Genomes and Genes
Experts and Doctors on gene expression regulation in Moscow, Russia
Locale: Moscow, Russia
Topic: gene expression regulation
- Shipounova I, Petrova T, Svinareva D, Momotuk K, Mikhailova E, Drize N. Alterations in hematopoietic microenvironment in patients with aplastic anemia. Clin Transl Sci. 2009;2:67-74 pubmed publisher..The physiologic status of the BM stromal microenvironment (MSC, CFU-F, and ACL of LTBMC) of AA patients was altered. ..
- Kopnin P, Ivanov A, Il inskaia G, Sablina A, Kopnin B, Chumakov P. [The protective role of p53 in Ras-induced transformation of REF52 cells]. Mol Biol (Mosk). 2003;37:458-71 pubmed..Thus, p53 prevented stable N-RAS-induced transformation of REF52 cells, arresting the cell cycle and expediting revertant selection. ..
- Kolomin T, Morozova M, Volkova A, Shadrina M, Andreeva L, Slominsky P, et al. The temporary dynamics of inflammation-related genes expression under tuftsin analog Selank action. Mol Immunol. 2014;58:50-5 pubmed publisher..This might indicate an active contribution of the dipeptide to the final effect of Selank. ..
- Klochkov D, Rincón Arano H, Ioudinkova E, Valadez Graham V, Gavrilov A, Recillas Targa F, et al. A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain. Mol Cell Biol. 2006;26:1589-97 pubmed
- Gogvadze E, Stukacheva E, Buzdin A, Sverdlov E. Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. J Virol. 2009;83:6098-105 pubmed publisher..The antisense transcripts formed from LTR promoter were shown to decrease the mRNA level of the corresponding genes. The human-specific regulation of these genes suggests their involvement in the evolutionary process. ..
- Illarionova A, Vinogradova T, Sverdlov E. Only those genes of the KIAA1245 gene subfamily that contain HERV(K) LTRs in their introns are transcriptionally active. Virology. 2007;358:39-47 pubmed..The expression of the LTR-containing genes in embryonic tissues might suggest their involvement in evolutionary events during primate speciation. ..
- Zavilgelsky G, Kotova V, Rastorguev S. Comparative analysis of anti-restriction activities of ArdA (ColIb-P9) and Ocr (T7) proteins. Biochemistry (Mosc). 2008;73:906-11 pubmed..It is shown that the dissociation constants K(d) for ArdA and Ocr proteins with EcoKI enzyme differ 1700-fold: K(d) (Ocr) = 10(-10) M, K(d) (ArdA) = 1.7.10(-7) M. ..
- Smekalova E, Kotelevtsev Y, LeBoeuf D, Shcherbinina E, Fefilova A, Zatsepin T, et al. lncRNA in the liver: Prospects for fundamental research and therapy by RNA interference. Biochimie. 2016;131:159-172 pubmed publisher..Different approaches for RNA delivery that can be used for functional studies in the lab and for clinical lncRNA based applications are critically discussed in this review. ..
- Stepanichev M, Lazareva N, Tukhbatova G, Salozhin S, Gulyaeva N. Transient disturbances in contextual fear memory induced by A?(25-35) in rats are accompanied by cholinergic dysfunction. Behav Brain Res. 2014;259:152-7 pubmed publisher..The data give an additional support to the concept of early impairments in the synthesis of proteins related to the cholinergic system as an important mechanism in amyloid-induced neuronal damage. ..
- Orlov S, Klimanova E, Tverskoi A, Vladychenskaya E, Smolyaninova L, Lopina O. Na⁺i,K⁺i-Dependent and -Independent Signaling Triggered by Cardiotonic Steroids: Facts and Artifacts. Molecules. 2017;22: pubmed publisher..We focus our review on the analysis of the relative impact Na⁺i,K⁺i-mediated and -independent pathways in cellular responses evoked by CTS. ..
