Publications

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Aging Dis (Aging Dis)

• Mitkevich VA, Barykin EP, Eremina S, Pani B, Katkova-Zhukotskaya O, Polshakov VI, Adzhubei AA, Kozin SA, Mironov AS, Makarov AA, Nudler E Zn-dependent beta-amyloid Aggregation and its Reversal by the Tetrapeptide HAEE. Aging Dis. 01 Apr 2023. 14(2):309-318
• Lazarev VF, Tsolaki M, Mikhaylova ER, Benken KA, Shevtsov MA, Nikotina AD, Lechpammer M, Mitkevich VA, Makarov AA, Moskalev AA, Kozin SA, Margulis BA, Guzhova IV, Nudler E Extracellular GAPDH Promotes Alzheimer Disease Progression by Enhancing Amyloid-beta Aggregation and Cytotoxicity. Aging Dis. 01 Aug 2021. 12(5):1223-1237

Annu Rev Biochem (Annu Rev Biochem)

• Nudler E RNA polymerase active center: the molecular engine of transcription. Annu Rev Biochem. 01 Jan 2009. 78:335-61

Biochem Biophys Res Commun (Biochem Biophys Res Commun)

• Lazarev VF, Nikotina AD, Mikhaylova ER, Nudler E, Polonik SG, Guzhova IV, Margulis BA Hsp70 chaperone rescues C6 rat glioblastoma cells from oxidative stress by sequestration of aggregating GAPDH. Biochem Biophys Res Commun. 12 Feb 2016. 470(3):766-771

Biochim Biophys Acta (Biochim Biophys Acta)

• Proshkin S, Mironov A, Nudler E Riboswitches in regulation of Rho-dependent transcription termination. Biochim Biophys Acta. 01 Oct 2014. 1839(10):974-977
• Svetlov V, Nudler E Basic mechanism of transcription by RNA polymerase II. Biochim Biophys Acta. 01 Jan 2013. 1829(1):20-8
• Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. Biochim Biophys Acta. 01 Feb 2013. 1829(2):187-98

Biochim Biophys Acta Gen Subj (Biochim Biophys Acta Gen Subj)

• Chung MC, Alem F, Hamer SG, Narayanan A, Shatalin K, Bailey C, Nudler E, Hakami RM S-nitrosylation of peroxiredoxin 1 contributes to viability of lung epithelial cells during Bacillus anthracis infection. Biochim Biophys Acta Gen Subj. 01 Jan 2017. 1861(1 Pt A):3019-3029

Bioconjug Chem (Bioconjug Chem)

• Kozlov M, Nudler E, Nikiforov V, Mustaev A Reactive rifampicin derivative able to damage transcription complex. Bioconjug Chem. 20 Mar 2013. 24(3):443-7

Bioessays (Bioessays)

• Gusarov I, Nudler E Glycogen at the Crossroad of Stress Resistance, Energy Maintenance, and Pathophysiology of Aging. Bioessays. 01 Sep 2018. 40(9):e1800033

Biophys J (Biophys J)

• Bezanilla M, Drake B, Nudler E, Kashlev M, Hansma PK, Hansma HG Motion and enzymatic degradation of DNA in the atomic force microscope. Biophys J. 01 Dec 1994. 67(6):2454-9
• O Maoileidigh D, Tadigotla VR, Nudler E, Ruckenstein AE A unified model of transcription elongation: what have we learned from single-molecule experiments? Biophys J. 02 Mar 2011. 100(5):1157-66

Brain Behav (Brain Behav)

• Rabow Z, Morningstar T, Showalter M, Heil H, Thongphanh K, Fan S, Chan J, Martinez-Cerdeno V, Berman R, Zagzag D, Nudler E, Fiehn O, Lechpammer M Exposure to DMSO during infancy alters neurochemistry, social interactions, and brain morphology in long-evans rats. Brain Behav. 01 May 2021. 11(5):e02146

Brain Pathol (Brain Pathol)

• Lechpammer M, Tran YP, Wintermark P, Martinez-Cerdeno V, Krishnan VV, Ahmed W, Berman RF, Jensen FE, Nudler E, Zagzag D Upregulation of cystathionine beta-synthase and p70S6K/S6 in neonatal hypoxic ischemic brain injury. Brain Pathol. 01 Jul 2017. 27(4):449-458

Cell (Cell)

