Genomes and Genes
Experts and Doctors on drosophila in Moscow, Russia
Locale: Moscow, Russia
- 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. ..
- Velikodvorskaia V, Lyozin G, Feder M, Evgen ev M. Unusual arrangement of the hsp68 locus in the virilis species group of Drosophila implicates evolutionary loss of an hsp68 gene. Genome. 2005;48:234-40 pubmed..Therefore, we suggest that the hsp68 locus may have arisen via duplication of the hsp70 locus (or vice versa) early in the history of the genus Drosophila, with 1 hsp68 copy subsequently lost in most other Drosophila species groups. ..
- Kulakovskiy I, Favorov A, Makeev V. Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinformatics. 2009;25:2318-25 pubmed publisher..Also we discuss possible overfitting of constructed motifs. Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM. ..
- Kyrchanova O, Ivlieva T, Toshchakov S, Parshikov A, Maksimenko O, Georgiev P. Selective interactions of boundaries with upstream region of Abd-B promoter in Drosophila bithorax complex and role of dCTCF in this process. Nucleic Acids Res. 2011;39:3042-52 pubmed publisher..Thus, the boundaries might be involved in supporting the specific interactions between iab enhancers and promoters of the bithorax complex. ..
- Shpiz S, Olovnikov I, Sergeeva A, Lavrov S, Abramov Y, Savitsky M, et al. Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons. Nucleic Acids Res. 2011;39:8703-11 pubmed publisher..Therefore piRNA-mediated transcriptional mode of silencing is involved in the control of retrotransposon expression in the Drosophila germline. ..
- Bonchuk A, Denisov S, Georgiev P, Maksimenko O. Drosophila BTB/POZ domains of "ttk group" can form multimers and selectively interact with each other. J Mol Biol. 2011;412:423-36 pubmed publisher..Unexpectedly, experiments in the Drosophila model system have not supported the role of GAF in organization of long-distance interaction between the yeast GAL4 activator and the white promoter. ..
- Panov V, Kuzmina J, Doronin S, Kopantseva M, Nabirochkina E, Georgieva S, et al. Transcription co-activator SAYP mediates the action of STAT activator. Nucleic Acids Res. 2012;40:2445-53 pubmed publisher..SAYP is necessary for stimulating STAT-driven transcription of numerous genes. Mutation of SAYP leads to maldevelopments similar to those observed in STAT mutants. Thus, SAYP is a novel co-activator mediating the action of STAT. ..
- 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. ..
- 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. ..
- 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. ..
- Gurskiy D, Orlova A, Vorobyeva N, Nabirochkina E, Krasnov A, Shidlovskii Y, et al. The DUBm subunit Sgf11 is required for mRNA export and interacts with Cbp80 in Drosophila. Nucleic Acids Res. 2012;40:10689-700 pubmed publisher..Thus, Sgf11 functions as a component of both SAGA DUBm and the mRNA biogenesis machinery. ..
- Olovnikov I, Ryazansky S, Shpiz S, Lavrov S, Abramov Y, Vaury C, et al. De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment. Nucleic Acids Res. 2013;41:5757-68 pubmed publisher..We show that transgene-derived hsp70 piRNAs stimulate in trans cleavage of cognate endogenous transcripts with subsequent processing of the non-homologous parts of these transcripts into piRNAs. ..
- Kalmykova A, Shevelyov Y, Dobritsa A, Gvozdev V. Acquisition and amplification of a testis-expressed autosomal gene, SSL, by the Drosophila Y chromosome. Proc Natl Acad Sci U S A. 1997;94:6297-302 pubmed..These results suggest that the acquisition of testis-specific autosomal genes may be important for the evolution of Drosophila as well as human Y chromosomes. ..
- 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...
- Golovnin A, Melnikova L, Volkov I, Kostuchenko M, Galkin A, Georgiev P. 'Insulator bodies' are aggregates of proteins but not of insulators. EMBO Rep. 2008;9:440-5 pubmed publisher..Hence, it is not the functional genomic insulators but rather aggregated proteins that make the so-called 'insulator bodies'. ..
- Kurshakova M, Maksimenko O, Golovnin A, Pulina M, Georgieva S, Georgiev P, et al. Evolutionarily conserved E(y)2/Sus1 protein is essential for the barrier activity of Su(Hw)-dependent insulators in Drosophila. Mol Cell. 2007;27:332-8 pubmed..Apparently, different domains of Su(Hw) recruit proteins responsible for enhancer-blocking and for the barrier activity. ..
- Minin A, Kulik A, Gyoeva F, Li Y, Goshima G, Gelfand V. Regulation of mitochondria distribution by RhoA and formins. J Cell Sci. 2006;119:659-70 pubmed..Thus, mitochondrial movement is controlled by the small GTPase RhoA and this control is mediated by formins. ..
- Garbuz D, Molodtsov V, Velikodvorskaia V, Evgen ev M, Zatsepina O. [Evolution of the response to heat shock in genus Drosophila]. Genetika. 2002;38:1097-109 pubmed..The evolutionary role of the variation in the number of hsp70 gene copies observed in the strains and species of genus Drosophila is discussed. ..