- Kyrchanova O, Leman D, Parshikov A, Fedotova A, Studitsky V, Maksimenko O, et al. New properties of Drosophila scs and scs' insulators. PLoS ONE. 2013;8:e62690 pubmed publisher..After analyzing many independent transgenic lines, we have concluded that transgenes carrying the scs insulator are rarely inserted into genomic regions that stimulate the white reporter expression in the eyes. ..
- Ivliev A, t Hoen P, van Roon Mom W, Peters D, Sergeeva M. Exploring the transcriptome of ciliated cells using in silico dissection of human tissues. PLoS ONE. 2012;7:e35618 pubmed publisher..Taken together, our large-scale analysis of gene coexpression networks identifies novel genes related to human cell cilia...
- Tukhvatulin A, Gitlin I, Shcheblyakov D, Artemicheva N, Burdelya L, Shmarov M, et al. Combined stimulation of Toll-like receptor 5 and NOD1 strongly potentiates activity of NF-ÎºB, resulting in enhanced innate immune reactions and resistance to Salmonella enterica serovar Typhimurium infection. Infect Immun. 2013;81:3855-64 pubmed publisher..Obtained results suggest that cooperation of NOD and TLR receptors is important for effective responses to microbial infection in vivo. ..
- Golovnin A, Melnick E, Mazur A, Georgiev P. Drosophila Su(Hw) insulator can stimulate transcription of a weakened yellow promoter over a distance. Genetics. 2005;170:1133-42 pubmed..The stimulatory activity depends on the number of Su(Hw)-binding sites. Mutational analysis demonstrates that only the DNA-binding domain and adjacent regions of the Su(Hw) protein are required for stimulation of yellow transcription. ..
- Lukhovitskaya N, Ignatovich I, Savenkov E, Schiemann J, Morozov S, Solovyev A. Role of the zinc-finger and basic motifs of chrysanthemum virus B p12 protein in nucleic acid binding, protein localization and induction of a hypersensitive response upon expression from a viral vector. J Gen Virol. 2009;90:723-33 pubmed publisher
- Kurshakova M, Krasnov A, Kopytova D, Shidlovskii Y, Nikolenko J, Nabirochkina E, et al. SAGA and a novel Drosophila export complex anchor efficient transcription and mRNA export to NPC. EMBO J. 2007;26:4956-65 pubmed..Thus, E(y)2 and Xmas-2 together with SAGA/TFTC function in the anchoring of a subset of transcription sites to the NPCs to achieve efficient transcription and mRNA export. ..
- Afanasyeva M, Putlyaeva L, Demin D, Kulakovskiy I, Vorontsov I, Fridman M, et al. The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region. PLoS ONE. 2017;12:e0172681 pubmed publisher..In a luciferase reporter assay, a kilobase-long genomic segment containing G but not A allele of rs12722489 demonstrated enhancer properties in MT-2 cell line, an HTLV-1 transformed human cell line with a regulatory T cell phenotype. ..
- Sakharov D, Maltseva D, Riabenko E, Shkurnikov M, Northoff H, Tonevitsky A, et al. Passing the anaerobic threshold is associated with substantial changes in the gene expression profile in white blood cells. Eur J Appl Physiol. 2012;112:963-72 pubmed publisher..In conclusion, a 15-min test to exhaustion was associated with substantially greater changes of gene expression than a 30-min test just below the AnT. ..
- Melnikova L, Kostuchenko M, Silicheva M, Georgiev P. Drosophila gypsy insulator and yellow enhancers regulate activity of yellow promoter through the same regulatory element. Chromosoma. 2008;117:137-45 pubmed..These finding suggest that proteins bound to the -100 to -69 sequence are essential for communication between the yellow promoter and upstream regulatory elements. ..
