2016

• Come Together: CRISPR-Cas Immunity Senses the Quorum. Semenova E, Severinov K. Molecular Cell 64, 2016, December 15, Pages 1102-1108.

• A Trojan-horse peptide-carboxymethyl-cytidine antibiotic from Bacillus amyloliquefaciens. Serebryakova M, Tsibulskaya D, Mokina O, Kulikovsky A, Nautiyal M, Van Aerschot A , Severinov K, DubileyS.   J. Am. Chem. Soc.,2016, 138(48), pp. 15690-15698  DOI: 10.1021/jacs.6b09853

• Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation  Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M,  Datsenko K, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin A,  Severinov K,  Semenova E. Nucleic Acids Research, 2016, vol.44, №22, 10849-10861, doi: 10.1093/nar/gkw914

• The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense.  Severinov K,  Ispolatov I, Semenova E. Front. Mol. Biosci. 2016, 31 August  | http://dx.doi.org/10.3389/fmolb.2016.00045

• Diversity of CRISPR-Cas-Mediated Mechanisms of Adaptive Immunity in Prokaryotes and Their Application in Biotechnology. Savitskaya E, Musharova O, Severinov K. Biochemistry (Mosc). 2016 Jul;81(7):653-61. doi: 10.1134/S0006297916070026.

• Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development. Li Q, Guo S, Jiang X, Bryk J, Naumann R, Enard W, Tomita M, Sugimoto M, Khaitovich P, Pääbo S. Proc Natl Acad Sci U S A. 2016 May 10;113(19):5358-63. doi: 10.1073/pnas.1519261113. Epub 2016 Apr 26.

• Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after introducing a restriction-modification system. Morozova N, Sabantsev A, Bogdanova E, Fedorova Y, Maikova A, Vedyaykin A, Rodic A, Djordjevic M, Khodorkovskii M, Severinov K  Nucleic Acids Res.2016 Jan 29;44(2):790-800. doi: 10.1093/nar/gkv1490. Epub 2015 Dec 19.

• Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex.  Semenova E, Savitskaya E, Musharova O, Strotskaya A, Vorontsova D, Datsenko K, Logacheva M, Severinov K. Proc Natl Acad Sci U S A. 2016, 7626–7631, doi: 10.1073/pnas.1602639113.

• C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Abudayyeh OO, Gootenberg J, Konermann S, Joung J, Slaymaker IM, Cox D, Shmakov S, Makarova K, Semenova E, Minakhin L, Severinov K, Regev A, Lander E, Koonin E, Zhang F.  Science, 2016 Aug 5;353(6299):aaf5573pii: aaf5573.

• The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. Lavysh D, Sokolova M, Minakhin L, Yakunina M, Artamonova T, Kozyavkin S, Makarova K, Koonin E, Severinov K. Virology. 2016 May 26;495:185-196. doi: 10.1016/j.virol.2016.04.030.

• Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova K, Koonin E, Ishitani R, Zhang F, Nureki O. Cell. 2016 May 5, Volume 165, Issue 4, p.949-962. pii: S0092-8674(16)30394-4. doi: 10.1016/j.cell.2016.04.003.

• Recent mobility of casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity. Krupovic M, Shmakov S, Makarova K, Forterre P, Koonin E. Genome Biol Evol. 2016 Jan 13;8(2):375-86. pii: evw006.

• Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow. Lopatina A, Medvedeva S, Shmakov S, Logacheva D, Krylenkov V, Severinov K. Front. Microbiol 2016. | doi: 10.3389/fmicb.2016.00398

• Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data. Kainov Y, Aushev V, Naumenko S, Tchevkina E, Bazykin G. Genome Biol Evol. 2016 Jul 2;8(6):1971-9. doi: 10.1093/gbe/evw137

• Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. Hahn J, Tsoy O, Thalmann S, Čuklina J, Gelfand M, Evguenieva-Hackenberg E. PLoS One. 2016 Oct 27;11(10):e0165429. doi: 10.1371/journal.pone.0165429. eCollection 2016.

• Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria. Tsoy O, Ravcheev D, Čuklina J, Gelfand M. Front Microbiol. 2016 Aug 26;7:1343. doi: 10.3389/fmicb.2016.01343. eCollection 2016.

• Evolution of the Exon-Intron Structure in Ciliate Genomes. Bondarenko V, Gelfand M. PLoS One. 2016 Sep 7;11(9):e0161476. doi: 10.1371/journal.pone.0161476. eCollection 2016.

• Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda). Ivanenko V, Antonenko E, Gelfand M, Yager J, Ferrari F. PeerJ. 2016 Aug 10;4:e2305. doi: 10.7717/peerj.2305. eCollection 2016.

• History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. Khrameeva E, Fudenberg G, Gelfand M, Mirny L. J Bioinform Comput Biol. 2016 Apr;14(2):1641002. doi: 10.1142/S021972001641002X. Epub 2016 Jan 28.

• Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Ulianov S, Khrameeva E, Gavrilov A, Flyamer I, Kos P, Mikhaleva E, Penin A, Logacheva M, Imakaev M, Chertovich A, Gelfand M, Shevelyov Y, Razin S. Genome Res. 2016 Jan;26(1):70-84. doi: 10.1101/gr.196006.115. Epub 2015 Oct 30.

• Changes in snoRNA and snRNA abundance in the human, chimpanzee, macaque and mouse brain. Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky B, Chen Y, Gelfand M, Khaitovich P. Genome Biol Evol., 2016 Mar 23;8(3):840-50pii: evw038.

• Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Flegontov P, Changmai P, Zidkova A, Logacheva M, Altınışık N, Flegontova O, Gelfand M, Gerasimov E, Khrameeva E, Konovalova O, Neretina T, Nikolsky Y, Starostin G, Stepanova V, Travinsky I, Tříska M, Tříska P, Tatarinova T. Sci Rep. 2016 Feb 11;6:20768. doi: 10.1038/srep20768.

• SOX2 Is the Determining Oncogenic Switch in Promoting Lung Squamous Cell Carcinoma from Different Cells of Origin. Ferone G, Song J, Sutherland K, Bhaskaran R, Monkhorst K, Lambooij J, Proost N, Gargiulo G, Berns A. Cancer Cell. 2016 Oct 10;30(4):519-532. doi: 10.1016/j.ccell.2016.09.001.

• Transcription Factor NFIB Is a Driver of Small Cell Lung Cancer Progression in Mice and Marks Metastatic Disease in Patients. Semenova E, Kwon M, Monkhorst K, Song J, Bhaskaran R, Krijgsman O, Kuilman T, Peters D, Buikhuisen W, Smit E, Pritchard C, Cozijnsen M, van der Vliet J, Zevenhoven J, Lambooij J, Proost N, van Montfort E, Velds A, Huijbers I, Berns A. Cell Rep. 2016 Jul 19;16(3):631-43. doi: 10.1016/j.celrep.2016.06.020.

• The steady progress of targeted therapies, promising advances for lung cancer. Bombardelli L, Berns A. Ecancermedicalscience. 2016 Apr 28;10:638. doi: 10.3332/ecancer.2016.638. Review.

• Sorting Out Antibiotics’ Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors. Osterman I, Komarova E, Shiryaev D, Korniltsev I, Khven I, Lukyanov D, Tashlitsky V, Serebryakova M, Efremenkova O, Ivanenkov Y, Bogdanov A, Sergiev P, Dontsova O. Antimicrob Agents Chemother. 2016, 60:7481-7489

• Peculiarities of Yeasts and Human Telomerase RNAs Processing. Rubtsova M, Vasilkova D, Naraykina Y, Dontsova O. Acta Naturae 2016;8:14-22.

• lncRNA in the liver: Prospects for fundamental research and therapy by RNA interference. Smekalova E, Kotelevtsev Y, Leboeuf D, Shcherbinina E, Fefilova A, Zatsepin T, Koteliansky V.  Biochimie. 2016. pii: S0300-9084(16)30116-X. doi: 10.1016/j.biochi.2016.06.007.

• Cy5/BHQ dye–quencher pairs in fluorogenic qPCR probes: effects of charge and hydrophobicity.  Farzan V, Aparin I, Veselova O, Podkolzin A, Shipulin G, Korshun V, Zatsepin T. Anal. Methods, 2016, 8, 5826-5831

• Lipid nanoparticles for targeted siRNA delivery – going from bench to bedside. Zatsepin T, Kotelevtsev Y, Koteliansky V.  Int J Nanomedicine. 2016 ;11:3077-86.

• TERRA mimicking ssRNAs prevail over the DNA substrate for telomerase in vitro due to interactions with the alternative binding site.  Azhibek D, Skvortsov D, Andreeva A, Zatsepin T, Arutyunyan A, Zvereva M, Dontsova O. J Mol Recognit.2016 Jun;29(6):242-7. doi: 10.1002/jmr.2521. Epub 2015 Dec 16.

• mRNA-Based Therapeutics – Advances and Perspectives. Sergeeva O, Koteliansky V, Zatsepin T. Biochemistry (Mosc). 2016 Jul;81(7):709-22. doi: 10.1134/S0006297916070075.

• Tetrahedral DNA conjugates from pentaerythritol-based polyazides. Ponomarenko A, Brylev V, Sapozhnikova K, Ustinov A, Prokhorenko I, Zatsepin T, Korshun V Tetrahedron 2016  72: 2386–2391.

• 1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay. Aparin I, Farzan V, Veselova O, Chistov A, Podkolzin A, Ustinov A, Shipulin G, Formanovsky A, Korshun V, Zatsepin T. Analyst. 2016 ;141(4):1331-8.

• Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Yin H, Song C, Dorkin J, Zhu L, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi M, Walsh S, Bogorad RL, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe S, Langer R, Xue W, Anderson D.  Nat Biotechnol. 2016 Mar;34(3):328-33.

