.molcel.2020.03.022DOI Listing
May 2020

The methylated way to translation.

Oncotarget 2017 Nov 25;8(55):93313-93314. Epub 2017 Oct 25.

Reuven Agami: Division of Oncogenomics, The Netherlands Cancer Institute, Oncode Institute, Amsterdam, The Netherlands; Department of Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.

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http://dx.doi.org/10.18632/oncotarget.22073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706795PMC
November 2017

Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation.

Cell 2017 04;169(2):326-337.e12

Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands. Electronic address:

Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. Here, we sought for a possible connection between transcription and translation. Employing an unbiased screen of multiple human promoters, we identified a positive effect of TATA box on translation and a general coupling between mRNA expression and translational efficiency. Using a CRISPR-Cas9-mediated approach, genome-wide analyses, and in vitro experiments, we show that the rate of transcription regulates the efficiency of translation. Furthermore, we demonstrate that mA modification of mRNAs is co-transcriptional and depends upon the dynamics of the transcribing RNAPII. Suboptimal transcription rates lead to elevated mA content, which may result in reduced translation. This study uncovers a general and widespread link between transcription and translation that is governed by epigenetic modification of mRNAs.
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http://dx.doi.org/10.1016/j.cell.2017.03.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388891PMC
April 2017

An Essential Role for COPI in mRNA Localization to Mitochondria and Mitochondrial Function.

Cell Rep 2016 Apr 7;15(3):540-549. Epub 2016 Apr 7.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel. Electronic address:

Nuclear-encoded mRNAs encoding mitochondrial proteins (mMPs) can localize directly to the mitochondrial surface, yet how mMPs target mitochondria and whether RNA targeting contributes to protein import into mitochondria and cellular metabolism are unknown. Here, we show that the COPI vesicle coat complex is necessary for mMP localization to mitochondria and mitochondrial function. COPI inactivation leads to reduced mMP binding to COPI itself, resulting in the dissociation of mMPs from mitochondria, a reduction in mitochondrial membrane potential, a decrease in protein import in vivo and in vitro, and severe deficiencies in mitochondrial respiration. Using a model mMP (OXA1), we observed that COPI inactivation (or mutation of the potential COPI-interaction site) led to altered mRNA localization and impaired cellular respiration. Overall, COPI-mediated mMP targeting is critical for mitochondrial protein import and function, and transcript delivery to the mitochondria or endoplasmic reticulum is regulated by cis-acting RNA sequences and trans-acting proteins.
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http://dx.doi.org/10.1016/j.celrep.2016.03.053DOI Listing
April 2016

Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to "MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system".

RNA 2016 May 11;22(5):660-6. Epub 2016 Mar 11.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.

The MS2 system has been extensively used to visualize single mRNA molecules in live cells and follow their localization and behavior. In their Letter to the Editor recently published, Garcia and Parker suggest that use of the MS2 system may yield erroneous mRNA localization results due to the accumulation of 3' decay products. Here we cite published works and provide new data which demonstrate that this is not a phenomenon general to endogenously expressed MS2-tagged transcripts, and that some of the results obtained in their study could have arisen from artifacts of gene expression.
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http://dx.doi.org/10.1261/rna.055095.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836641PMC
May 2016

Production of bone formation-regulating factors by osteoclasts in vitro does not correlate with the radiographic disease progression in patients with ankylosing spondylitis.

Joint Bone Spine 2016 Jul 6;83(4):468-9. Epub 2015 Oct 6.

Internal Medicine A, Bnai Zion Medical Center, 47, Golomb Street, Haifa 31048, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa 31048, Israel.

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http://dx.doi.org/10.1016/j.jbspin.2015.06.008DOI Listing
July 2016

Transcription initiation determines its end.

Mol Cell 2015 Jan;57(2):205-6

Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Erasmus MC, Rotterdam University, 3000 CA Rotterdam, The Netherlands. Electronic address:

A new study published in this issue of Molecular Cell (Oktaba et al., 2015) suggests widespread involvement of promoters in the regulation of alternative cleavage and polyadenylation of mRNAs in Drosophila neurons.
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http://dx.doi.org/10.1016/j.molcel.2015.01.006DOI Listing
January 2015

Translation- and SRP-independent mRNA targeting to the endoplasmic reticulum in the yeast Saccharomyces cerevisiae.