• Serganov A, Nudler E A decade of riboswitches. Cell. 17 Jan 2013. 152(1-2):17-24
• Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell. 27 Nov 2002. 111(5):747-56
• Sedlyarova N, Shamovsky I, Bharati BK, Epshtein V, Chen J, Gottesman S, Schroeder R, Nudler E sRNA-Mediated Control of Transcription Termination in E. coli. Cell. 22 Sep 2016. 167(1):111-121.e13
• Gusarov I, Gautier L, Smolentseva O, Shamovsky I, Eremina S, Mironov A, Nudler E Bacterial nitric oxide extends the lifespan of C. elegans. Cell. 14 Feb 2013. 152(4):818-30
• Nudler E Flipping riboswitches. Cell. 14 Jul 2006. 126(1):19-22
• Kashlev M, Nudler E, Goldfarb A, White T, Kutter E Bacteriophage T4 Alc protein: a transcription termination factor sensing local modification of DNA. Cell. 08 Oct 1993. 75(1):147-54
• Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Cell. 10 May 2023. epub ahead of print
• Dutta D, Shatalin K, Epshtein V, Gottesman ME, Nudler E Linking RNA polymerase backtracking to genome instability in E. coli. Cell. 19 Aug 2011. 146(4):533-43
• Nudler E, Kashlev M, Nikiforov V, Goldfarb A Coupling between transcription termination and RNA polymerase inchworming. Cell. 05 May 1995. 81(3):351-7
• Bar-Nahum G, Epshtein V, Ruckenstein AE, Rafikov R, Mustaev A, Nudler E A ratchet mechanism of transcription elongation and its control. Cell. 28 Jan 2005. 120(2):183-93
• Nudler E, Mustaev A, Lukhtanov E, Goldfarb A The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell. 04 Apr 1997. 89(1):33-41
• Nudler E RNA polymerase backtracking in gene regulation and genome instability. Cell. 22 Jun 2012. 149(7):1438-45
• Svetlov V, Nudler E Unfolding the bridge between transcription and translation. Cell. 20 Jul 2012. 150(2):243-5
• Bar-Nahum G, Nudler E Isolation and characterization of sigma(70)-retaining transcription elongation complexes from Escherichia coli. Cell. 24 Aug 2001. 106(4):443-51
• Gusarov I, Nudler E Control of intrinsic transcription termination by N and NusA: the basic mechanisms. Cell. 16 Nov 2001. 107(4):437-49

Cell Microbiol (Cell Microbiol)

• Shen X, Banga S, Liu Y, Xu L, Gao P, Shamovsky I, Nudler E, Luo ZQ Targeting eEF1A by a Legionella pneumophila effector leads to inhibition of protein synthesis and induction of host stress response. Cell Microbiol. 01 Jun 2009. 11(6):911-26

Cell Mol Life Sci (Cell Mol Life Sci)

• Shamovsky I, Nudler E New insights into the mechanism of heat shock response activation. Cell Mol Life Sci. 01 Mar 2008. 65(6):855-61

Cell Stem Cell (Cell Stem Cell)

• Muto T, Guillamot M, Yeung J, Fang J, Bennett J, Nadorp B, Lasry A, Redondo LZ, Choi K, Gong Y, Walker CS, Hueneman K, Bolanos LC, Barreyro L, Lee LH, Greis KD, Vasyliev N, Khodadadi-Jamayran A, Nudler E, Lujambio A, Lowe SW, Aifantis I, Starczynowski DT TRAF6 functions as a tumor suppressor in myeloid malignancies by directly targeting MYC oncogenic activity. Cell Stem Cell. 03 Feb 2022. 29(2):298-314.e9

Cell Stress Chaperones (Cell Stress Chaperones)

• Bobkova N, Guzhova I, Margulis B, Nesterova I, Medvinskaya N, Samokhin A, Alexandrova I, Garbuz D, Nudler E, Evgen'ev M Dynamics of endogenous Hsp70 synthesis in the brain of olfactory bulbectomized mice. Cell Stress Chaperones. 01 Jan 2013. 18(1):109-18

Circulation (Circulation)

• Rafikova O, Sokolova E, Rafikov R, Nudler E Control of plasma nitric oxide bioactivity by perfluorocarbons: physiological mechanisms and clinical implications. Circulation. 07 Dec 2004. 110(23):3573-80

Cold Spring Harb Symp Quant Biol (Cold Spring Harb Symp Quant Biol)

• Korzheva N, Mustaev A, Nudler E, Nikiforov V, Goldfarb A Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harb Symp Quant Biol. 01 Jan 1998. 63:337-45

Commun Biol (Commun Biol)

• Nadon JF, Epshtein V, Cameron E, Samatov MR, Vasenko AS, Nudler E, Lafontaine DA Site-specific photolabile roadblocks for the study of transcription elongation in biologically complex systems. Commun Biol. 12 May 2022. 5(1):457
• Ruff SE, Vasilyev N, Nudler E, Logan SK, Garabedian MJ PIM1 phosphorylation of the androgen receptor and 14-3-3 zeta regulates gene transcription in prostate cancer. Commun Biol. 25 Oct 2021. 4(1):1221