- Vorobyeva N, Soshnikova N, Kuzmina J, Kopantseva M, Nikolenko J, Nabirochkina E, et al. The novel regulator of metazoan development SAYP organizes a nuclear coactivator supercomplex. Cell Cycle. 2009;8:2152-6 pubmed..We suggest that nuclear supercomplexes may be important means of gene-specific regulation of transcription during development. ..
- 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. ..
- Evgen ev M, Zatsepina O, Garbuz D, Lerman D, Velikodvorskaya V, Zelentsova E, et al. Evolution and arrangement of the hsp70 gene cluster in two closely related species of the virilis group of Drosophila. Chromosoma. 2004;113:223-32 pubmed publisher..virilis and D. lummei followed by loss of hsp70 genes in D. lummei. These and other data for hsp70 in Drosophila suggest that evolutionary adaptation has repeatedly modified hsp70 copy number by several different genetic mechanisms...
- Korochkin L. [New approaches in developmental genetics and gene therapy: xenotransplantation of Drosophila embryonic nerve cells into the brain of vertebrate animals]. Genetika. 2000;36:1436-42 pubmed..The results obtained are of interest with regard to neurosurgery, because they may be used to prevent formation of glial scar, an important factor in successful neurotransplantation. ..
- 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. ..
- 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. ..
- Mitashov V, Koussulakos S. [Molecular mechanisms of development and differentiation of eye structures in Drosophila and vertebrates]. Ontogenez. 2001;32:14-28 pubmed..The hypothesis of the monophyletic origin of eyes has been substantiated by the results of molecular investigations. ..
- Golovnin A, Biryukova I, Birukova I, Romanova O, Silicheva M, Parshikov A, et al. An endogenous Su(Hw) insulator separates the yellow gene from the Achaete-scute gene complex in Drosophila. Development. 2003;130:3249-58 pubmed..Genetic analysis shows that at least two proteins, Suppressor of Hairy wing and Modifier of MDG4, required for the activity of this insulator, are involved in the transcriptional regulation of Achaete-scute. ..
- Melnikova L, Juge F, Gruzdeva N, Mazur A, Cavalli G, Georgiev P. Interaction between the GAGA factor and Mod(mdg4) proteins promotes insulator bypass in Drosophila. Proc Natl Acad Sci U S A. 2004;101:14806-11 pubmed..Our data provide direct evidence that heterologous insulators can be bypassed by distal enhancers and identify the interaction between GAF and Mod(mdg4) as a possible means to regulate insulator activity. ..
- Seplyarskiy V, Kharchenko P, Kondrashov A, Bazykin G. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol. 2012;29:1943-55 pubmed publisher..Genome segments with locally elevated mutation rates possess lower values of ?; however, a substantial fraction of variation in ? cannot be directly explained by the local mutation rates...
- 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. ..
- Erokhin M, Davydova A, Kyrchanova O, Parshikov A, Georgiev P, Chetverina D. Insulators form gene loops by interacting with promoters in Drosophila. Development. 2011;138:4097-106 pubmed publisher..Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription...
- Shpiz S, Kwon D, Uneva A, Kim M, Klenov M, Rozovsky Y, et al. Characterization of Drosophila telomeric retroelement TAHRE: transcription, transpositions, and RNAi-based regulation of expression. Mol Biol Evol. 2007;24:2535-45 pubmed..Taking into account a common pattern of HeT-A and TAHRE expression, one may consider TAHRE as a source of reverse transcriptase enzymatic activity for HeT-A transpositions in ovaries. ..
- Shpiz S, Kwon D, Rozovsky Y, Kalmykova A. rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus. Nucleic Acids Res. 2009;37:268-78 pubmed publisher..Finally, this regulation occurs in the nucleus since disruption of the rasiRNA pathway leads to an accumulation of TART and HeT-A transcripts in germ cell nuclei. ..
- Kalmykova A, Kwon D, Rozovsky Y, Hueber N, Capy P, Maisonhaute C, et al. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol Biol Evol. 2004;21:2281-9 pubmed..Thus, expansion of the recently evolved genomic variants of the LTR retrotransposon 1731 possessing a new translation strategy, duplication in the U3 region, and extended profile of expression is revealed. ..
- Gruzdeva N, Kyrchanova O, Parshikov A, Kullyev A, Georgiev P. The Mcp element from the bithorax complex contains an insulator that is capable of pairwise interactions and can facilitate enhancer-promoter communication. Mol Cell Biol. 2005;25:3682-9 pubmed
- Abramov Y, Shatskikh A, Maksimenko O, Bonaccorsi S, Gvozdev V, Lavrov S. The Differences Between Cis- and Trans-Gene Inactivation Caused by Heterochromatin in Drosophila. Genetics. 2016;202:93-106 pubmed publisher..We demonstrate that trans-inactivation is followed by de novo HP1a accumulation in the affected transgene; trans-inactivation is specifically favored by the chromatin remodeler SAYP and prevented by Argonaute AGO2. ..
- Kyrchanova O, Chetverina D, Maksimenko O, Kullyev A, Georgiev P. Orientation-dependent interaction between Drosophila insulators is a property of this class of regulatory elements. Nucleic Acids Res. 2008;36:7019-28 pubmed publisher..These results suggest that insulator proteins can support selective interactions between distant regulatory elements...