Mol Biol Cell 2013 Oct 31;24(19):3069-84. Epub 2013 Jul 31.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.

mRNAs encoding secreted/membrane proteins (mSMPs) are believed to reach the endoplasmic reticulum (ER) in a translation-dependent manner to confer protein translocation. Evidence exists, however, for translation- and signal recognition particle (SRP)-independent mRNA localization to the ER, suggesting that there are alternate paths for RNA delivery. We localized endogenously expressed mSMPs in yeast using an aptamer-based RNA-tagging procedure and fluorescence microscopy. Unlike mRNAs encoding polarity and secretion factors that colocalize with cortical ER at the bud tip, mSMPs and mRNAs encoding soluble, nonsecreted, nonpolarized proteins localized mainly to ER peripheral to the nucleus (nER). Synthetic nontranslatable uracil-rich mRNAs were also demonstrated to colocalize with nER in yeast. This mRNA-ER association was verified by subcellular fractionation and reverse transcription-PCR, single-molecule fluorescence in situ hybridization, and was not inhibited upon SRP inactivation. To better understand mSMP targeting, we examined aptamer-tagged USE1, which encodes a tail-anchored membrane protein, and SUC2, which encodes a soluble secreted enzyme. USE1 and SUC2 mRNA targeting was not abolished by the inhibition of translation or removal of elements involved in translational control. Overall we show that mSMP targeting to the ER is both translation- and SRP-independent, and regulated by cis elements contained within the message and trans-acting RNA-binding proteins (e.g., She2, Puf2).
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http://dx.doi.org/10.1091/mbc.E13-01-0038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784381PMC
October 2013

K2CaV2O7: a pyrovanadate with a new layered type of structure in the A2BV2O7 family.

Dalton Trans 2013 Jan;42(4):1057-64

Institute of Solid State Chemistry, Ural Branch of the Russian Academy of Sciences, 91 Pervomayskaya str., Ekaterinburg GSP-145, 620990, Russia.

The crystal structure of K(2)CaV(2)O(7) prepared by a conventional solid-state reaction has been solved by a direct method and refined using Rietveld full profile fitting based on X-ray powder diffraction data. This compound crystallises in the triclinic space group (P1, Z = 2) with unit cell constants a = 7.1577(1) Å, b = 10.5104(2) Å, c = 5.8187(1) Å, α = 106.3368(9)°, β = 106.235(1)°, γ = 71.1375(9)°. The structure can be described as infinite undulating CaV(2)O(7)(2-) layers parallel to the ac plane, which consist of pairs of edge-sharing CaO(6) octahedra connected to each other through V(2)O(7) pyrogroups. The potassium atoms are positioned in two sites between the layers, with a distorted IX-fold coordination of oxygen atoms. The chemical composition obtained from the structural solution was confirmed by energy-dispersive X-ray analysis. The stability of compounds in the family of alkali metal calcium pyrovanadates is discussed based on an analysis of the correlation between anion and cation sizes and theoretical first-principles calculations.
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http://dx.doi.org/10.1039/c2dt31246hDOI Listing
January 2013

RaPID: an aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes.

Methods Mol Biol 2011 ;714:387-406

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

RNA metabolism involves regulatory processes, such as transcription, splicing, nuclear export, transport and localization, association with sites of RNA modification, silencing and decay, and necessitates a wide variety of diverse RNA-interacting proteins. These interactions can be direct via RNA-binding proteins (RBPs) or indirect via other proteins and RNAs that form ribonucleoprotein complexes that together control RNA fate. While pull-down methods for the isolation of known RBPs are commonly used, strategies have also been described for the direct isolation of messenger RNAs (mRNAs) and their associated factors. The latter techniques allow for the identification of interacting proteins and RNAs, but most suffer from problems of low sensitivity and high background. Here we describe a simple and highly effective method for RNA purification and identification (RaPID) that allows for the isolation of specific mRNAs of interest from yeast and mammalian cells, and subsequent analysis of the associated proteins and RNAs using mass spectrometry and reverse transcription-PCR, respectively. This method employs the MS2 coat RBP fused to both GFP and streptavidin-binding protein to precipitate MS2 aptamer-tagged RNAs using immobilized streptavidin.
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http://dx.doi.org/10.1007/978-1-61779-005-8_24DOI Listing
July 2011

A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes.