Curr Opin Microbiol (Curr Opin Microbiol)

• Luhachack L, Nudler E Bacterial gasotransmitters: an innate defense against antibiotics. Curr Opin Microbiol. 01 Oct 2014. 21:13-7
• McGary K, Nudler E RNA polymerase and the ribosome: the close relationship. Curr Opin Microbiol. 01 Apr 2013. 16(2):112-7
• Kamarthapu V, Nudler E Rethinking transcription coupled DNA repair. Curr Opin Microbiol. 01 Apr 2015. 24:15-20
• Borukhov S, Nudler E RNA polymerase holoenzyme: structure, function and biological implications. Curr Opin Microbiol. 01 Apr 2003. 6(2):93-100

Curr Opin Struct Biol (Curr Opin Struct Biol)

• Svetlov V, Nudler E Macromolecular micromovements: how RNA polymerase translocates. Curr Opin Struct Biol. 01 Dec 2009. 19(6):701-7

DNA Repair (Amst) (DNA Repair (Amst))

• Pani B, Nudler E Mechanistic insights into transcription coupled DNA repair. DNA Repair (Amst). 01 Aug 2017. 56:42-50

EMBO J (EMBO J)

• Svetlov V, Nudler E Clamping the clamp of RNA polymerase. EMBO J. 06 Apr 2011. 30(7):1190-1
• Svetlov V, Nudler E Towards the unified principles of transcription termination. EMBO J. 03 Feb 2020. 39(3):e104112
• Epshtein V, Toulme F, Rahmouni AR, Borukhov S, Nudler E Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J. 15 Sep 2003. 22(18):4719-27

Elife (Elife)

• Demo G, Rasouly A, Vasilyev N, Svetlov V, Loveland AB, Diaz-Avalos R, Grigorieff N, Nudler E, Korostelev AA Structure of RNA polymerase bound to ribosomal 30S subunit. Elife. 13 Oct 2017. 6:epub ahead of print
• Vera M, Pani B, Griffiths LA, Muchardt C, Abbott CM, Singer RH, Nudler E The translation elongation factor eEF1A1 couples transcription to translation during heat shock response. Elife. 16 Sep 2014. 3:e03164

Environ Microbiol (Environ Microbiol)

• Shenhar Y, Rasouly A, Biran D, Ron EZ Adaptation of Escherichi coli to elevated temperatures involves a change in stability of heat shock gene transcripts. Environ Microbiol. 01 Dec 2009. 11(12):2989-97
• Oberpichler I, Rosen R, Rasouly A, Vugman M, Ron EZ, Lamparter T Light affects motility and infectivity of Agrobacterium tumefaciens. Environ Microbiol. 01 Aug 2008. 10(8):2020-9

Exp Neurol (Exp Neurol)

• Ekimova IV, Plaksina DV, Pastukhov YF, Lapshina KV, Lazarev VF, Mikhaylova ER, Polonik SG, Pani B, Margulis BA, Guzhova IV, Nudler E New HSF1 inducer as a therapeutic agent in a rodent model of Parkinson's disease. Exp Neurol. 01 Aug 2018. 306:199-208

Front Microbiol (Front Microbiol)

• Patlan-Vazquez AG, Ayala-Garcia VM, Vallin C, Cortes J, Vasquez-Morales SG, Robleto EA, Nudler E, Pedraza-Reyes M Dynamics of Mismatch and Alternative Excision-Dependent Repair in Replicating Bacillus subtilis DNA Examined Under Conditions of Neutral Selection. Front Microbiol. 01 Jan 2022. 13:866089

Genes Cells (Genes Cells)

• Nudler E, Gottesman ME Transcription termination and anti-termination in E. coli. Genes Cells. 01 Aug 2002. 7(8):755-68

Genes Dev (Genes Dev)

• Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev. 15 Nov 2007. 21(22):2874-9

In Silico Biol (In Silico Biol)

• Bergig O, Barash D, Nudler E, Kedem K STR2: a structure to string approach for locating G-box riboswitch shapes in pre-selected genes. In Silico Biol. 01 Jan 2004. 4(4):593-604

Infect Immun (Infect Immun)

• Toliver-Kinsky T, Cui W, Toro G, Lee SJ, Shatalin K, Nudler E, Szabo C H2S: a Bacterial Defense Mechanism Against the Host Immune Response. Infect Immun. 15 Oct 2018. epub ahead of print

J Alzheimers Dis (J Alzheimers Dis)