- Kyrchanova O, Toshchakov S, Parshikov A, Georgiev P. Study of the functional interaction between Mcp insulators from the Drosophila bithorax complex: effects of insulator pairing on enhancer-promoter communication. Mol Cell Biol. 2007;27:3035-43 pubmed..These results indicate that the relative placement and orientation of insulator-like elements can determine proper enhancer-promoter communication. ..
- Tokarev K, Tiunova A, Scharff C, Anokhin K. Food for song: expression of c-Fos and ZENK in the zebra finch song nuclei during food aversion learning. PLoS ONE. 2011;6:e21157 pubmed publisher..These findings underscore the previously advanced notion that the specialized forebrain pre-motor nuclei controlling song evolved from circuits involved in behaviors related to feeding. ..
- Zobacheva P, Kulliev A, Georgiev P, Mel nikova L. Interaction between zeste binding sites does not block isolated yellow enhancers in Drosophila melanogaster. Dokl Biochem Biophys. 2003;391:229-31 pubmed
- Sofronova S, Gaynullina D, Shvetsova A, Borzykh A, Selivanova E, Kostyunina D, et al. Antenatal/early postnatal hypothyroidism alters arterial tone regulation in 2-week-old rats. J Endocrinol. 2017;235:137-151 pubmed publisher..Such alterations disturb perinatal cardiovascular homeostasis and might lead to cardiovascular pathologies in adulthood. ..
- Skoblov M, Shakhbazov K, Oshchepkov D, Guskova A, Ivanov D, Rubtsov P, et al. Human RFP2 gene promoter: unique structure and unusual strength. Biochem Biophys Res Commun. 2006;342:859-66 pubmed..A "minimized" version of the RFP2 promoter could be used for overexpression of the various transgenes in the mammalian cells. ..
- Kuprash D, Osipovich O, Pokholok D, Alimzhanov M, Biragyn A, Turetskaya R, et al. Functional analysis of the lymphotoxin-beta promoter. Sequence requirements for PMA activation. J Immunol. 1996;156:2465-72 pubmed..We propose that the interaction between the members of NF-kappaB and Ets families of transcription factors and their cognate sites in the promoter is the major determinant of inducible expression of the LT-beta gene in Jurkat cells. ..
- Timofeeva A, Goryunova L, Khaspekov G, Kovalevskii D, Scamrov A, Bulkina O, et al. Altered gene expression pattern in peripheral blood leukocytes from patients with arterial hypertension. Ann N Y Acad Sci. 2006;1091:319-35 pubmed..Gene expression pattern of the majority of genes was similar in AH patients independent of the disease stage and used hypotensive therapy, but was clearly different from that of normotensive subjects. ..
- Kibardin A, Mirkina I, Zakeeva I, Baranova E, Georgiev G, Kiselev S. [Expression analysis of proteins encoded by genes of the tag7/tagL (PGRP-S,L) family in human peripheral blood cells]. Genetika. 2003;39:244-9 pubmed..Expression regulation by several factors was demonstrated. ..
- Kovaleva I, Garaeva A, Chumakov P, Evstafieva A. Intermedin/adrenomedullin 2 is a stress-inducible gene controlled by activating transcription factor 4. Gene. 2016;590:177-85 pubmed publisher..Since ADM2 was shown to inhibit ATF4 expression during myocardial ER stress, a feedback mechanism could be proposed for the ADM2 regulation under ER stress conditions. ..
- Kryukova E, Shelukhina I, Kolacheva A, Alieva A, Shadrina M, Slominsky P, et al. [Possible involvement of neuronal nicotinic acetylcholine receptors in compensatory brain mechanisms at early stages of Parkinson's disease]. Biomed Khim. 2017;63:241-247 pubmed publisher..Poluchennye dannye ob izmeneniiakh urovnia mRNK ili funktsional'nykh kholinoretseptorov svidetel'stvuiut o vozmozhnom uchastii nAKhR v kompensatornykh mekhanizmakh na rannikh stadiiakh BP. ..