RNA 2010 Nov 28;16(11):2277-90. Epub 2010 Sep 28.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.

Intracellular mRNA targeting and localized translation are potential determinants for protein localization. To facilitate targeting, mRNAs possess specific cis-acting sequence motifs that are recognized by trans-acting RNA-binding proteins (RBPs). While many mRNAs are trafficked, our knowledge of the RBPs involved and presence of additional transcripts within these ribonucleoprotein (RNP) complexes is limited. To facilitate the identification of RBPs and transcripts that bind to specific mRNAs, we developed RNA-binding protein purification and identification (RaPID), a novel technique that allows for the affinity purification of MS2 aptamer-tagged mRNAs and subsequent detection of bound RBPs and transcripts using mass-spectometry and RT-PCR, respectively. RaPID effectively isolated specific mRNAs from both yeast and mammalian cells, and identified known mRNA-RBP interactions (e.g., ASH1-She2; β-Actin-IMP1). By isolating tagged OXA1 mRNA using RaPID, we could identify a yeast COPI subunit (i.e., Sec27) as a candidate interacting protein. This finding was strengthened by the observation that a portion of OXA1 mRNA was delocalized in a sec27-1 temperature-sensitive mutant at restrictive temperatures. Finally, RaPID could also be used to show biochemically the coexistence of different RNA species within the same RNP complex (e.g., coprecipitation of the yeast SRO7, WSC2, SEC3, and IST2 mRNAs with ASH1 mRNA) for the first time.
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http://dx.doi.org/10.1261/rna.2091710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957065PMC
November 2010

Role of PP2Calpha in cell growth, in radio- and chemosensitivity, and in tumorigenicity.

Mol Cancer 2007 Oct 17;6:65. Epub 2007 Oct 17.

Department of Innovative Cancer Diagnosis and Therapy, Clinical Cooperation Unit Radiotherapeutic Oncology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.

Background: PP2Calpha is the representative member of the type 2C family of protein phosphatases, and it has recently been implicated in the regulation of p53-, TGFbeta-, cyclin-dependent kinase- and apoptosis-signaling. To investigate the role of PP2Calpha in cell growth and in radio- and chemosensitivity, wild type and PP2Calpha siRNA-expressing MCF7 cells were subjected to several different viability and cell cycle analyses, both under basal conditions and upon treatment with radio- and chemotherapy. By comparing the growth of tumors established from both types of cells, we also evaluated the involvement of PP2Calpha in tumorigenesis.

Results: It was found that knockdown of PP2Calpha did not affect the proliferation, the clonogenic survival and the membrane integrity of MCF7 cells. In addition, it did not alter their radio- and chemosensitivity. For PP2Calpha siRNA-expressing MCF7 cells, the number of cells in the G0/G1 phase of the cell cycle was reduced, the induction of the G1 block was attenuated, the number of cells in G2/M was increased, and the induction of the G2 block was enhanced. The tumorigenic potential of PP2Calpha siRNA-expressing MCF7 cells was found to be higher than that of wild type MCF7 cells, and the in vivo proliferation of these cells was found to be increased.

Conclusion: Based on these findings, we conclude that PP2Calpha is not involved in controlling cell growth and radio- and chemosensitivity in vitro. It does, however, play a role in the regulation of the cell cycle, in the induction of cell cycle checkpoints and in tumorigenesis. The latter notion implies that PP2Calpha may possess tumor-suppressing properties, and it thereby sets the stage for more elaborate analyses on its involvement in the development and progression of cancer.
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http://dx.doi.org/10.1186/1476-4598-6-65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2100065PMC
October 2007