• Bobkova NV, Garbuz DG, Nesterova I, Medvinskaya N, Samokhin A, Alexandrova I, Yashin V, Karpov V, Kukharsky MS, Ninkina NN, Smirnov AA, Nudler E, Evgen'ev M Therapeutic effect of exogenous hsp70 in mouse models of Alzheimer's disease. J Alzheimers Dis. 01 Jan 2014. 38(2):425-35

J Am Soc Mass Spectrom (J Am Soc Mass Spectrom)

• Abolhasani Khaje N, Mobley CK, Misra SK, Miller L, Li Z, Nudler E, Sharp JS Variation in FPOP Measurements Is Primarily Caused by Poor Peptide Signal Intensity. J Am Soc Mass Spectrom. 01 Sep 2018. 29(9):1901-1907

J Bacteriol (J Bacteriol)

• Rasouly A, Schonbrun M, Shenhar Y, Ron EZ YbeY, a heat shock protein involved in translation in Escherichia coli. J Bacteriol. 01 Apr 2009. 191(8):2649-55
• Rasouly A, Davidovich C, Ron EZ The heat shock protein YbeY is required for optimal activity of the 30S ribosomal subunit. J Bacteriol. 01 Sep 2010. 192(18):4592-6
• Rasouly A, Shenhar Y, Ron EZ Thermoregulation of Escherichia coli hchA transcript stability. J Bacteriol. 01 Aug 2007. 189(15):5779-81

J Biol Chem (J Biol Chem)

• Gusarov I, Starodubtseva M, Wang ZQ, McQuade L, Lippard SJ, Stuehr DJ, Nudler E Bacterial nitric-oxide synthases operate without a dedicated redox partner. J Biol Chem. 09 May 2008. 283(19):13140-7
• Artsimovitch I, Svetlov V, Nemetski SM, Epshtein V, Cardozo T, Nudler E Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop. J Biol Chem. 18 Nov 2011. 286(46):40395-400
• van Sorge NM, Beasley FC, Gusarov I, Gonzalez DJ, von Kockritz-Blickwede M, Anik S, Borkowski AW, Dorrestein PC, Nudler E, Nizet V Methicillin-resistant Staphylococcus aureus bacterial nitric-oxide synthase affects antibiotic sensitivity and skin abscess development. J Biol Chem. 01 Mar 2013. 288(9):6417-26

J Mol Biol (J Mol Biol)

• Nudler E Transcription elongation: structural basis and mechanisms. J Mol Biol. 23 Apr 1999. 288(1):1-12

Methods Enzymol (Methods Enzymol)

• Nudler E, Gusarov I, Bar-Nahum G Methods of walking with the RNA polymerase. Methods Enzymol. 01 Jan 2003. 371:160-9
• Nudler E, Gusarov I Analysis of the intrinsic transcription termination mechanism and its control. Methods Enzymol. 01 Jan 2003. 371:369-82
• Nudler E, Avetissova E, Korzheva N, Mustaev A Characterization of protein-nucleic acid interactions that are required for transcription processivity. Methods Enzymol. 01 Jan 2003. 371:179-90
• Epshtein V, Kamarthapu V, Nudler E Strategies and Methods of Transcription-Coupled Repair Studies In Vitro and In Vivo. Methods Enzymol. 01 Jan 2017. 591:287-306
• Kashlev M, Nudler E, Severinov K, Borukhov S, Komissarova N, Goldfarb A Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase. Methods Enzymol. 01 Jan 1996. 274:326-34

Methods Mol Biol (Methods Mol Biol)

• Mironov A, Epshtein V, Nudler E Transcriptional approaches to riboswitch studies. Methods Mol Biol. 01 Jan 2009. 540:39-51
• Shamovsky I, Nudler E Isolation and characterization of the heat shock RNA 1. Methods Mol Biol. 01 Jan 2009. 540:265-79

Mob DNA (Mob DNA)

• Briggs EM, Mita P, Sun X, Ha S, Vasilyev N, Leopold ZR, Nudler E, Boeke JD, Logan SK Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9. Mob DNA. 23 Aug 2021. 12(1):21

Mol Biosyst (Mol Biosyst)

• Kulikova AA, Tsvetkov PO, Indeykina MI, Popov IA, Zhokhov SS, Golovin AV, Polshakov VI, Kozin SA, Nudler E, Makarov AA Phosphorylation of Ser8 promotes zinc-induced dimerization of the amyloid-beta metal-binding domain. Mol Biosyst. 01 Oct 2014. 10(10):2590-6

Mol Cell (Mol Cell)