- Kyrchanova O, Georgiev P. Chromatin insulators and long-distance interactions in Drosophila. FEBS Lett. 2014;588:8-14 pubmed publisher..It has also become apparent that enhancer blocking is only one of several functional activities of known insulator proteins, which also contribute to the organization of chromosome architecture and the integrity of regulatory elements. ..
- Savitsky M, Kravchuk O, Melnikova L, Georgiev P. Heterochromatin protein 1 is involved in control of telomere elongation in Drosophila melanogaster. Mol Cell Biol. 2002;22:3204-18 pubmed..The Drosophila lines bearing the Su(var)2-5 mutations maintain extremely long telomeres consisting of HeT-A and TART for many generations. Thus, HP1 plays an important role in the control of telomere elongation in D. melanogaster. ..
- Ryazansky S, Radion E, Mironova A, Akulenko N, Abramov Y, Morgunova V, et al. Natural variation of piRNA expression affects immunity to transposable elements. PLoS Genet. 2017;13:e1006731 pubmed publisher..We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon HeT-A, which we have observed in one particular transposon-resistant R strain. ..
- Chetverina D, Savitskaya E, Maksimenko O, Melnikova L, Zaytseva O, Parshikov A, et al. Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs. Nucleic Acids Res. 2008;36:929-37 pubmed
- Feoktistova E, Skamrov A, Goryunova L, Khaspekov G, Osyaeva M, Rodnenkov O, et al. [Analysis of gene expression pattern in peripheral blood leukocytes during experimental heat wave]. Biomed Khim. 2017;63:139-146 pubmed publisher..Pri teplovom vozde?stvii dlia genov EGR2, EGR3 uvelichenie urovnia ékspressii otmecheno u vsekh 6 ispytuemykh, a dlia genov EGR1, SIRT1, CYP51A1, MAPK9, BAG5, MNDA – u piati iz 6 ispytuemykh. ..
- Alexandrov P, Cui J, Lukiw W. Hypoxia-sensitive domain in the human cytosolic phospholipase A2 promoter. Neuroreport. 2006;17:303-7 pubmed
- Feng T, Yamamoto A, Wilkins S, Sokolova E, Yates L, MÃ¼nzel M, et al. Optimal translational termination requires C4 lysyl hydroxylation of eRF1. Mol Cell. 2014;53:645-54 pubmed publisher..These findings further highlight the role of 2-oxoglutarate/Fe(II) oxygenases in fundamental cellular processes and provide additional evidence that ensuring fidelity of protein translation is a major role of hydroxylation. ..
- Belenkaya T, Soldatov A, Nabirochkina E, Biryukova I, Birjukova I, Georgieva S, et al. P-Element insertion at the polyhomeotic gene leads to formation of a novel chimeric protein that negatively regulates yellow gene expression in P-element-induced alleles of Drosophila melanogaster. Genetics. 1998;150:687-97 pubmed..The P-PH, Polycomb (PC), and Posterior sex combs (PSC) proteins were immunohistochemically detected on polytene chromosomes in the regions of P-element insertions. ..
- Kulakovskiy I, Belostotsky A, Kasianov A, Esipova N, Medvedeva Y, Eliseeva I, et al. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinformatics. 2011;27:2621-4 pubmed publisher..We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. firstname.lastname@example.org Supplementary data are available at Bioinformatics online. ..
- Kostyuk S, Smirnova T, Efremova L, Konkova M, Alekseeva A, Kameneva L, et al. Enhanced expression of iNOS in human endothelial cells during long-term culturing with extracellular DNA fragments. Bull Exp Biol Med. 2010;149:191-5 pubmed..Activation of these receptors by extracellular DNA fragments stimulates expression of the adapter protein MyD88. ..
- Melnikova L, Kulikov A, Georgiev P. Interactions between cut wing mutations and mutations in zeste, and the enhancer of yellow and Polycomb group genes of Drosophila melanogaster. Mol Gen Genet. 1996;252:230-6 pubmed..The results are discussed in terms of the role of long-distance interactions and DNA compaction in transcriptional control of the cut locus. ..