• RNAi-nanoparticulate manipulation of gene expression as a new functional genomics tool in the liver Yin H, Bogorad R, Barnes C, Walsh S, Zhuang I, Nonaka H, Ruda V, Kuchimanchi S, Nechev L, Akinc A, Xue W, Zerial M, Langer R, Anderson D, Koteliansky V. J Hepatol. 2016 Apr;64(4):899-907.

• N6-Methylated Adenosine in RNA: From Bacteria to Humans. Sergiev P, Golovina A, Osterman I, Nesterchuk M, Sergeeva O, Chugunova A, Evfratov S, Andreianova E, Pletnev P, Laptev I, Petriukov K, Navalayeu T, Koteliansky V, Bogdanov A, Dontsova O.  J Mol Biol. 2016 May 22;428(10 Pt B):2134-45

• Di Schiavi E. A Caenorhabditis elegans model to study dopamine transporter deficiency syndrome. Illiano P, Lanzo A, Leo D, Paglione M, Zampi G, Gainetdinov R,  Eur J Neurosci. 2016 Aug 13. doi: 10.1111/ejn.13366.

•  Genetic and environmental modulation of neurodevelopmental disorders: Translational insights from labs to beds. Homberg J, Kyzar E, Scattoni M, Norton W, Pittman J, Gaikwad S, Nguyen M, Poudel M, Ullmann J, Diamond D, Kaluyeva A, Parker M, Brown R, Song C, Gainetdinov R, Gottesman I, Kalueff A. Brain Res Bull. 2016 Jul;125:79-91. doi: 10.1016/j.brainresbull.2016.04.015.

• Analysis of the cleavage mechanism by protein-only RNase P using precursor tRNA substrates with modifications at the cleavage site Walczyk D, Gößringer M, Rossmanith W, Zatsepin T, Oretskaya T, Hartmann R,  J. Mol. Biol. 2016, 428(24 Pt B), 4917-4928

• Adenylyl cyclase activating polypeptide reduces phosphorylation and toxicity of the polyglutamine-expanded androgen receptor in spinobulbar muscular atrophy. Polanco M, Parodi S, Piol D, Stack C, Chivet M, Contestabile A, Miranda H, Lievens P, Espinoza S, Jochum T, Rocchi A, Grunseich C, Gainetdinov R, Cato A, Lieberman A, La Spada A, Sambataro F, Fischbeck K, Gozes I, Pennuto M. Sci Transl Med. 2016 Dec 21

• Hit-to-Lead Optimization of Mouse Trace Amine Associated Receptor 1 (mTAAR1) Agonists with a Diphenylmethane-Scaffold: Design, Synthesis, and Biological Study. Chiellini G, Nesi G, Sestito S, Chiarugi S, Runfola M, Espinoza S, Sabatini M, Bellusci L, Laurino A, Cichero E, Gainetdinov R, Fossa P, Raimondi L, Zucchi R, Rapposelli S. J Med Chem. 2016 Nov 10

• Dopamine transporter mutant animals: a translational perspective. Efimova E, Gainetdinov R, Budygin E, Sotnikova T. J Neurogenet. 2016 Mar doi: 10.3109/01677063.2016.1144751.

• G protein-coupled receptor kinases as regulators of dopamine receptor functions. Gurevich E, Gainetdinov R, Gurevich V. Pharmacol Res. 2016 Sep doi: 10.1016/j.phrs.2016.05.010. Epub 2016 May 10.

• Understanding autism and other neurodevelopmental disorders through experimental translational neurobehavioral models. Homberg J, Kyzar E, Nguyen M, Norton W, Pittman J, Poudel M, Gaikwad S, Nakamura S, Koshiba M, Yamanouchi H, Scattoni M, Ullman J, Diamond D, Kaluyeva A, Parker M, Klimenko V, Apryatin S, Brown R, Song C, Gainetdinov R, Gottesman I, Kalueff A. Neurosci Biobehav Rev. 2016

• Increased context-dependent conditioning to amphetamine in mice lacking TAAR. Sukhanov I, Caffino L, Efimova E, Espinoza S, Sotnikova T, Cervo L, Fumagalli F, Gainetdinov RR. Pharmacol Res. 2016 Jan
  

• Molecular beacons with JOE dye: Influence of linker and 3′ couple quencher. Tsybulsky D, Kvach M, Ryazantsev D, Aparin I, Stakheev A, Prokhorenko I, Martynenko Y, Gontarev S, Formanovsky A, Zatsepin T, Shmanai V, Korshun V, Zavriev S. Mol Cell Probes. 2016 Oct.

• Small-molecule PSMA ligands. Current state, SAR and perspectives. Machulkin A, Ivanenkov Y, Aladinskaya A, Veselov M, Aladinskiy V, Beloglazkina E, Koteliansky V, Shakhbazyan A, Sandulenko Y, Majouga A. J Drug Target. 2016 Sep