• Shamovsky I, Nudler E Modular RNA heats up. Mol Cell. 29 Feb 2008. 29(4):415-7
• Gusarov I, Nudler E Protein S-Nitrosylation: Enzymatically Controlled, but Intrinsically Unstable, Post-translational Modification. Mol Cell. 01 Feb 2018. 69(3):351-353
• Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E Pre-termination Transcription Complex: Structure and Function. Mol Cell. 01 Dec 2020. epub ahead of print
• Sedlyarova N, Rescheneder P, Magan A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. Mol Cell. 06 Jul 2017. 67(1):30-43.e6
• Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E An allosteric path to transcription termination. Mol Cell. 28 Dec 2007. 28(6):991-1001
• Rasouly A, Nudler E RNA polymerase and ppGpp deliver a one-two punch to antibiotics. Mol Cell. 20 Apr 2023. 83(8):1204-1205
• Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Mol Cell. 17 Aug 2023. 83(16):2872-2883.e7
• Sekine S, Murayama Y, Svetlov V, Nudler E, Yokoyama S The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions. Mol Cell. 05 Feb 2015. 57(3):408-21
• Gusarov I, Nudler E The mechanism of intrinsic transcription termination. Mol Cell. 01 Apr 1999. 3(4):495-504
• Kandel ES, Nudler E Template switching by RNA polymerase II in vivo. Evidence and implications from a retroviral system. Mol Cell. 01 Dec 2002. 10(6):1495-502
• Valencia-Sanchez MI, De Ioannes P, Wang M, Vasilyev N, Chen R, Nudler E, Armache JP, Armache KJ Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination. Mol Cell. 08 Apr 2019. epub ahead of print
• Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E Persistence of backtracking by human RNA polymerase II. Mol Cell. 06 Feb 2024. epub ahead of print

Mol Microbiol (Mol Microbiol)

• Svetlov V, Nudler E Reading of the non-template DNA by transcription elongation factors. Mol Microbiol. 01 Aug 2018. 109(4):417-421

Nat Commun (Nat Commun)

• Gusarov I, Shamovsky I, Pani B, Gautier L, Eremina S, Katkova-Zhukotskaya O, Mironov A, Makarov Acapital A, Cyrillic, Nudler E Dietary thiols accelerate aging of C. elegans. Nat Commun. 15 Jul 2021. 12(1):4336
• Martinez B, Bharati BK, Epshtein V, Nudler E Pervasive Transcription-coupled DNA repair in E. coli. Nat Commun. 30 Mar 2022. 13(1):1702
• Gusarov I, Pani B, Gautier L, Smolentseva O, Eremina S, Shamovsky I, Katkova-Zhukotskaya O, Mironov A, Nudler E Glycogen controls Caenorhabditis elegans lifespan and resistance to oxidative stress. Nat Commun. 19 Jun 2017. 8:15868
• Schneider JA, Craven TW, Kasper AC, Yun C, Haugbro M, Briggs EM, Svetlov V, Nudler E, Knaut H, Bonneau R, Garabedian MJ, Kirshenbaum K, Logan SK Design of Peptoid-peptide Macrocycles to Inhibit the beta-catenin TCF Interaction in Prostate Cancer. Nat Commun. 23 Oct 2018. 9(1):4396
• Luhachack L, Rasouly A, Shamovsky I, Nudler E Transcription factor YcjW controls the emergency H2S production in E. coli. Nat Commun. 28 Jun 2019. 10(1):2868
• Grau D, Zhang Y, Lee CH, Valencia-Sanchez M, Zhang J, Wang M, Holder M, Svetlov V, Tan D, Nudler E, Reinberg D, Walz T, Armache KJ Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction. Nat Commun. 29 Jan 2021. 12(1):714

Nat Microbiol (Nat Microbiol)

• Rasouly A, Shamovsky Y, Epshtein V, Tam K, Vasilyev N, Hao Z, Quarta G, Pani B, Li L, Vallin C, Shamovsky I, Krishnamurthy S, Shtilerman A, Vantine S, Torres VJ, Nudler E Analysing the fitness cost of antibiotic resistance to identify targets for combination antimicrobials. Nat Microbiol. 25 Oct 2021. epub ahead of print

Nat Struct Mol Biol (Nat Struct Mol Biol)