- Tumanov A, Grivennikov S, Kruglov A, Shebzukhov Y, Koroleva E, Piao Y, et al. Cellular source and molecular form of TNF specify its distinct functions in organization of secondary lymphoid organs. Blood. 2010;116:3456-64 pubmed publisher..Thus, the maintenance of each type of secondary lymphoid organ is orchestrated by distinct contributions of membrane-bound and soluble TNF produced by B and T lymphocytes. ..
- Makeev V, Lifanov A, Nazina A, Papatsenko D. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res. 2003;31:6016-26 pubmed..We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes. ..
- Kuprash D, Alimzhanov M, Tumanov A, Grivennikov S, Shakhov A, Drutskaya L, et al. Redundancy in tumor necrosis factor (TNF) and lymphotoxin (LT) signaling in vivo: mice with inactivation of the entire TNF/LT locus versus single-knockout mice. Mol Cell Biol. 2002;22:8626-34 pubmed..Thus, our data support the notion that TNF and LT have largely nonredundant functions in vivo. ..
- Zolotarev N, Maksimenko O, Kyrchanova O, Sokolinskaya E, Osadchiy I, Girardot C, et al. Opbp is a new architectural/insulator protein required for ribosomal gene expression. Nucleic Acids Res. 2017;45:12285-12300 pubmed publisher..Rather than having a constitutive role, Opbp represents a new type of architectural protein with a very restricted, yet essential, function in regulation of housekeeping gene expression. ..
- Ilyushina N, Lugovtsev V, Samsonova A, Sheikh F, Bovin N, Donnelly R. Generation and characterization of interferon-lambda 1-resistant H1N1 influenza A viruses. PLoS ONE. 2017;12:e0181999 pubmed publisher..Our findings demonstrate that influenza viruses can develop increased resistance to the antiviral activity of type III interferons. ..
- Buchman V, Ninkina N, Bogdanov Y, Bortvin A, Akopian H, Kiselev S, et al. Differential splicing creates a diversity of transcripts from a neurospecific developmentally regulated gene encoding a protein with new zinc-finger motifs. Nucleic Acids Res. 1992;20:5579-85 pubmed..Several differential splicing variants were found, each of which influences the structure of the encoded protein. ..
- Golovnin A, Volkov I, Georgiev P. SUMO conjugation is required for the assembly of Drosophila Su(Hw) and Mod(mdg4) into insulator bodies that facilitate insulator complex formation. J Cell Sci. 2012;125:2064-74 pubmed publisher..These results suggest that insulator bodies function as a depot of sumoylated proteins that are involved in insulation and can facilitate insulator complex formation, but are nonessential for insulator action. ..
- Kopnin B, Stromskaya T, Kondratov R, Ossovskaya V, Pugacheva E, Rybalkina E, et al. Influence of exogenous ras and p53 on P-glycoprotein function in immortalized rodent fibroblasts. Oncol Res. 1995;7:299-306 pubmed..abstract truncated at 250 words) ..
- Kravchenko I, Furalyov V, Lisitsina E, Popov V. Stimulation of mechano-growth factor expression by second messengers. Arch Biochem Biophys. 2011;507:323-31 pubmed publisher..Implication of protein kinase A and protein kinase C in MGF synthesis stimulation and a cross-talk between two signaling systems is discussed. ..
- Tonevitsky E, Trushkin E, Shkurnikov M, Akimov E, Sakharov D. Changed profile of splicing regulator genes expression in response to exercise. Bull Exp Biol Med. 2009;147:733-6 pubmed..The role of the detected regulators in initiation of splisosome assembly under conditions of maximally intensive exercise is discussed. ..