• Valencia-Sanchez MI, Abini-Agbomson S, Wang M, Lee R, Vasilyev N, Zhang J, De Ioannes P, La Scola B, Talbert P, Henikoff S, Nudler E, Erives A, Armache KJ The structure of a virus-encoded nucleosome. Nat Struct Mol Biol. 01 May 2021. 28(5):413-417
• Cai SW, Zinder JC, Svetlov V, Bush MW, Nudler E, Walz T, de Lange T Cryo-EM structure of the human CST-Polalpha/primase complex in a recruitment state. Nat Struct Mol Biol. 16 May 2022. epub ahead of print
• Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Nat Struct Mol Biol. 01 Jul 2018. 25(7):616-622
• Wade JT, Castro Roa D, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol. 01 Sep 2006. 13(9):806-14
• Helmrich A, Ballarino M, Nudler E, Tora L Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol. 01 Apr 2013. 20(4):412-8
• Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, Afanaseva E, Mironov A, Serganov A, Nudler E Control of transcription elongation and DNA repair by alarmone ppGpp. Nat Struct Mol Biol. 01 May 2023. 30(5):600-607
• Vasilyev N, Liu MMJ, Epshtein V, Shamovsky I, Nudler E General transcription factor from Escherichia coli with a distinct mechanism of action. Nat Struct Mol Biol. 04 Jan 2024. epub ahead of print
• Svetlov V, Nudler E Jamming the ratchet of transcription. Nat Struct Mol Biol. 01 Aug 2008. 15(8):777-9
• Svetlov V, Nudler E Looking for a promoter in 3D. Nat Struct Mol Biol. 01 Feb 2013. 20(2):141-2

Nature (Nature)

• Bharati BK, Gowder M, Zheng F, Alzoubi K, Svetlov V, Kamarthapu V, Weaver JW, Epshtein V, Vasilyev N, Shen L, Zhang Y, Nudler E Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Nature. 30 Mar 2022. epub ahead of print
• Epshtein V, Kamarthapu V, McGary K, Svetlov V, Ueberheide B, Proshkin S, Mironov A, Nudler E UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature. 16 Jan 2014. 505(7483):372-7
• Belogurov GA, Vassylyeva MN, Sevostyanova A, Appleman JR, Xiang AX, Lira R, Webber SE, Klyuyev S, Nudler E, Artsimovitch I, Vassylyev DG Transcription inactivation through local refolding of the RNA polymerase structure. Nature. 15 Jan 2009. 457(7227):332-5
• Epshtein V, Dutta D, Wade J, Nudler E An allosteric mechanism of Rho-dependent transcription termination. Nature. 14 Jan 2010. 463(7278):245-9
• Jee J, Rasouly A, Shamovsky I, Akivis Y, Steinman SR, Mishra B, Nudler E Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing. Nature. 30 Jun 2016. 534(7609):693-6
• Shamovsky I, Ivannikov M, Kandel ES, Gershon D, Nudler E RNA-mediated response to heat shock in mammalian cells. Nature. 23 Mar 2006. 440(7083):556-60
• Yang KB, Cameranesi M, Gowder M, Martinez C, Shamovsky Y, Epshtein V, Hao Z, Nguyen T, Nirenstein E, Shamovsky I, Rasouly A, Nudler E High-resolution landscape of an antibiotic binding site. Nature. 30 Aug 2023. epub ahead of print

Nucleic Acids Res (Nucleic Acids Res)

• Magan A, Amman F, El-Isa F, Hartl N, Shamovsky I, Nudler E, Schroeder R, Sedlyarova N iRAPs curb antisense transcription in E. coli. Nucleic Acids Res. 18 Nov 2019. 47(20):10894-10905

PLoS One (PLoS One)

• Garbuz DG, Astakhova LN, Zatsepina OG, Arkhipova IR, Nudler E, Evgen'ev MB Functional organization of hsp70 cluster in camel (Camelus dromedarius) and other mammals. PLoS One. 01 Jan 2011. 6(11):e27205

Plant Mol Biol (Plant Mol Biol)

• Vitlin A, Weiss C, Demishtein-Zohary K, Rasouly A, Levin D, Pisanty-Farchi O, Breiman A, Azem A Chloroplast beta chaperonins from A. thaliana function with endogenous cpn10 homologs in vitro. Plant Mol Biol. 01 Sep 2011. 77(1-2):105-15

Proc Natl Acad Sci U S A (Proc Natl Acad Sci U S A)

• Mejia YX, Nudler E, Bustamante C Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase. Proc Natl Acad Sci U S A. 20 Jan 2015. 112(3):743-8
• Rasouly A, Nudler E Antibiotic killing through oxidized nucleotides. Proc Natl Acad Sci U S A. 27 Feb 2018. 115(9):1967-1969
• Mironov A, Seregina T, Nagornykh M, Luhachack LG, Korolkova N, Lopes LE, Kotova V, Zavilgelsky G, Shakulov R, Shatalin K, Nudler E Mechanism of H2S-mediated protection against oxidative stress in Escherichia coli. Proc Natl Acad Sci U S A. 06 Jun 2017. 114(23):6022-6027
• Bobkova NV, Evgen'ev M, Garbuz DG, Kulikov AM, Morozov A, Samokhin A, Velmeshev D, Medvinskaya N, Nesterova I, Pollock A, Nudler E Exogenous Hsp70 delays senescence and improves cognitive function in aging mice. Proc Natl Acad Sci U S A. 29 Dec 2015. 112(52):16006-11
• Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, Nudler E, Groisman EA Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci U S A. 03 Apr 2012. 109(14):5376-81
• Shatalin K, Gusarov I, Avetissova E, Shatalina Y, McQuade LE, Lippard SJ, Nudler E Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages. Proc Natl Acad Sci U S A. 22 Jan 2008. 105(3):1009-13
• Hausladen A, Rafikov R, Angelo M, Singel DJ, Nudler E, Stamler JS Assessment of nitric oxide signals by triiodide chemiluminescence. Proc Natl Acad Sci U S A. 13 Feb 2007. 104(7):2157-62
• Mirkin EV, Castro Roa D, Nudler E, Mirkin SM Transcription regulatory elements are punctuation marks for DNA replication. Proc Natl Acad Sci U S A. 09 May 2006. 103(19):7276-81
• Tadigotla VR, O Maoileidigh D, Sengupta AM, Epshtein V, Ebright RH, Nudler E, Ruckenstein AE Thermodynamic and kinetic modeling of transcriptional pausing. Proc Natl Acad Sci U S A. 21 Mar 2006. 103(12):4439-44
• Gusarov I, Nudler E NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria. Proc Natl Acad Sci U S A. 27 Sep 2005. 102(39):13855-60
• Epshtein V, Mironov AS, Nudler E The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci U S A. 29 Apr 2003. 100(9):5052-6
• Rafikova O, Rafikov R, Nudler E Catalysis of S-nitrosothiols formation by serum albumin: the mechanism and implication in vascular control. Proc Natl Acad Sci U S A. 30 Apr 2002. 99(9):5913-8
• Nedospasov A, Rafikov R, Beda N, Nudler E An autocatalytic mechanism of protein nitrosylation. Proc Natl Acad Sci U S A. 05 Dec 2000. 97(25):13543-8
• Gragerov A, Nudler E, Komissarova N, Gaitanaris GA, Gottesman ME, Nikiforov V Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli. Proc Natl Acad Sci U S A. 01 Nov 1992. 89(21):10341-4
• Rasouly A, Nudler E Reactive oxygen species as the long arm of bactericidal antibiotics. Proc Natl Acad Sci U S A. 14 May 2019. 116(20):9696-9698
• Hou L, Wang Y, Liu Y, Zhang N, Shamovsky I, Nudler E, Tian B, Dynlacht BD Paf1C regulates RNA polymerase II progression by modulating elongation rate. Proc Natl Acad Sci U S A. 27 Jun 2019. epub ahead of print
• Alexander Mironov, Tatyana Seregina, Konstantin Shatalin, Maxim Nagornykh, Rustem Shakulov, Evgeny Nudler CydDC functions as a cytoplasmic cystine reductase to sensitize Escherichia coli to oxidative stress and aminoglycosides Proc Natl Acad Sci U S A. 08 Sep 2020. epub
• Zinder JC, Olinares PDB, Svetlov V, Bush MW, Nudler E, Chait BT, Walz T, de Lange T Shelterin is a dimeric complex with extensive structural heterogeneity. Proc Natl Acad Sci U S A. 02 Aug 2022. 119(31):e2201662119
• Rasouly A, Nudler E The very hungry bactericidal antibiotics. Proc Natl Acad Sci U S A. 12 Jul 2022. 119(28):e2208035119

Res Microbiol (Res Microbiol)

• Katz C, Rasouly A, Gur E, Shenhar Y, Biran D, Ron EZ Temperature-dependent proteolysis as a control element in Escherichia coli metabolism. Res Microbiol. 01 Nov 2009. 160(9):684-6
• Rasouly A, Ron EZ Interplay between the heat shock response and translation in Escherichia coli. Res Microbiol. 01 May 2009. 160(4):288-96
• Ionescu M, Elgrably-Weiss M, Elad T, Rasouly A, Yagur-Kroll S, Belkin S Negative regulation of sigma(70)-driven promoters by sigma(70). Res Microbiol. 01 Jun 2011. 162(5):461-9

Sci Adv (Sci Adv)

• Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1. Sci Adv. 09 Aug 2023. 9(32):eadg9832
• Escobar TM, Yu JR, Liu S, Lucero K, Vasilyev N, Nudler E, Reinberg D Inheritance of repressed chromatin domains during S phase requires the histone chaperone NPM1. Sci Adv. 29 Apr 2022. 8(17):eabm3945

Sci Rep (Sci Rep)

• Smolentseva O, Gusarov I, Gautier L, Shamovsky I, DeFrancesco AS, Losick R, Nudler E Mechanism of biofilm-mediated stress resistance and lifespan extension in C. elegans. Sci Rep. 02 Aug 2017. 7(1):7137