- Vorobyeva N, Nikolenko J, Nabirochkina E, Krasnov A, Shidlovskii Y, Georgieva S. SAYP and Brahma are important for 'repressive' and 'transient' Pol II pausing. Nucleic Acids Res. 2012;40:7319-31 pubmed publisher..SAYP is essential for Ser2 phosphorylation and transcription elongation. Thus, SAYP as part of the Brahma complex participates in both 'repressive' and 'transient' Pol II pausing. ..
- Melnikova L, Georgiev P. Enhancer of terminal gene conversion, a new mutation in Drosophila melanogaster that induces telomere elongation by gene conversion. Genetics. 2002;162:1301-12 pubmed..Thus, the E(tc) mutation plays a significant role in the control of telomere elongation in D. melanogaster. ..
- Dergunova L, Raevskaya N, Vladychenskaya I, Limborska S. Hmob3 brain-specific sequence is a part of phylogenetically conserved human MAP1B gene 3'-untranslated region. Biomol Eng. 2003;20:91-6 pubmed..Using Hmob3 as a probe in the Northern blot analysis, we have revealed two different types of transcripts for brain and kidney mRNA samples; in the skeletal muscle sample we detected both transcripts. ..
- Savitskaya E, Melnikova L, Kostuchenko M, Kravchenko E, Pomerantseva E, Boikova T, et al. Study of long-distance functional interactions between Su(Hw) insulators that can regulate enhancer-promoter communication in Drosophila melanogaster. Mol Cell Biol. 2006;26:754-61 pubmed..Some inferences concerning the possible modes of insulator action are made from collating the new data and the relevant literature, with tentative schemes illustrating the regulatory situations in particular model constructs. ..
- Belen kaia T, Georgiev P. [Role of the "enhancer of yellow" genes in the regulation of expression of the "yellow" gene in Drosophila melanogaster]. Genetika. 1999;35:432-7 pubmed..When introduced at +2490 from the transcription initiation site, the su(Hw) insulator becomes able to block interactions between the bristle enhancer and yellow promoter, not separating them from each other. ..
- Simonova O. [A novel trans-regulatory locus in Drosophila]. Genetika. 2000;36:1464-74 pubmed..A possible role of the new locus in organogenesis, neurogenesis, and embryonic development is discussed on the basis of experimental findings...
- Karpova O, Karger E, Kozlovskii S, Dorokhov Y, Rodionova N, Atabekov I. Role of C- and N-terminal mutations of the movement protein of tobacco mosaic virus in activation of complexes between the transport protein and viral RNA that are not translated in vitro. Dokl Biochem Biophys. 2004;397:224-7 pubmed
- Rodin S, Kyrchanova O, Pomerantseva E, Parshikov A, Georgiev P. New properties of Drosophila fab-7 insulator. Genetics. 2007;177:113-21 pubmed..It seems likely that Fab-7 strengthens the relatively weak white promoter, which leads to the efficient enhancer-promoter interaction and insulator bypass...
- Tchurikov N, Kretova O, Sosin D, Zykov I, Zhimulev I, Kravatsky Y. Genome-wide profiling of forum domains in Drosophila melanogaster. Nucleic Acids Res. 2011;39:3667-85 pubmed publisher..The data on the global mapping of forum domains revealed a strong correlation between fragmentation sites in chromosomes, particular sets of mobile elements and regions of intercalary heterochromatin. ..
- Kostyuk S, Ermakov A, Alekseeva A, Smirnova T, Glebova K, Efremova L, et al. Role of extracellular DNA oxidative modification in radiation induced bystander effects in human endotheliocytes. Mutat Res. 2012;729:52-60 pubmed publisher..We found that the cellular responses to all three stimuli described above are essentially similar. We conclude that irradiation-related oxidation of the ecDNA is an important component of the ecDNA-mediated bystander effect. ..
- Nikulova A, Favorov A, Sutormin R, Makeev V, Mironov A. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res. 2012;40:e93 pubmed publisher..Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila. ..