Sci STKE (Sci STKE)

• Shamovsky I, Nudler E Gene control by large noncoding RNAs. Sci STKE. 03 Oct 2006. 2006(355):pe40

Sci Signal (Sci Signal)

• Gusarov I, Nudler E S-nitrosylation signaling in Escherichia coli. Sci Signal. 12 Jun 2012. 5(228):pe26

Science (Science)

• Kamarthapu V, Epshtein V, Benjamin B, Proshkin S, Mironov A, Cashel M, Nudler E ppGpp couples transcription to DNA repair in E. coli. Science. 20 May 2016. 352(6288):993-6
• Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science. 24 Apr 2020. 368(6489):epub ahead of print
• Shatalin K, Nuthanakanti A, Kaushik A, Shishov D, Peselis A, Shamovsky I, Pani B, Lechpammer M, Vasilyev N, Shatalina E, Rebatchouk D, Mironov A, Fedichev P, Serganov A, Nudler E Inhibitors of bacterial H2S biogenesis targeting antibiotic resistance and tolerance. Science. 11 Jun 2021. 372(6547):1169-1175
• Nudler E, Goldfarb A, Kashlev M Discontinuous mechanism of transcription elongation. Science. 05 Aug 1994. 265(5173):793-6
• Nudler E, Avetissova E, Markovtsov V, Goldfarb A Transcription processivity: protein-DNA interactions holding together the elongation complex. Science. 12 Jul 1996. 273(5272):211-7
• Nudler E, Gusarov I, Avetissova E, Kozlov M, Goldfarb A Spatial organization of transcription elongation complex in Escherichia coli. Science. 17 Jul 1998. 281(5375):424-8
• Epshtein V, Nudler E Cooperation between RNA polymerase molecules in transcription elongation. Science. 02 May 2003. 300(5620):801-5
• Cardinale CJ, Washburn RS, Tadigotla VR, Brown LM, Gottesman ME, Nudler E Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science. 16 May 2008. 320(5878):935-8
• Shatalin K, Shatalina E, Mironov A, Nudler E H2S: a universal defense against antibiotics in bacteria. Science. 18 Nov 2011. 334(6058):986-90
• Gusarov I, Shatalin K, Starodubtseva M, Nudler E Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science. 11 Sep 2009. 325(5946):1380-4
• Proshkin S, Rahmouni AR, Mironov A, Nudler E Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science. 23 Apr 2010. 328(5977):504-8

Structure (Structure)

• Chou HT, Apelt L, Farrell DP, White SR, Woodsmith J, Svetlov V, Goldstein JS, Nager AR, Li Z, Muller J, Dollfus H, Nudler E, Stelzl U, DiMaio F, Nachury MV, Walz T The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach. Structure. 03 Sep 2019. 27(9):1384-1394.e4

Transcription (Transcription)

• Svetlov V, Artsimovitch I, Nudler E Response to Klyuyev and Vassylyev: on the mechanism of tagetitoxin inhibition of transcription. Transcription. 01 Mar 2012. 3(2):51-5
• Sekine S, Murayama Y, Svetlov V, Nudler E, Yokoyama S Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations. Transcription. 01 Jan 2015. 6(3):56-60
• Hao Z, Svetlov V, Nudler E Rho-dependent transcription termination: a revisionist view. Transcription. 01 Aug 2021. 12(4):171-181
• Nedialkov YA, Nudler E, Burton ZF RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription. 01 Sep 2012. 3(5):260-9

Trends Biochem Sci (Trends Biochem Sci)

• Nudler E Transcription-coupled global genomic repair in E. coli. Trends Biochem Sci. 07 Aug 2023. epub ahead of print
• Nudler E, Mironov AS The riboswitch control of bacterial metabolism. Trends Biochem Sci. 01 Jan 2004. 29(1):11-7

Trends Genet (Trends Genet)

• Rasouly A, Pani B, Nudler E A Magic Spot in Genome Maintenance. Trends Genet. 01 Jan 2017. 33(1):58-67

Trends Microbiol (Trends Microbiol)

• Borukhov S, Nudler E RNA polymerase: the vehicle of transcription. Trends Microbiol. 01 Mar 2008. 16(3):126-34

bioRxiv (bioRxiv)

• Wang B, Svetlov V, Wolf YI, Koonin EV, Nudler E, Artsimovitch I Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides. bioRxiv. 28 Apr 2021. epub ahead of print

mBio (mBio)

• Wang B, Svetlov V, Wolf YI, Koonin EV, Nudler E, Artsimovitch I Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides. mBio. 29 Jun 2021. 12(3):e0142321