Tatyana Azhikina

Institute of Bioorganic Chemistry

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Elena G. Salina

A N Bach Institute of Biochemistry

Timofey Skvortsov

Queen's University Belfast

Oksana S. Bychenko

Institute of Bioorganic Chemistry

Artem Grigorov

Institute of Bioorganic Chemistry

Dmitriy Ignatov

Max Planck Unit for the Science of Pathogens

Arseny S. Kaprelyants

A N Bach Institute of Biochemistry

Yu. V. Skvortsova

Institute of Bioorganic Chemistry

E. D. Sverdlov

Kurchatov Institute

Alexander Apt

Central Scientific Research Institute of Tuberculosis Russian Academy of Medical Sciences

ЕД

Е. Д. Свердлов

Kurchatov Institute

Cooperative Institutions

Russian Academy of Sciences

105

Institute of Bioorganic Chemistry

Central Scientific Research Institute of Tuberculosis Russian Academy of Medical Sciences

Lomonosov Moscow State University

Ministry of Health of the Russian Federation

A N Bach Institute of Biochemistry

Federal Center Research Fundamentals of Biotechnology

Institute of Molecular Genetics

University of Pavia

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Dam methylase accessibility as an instrument for analysis of mammalian chromatin structure

Epigenetics (2011)

С. С. Буланенкова Alena Kozlova E. S. Kotova E. V. Snezhkov Tatyana Azhikina

For a 140-kb human genome locus, an analysis of the distribution of Dam methylase accessible sites, DNase I sensitive and resistant regions, unmethylated CpG sites and acetylated histone H3 molecules was performed and compared with transcriptional activity of the genes within the locus. A direct correlation was found between the extent of Dam methylation and C5 cytosine (CpG) methylation. It was also demonstrated that promoter regions of all highly and moderately transcribed genes are highly accessible to methylation by Dam methylase. In contrast, promoters of non-transcribed genes showed a very low extent of Dam methylation. Promoter regions of non-transcribed genes were also highly CpG methylated, and the promoter and more distant 5‘-regions of the housekeeping gene COX6B1 were substantially CpG-demethylated. Some highly Dam methylase accessible regions are present in the intergenic regions of the locus suggesting that the latter contain either unidentified non-coding transcripts or extended regulatory elements like locus control regions.

CpG site

Intergenic region

Housekeeping gene

10.4161/epi.6.9.16476

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РОЛЬ МАЛЫХ НЕКОДИРУЮЩИХ РНК NCRV11733 ПРИ АДАПТАЦИИ МИКОБАКТЕРИЙ К СТРЕССУ, "Вестник Центрального научно-исследовательского института туберкулеза"

Вестник ЦНИИТ (2017)

Artem Grigorov А.С. Мазурова Elena G. Salina К.Б. Майоров Н. Н. Логунова

10.7868/s2587667817010101

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Mycobacterium tuberculosis Transcriptome Profiling in Mice with Genetically Different Susceptibility to Tuberculosis

Acta Naturae (2013)

Timofey Skvortsov Dmitriy Ignatov Konstantin B. Majorov Alexander Apt Tatyana Azhikina

Whole transcriptome profiling is now almost routinely used in various fields of biology, including microbiology. In vivo transcriptome studies usually provide relevant information about the biological processes in the organism and thus are indispensable for the formulation of hypotheses, testing, and correcting. In this study, we describe the results of genome-wide transcriptional profiling of the major human bacterial pathogen M. tuberculosis during its persistence in lungs. Two mouse strains differing in their susceptibility to tuberculosis were used for experimental infection with M. tuberculosis. Mycobacterial transcriptomes obtained from the infected tissues of the mice at two different time points were analyzed by deep sequencing and compared. It was hypothesized that the changes in the M. tuberculosis transcriptome may attest to the activation of the metabolism of lipids and amino acids, transition to anaerobic respiration, and increased expression of the factors modulating the immune response. A total of 209 genes were determined whose expression increased with disease progression in both host strains (commonly upregulated genes, CUG). Among them, the genes related to the functional categories of lipid metabolism, cell wall, and cell processes are of great interest. It was assumed that the products of these genes are involved in M. tuberculosis adaptation to the host immune system defense, thus being potential targets for drug development.

10.32607/20758251-2013-5-2-62-69

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Role of Small Noncoding RNAs in Bacterial Metabolism

Biochemistry (Moscow) (2015)

Tatyana Azhikina Dmitriy Ignatov Elena G. Salina Mikhail V. Fursov Arseny S. Kaprelyants

Transcription

Riboswitch

10.1134/s0006297915130015

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Citations (10)

Alterations in Proteostasis System Components in Peripheral Blood Mononuclear Cells in Parkinson Disease: Focusing on the HSP70 and p62 Levels

Biomolecules (2022)

Julia D. Vavilova Anna A. Boyko Natalya I. Troyanova Н.В. Пономарева В. Ф. Фокин

Parkinson disease (PD) is attributed to a proteostasis disorder mediated by α-synuclein accumulating in a specific brain region. PD manifestation is often related to extraneuronal alterations, some of which could be used as diagnostic or prognostic PD biomarkers. In this work, we studied the shifts in the expression of proteostasis-associated chaperones of the HSP70 family and autophagy-dependent p62 protein values in the peripheral blood mononuclear cells (PBMC) of mild to moderate PD patients. Although we did not detect any changes in the intracellular HSP70 protein pool in PD patients compared to non-PD controls, an increase in the transcriptional activity of the stress-associated HSPA1A/B and HSPA6 genes was observed in these cells. Basal p62 content was found to be increased in PD patients' PBMC, similarly to the p62 level in substantia nigra neural cells in PD. Moreover, the spontaneous apoptosis level was increased among PBMC and positively correlated with the p62 intracellular level in the PD group. A combined HSPA6- and p62-based analysis among 26 PD patients and 36 age-matched non-PD controls pointed out the diagnostic significance of these markers, with intermediate sensitivity and high specificity of this combination when observing patients diagnosed with PD.

Proteostasis

10.3390/biom12040493

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Citations (7)

Additional file 6: Table S6. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

Figshare (2015)

Dmitriy Ignatov Elena G. Salina Mikhail Fursov Timofey Skvortsov Tatyana Azhikina

Functional enrichments analysis. Functional enrichment analysis was performed using the GOseq package [76] and functional categories from the TubercuList and PATRIC databases [33, 34]. The lists of differentially expressed (up- and down-regulated) genes were generated by the comparison of the following samples: DE vs. Log, DM vs. DE, and DL vs. DM. For each functional category, the number of differentially expressed genes, the total number of genes in the category, and the adjusted p-value of overrepresentation are shown. (XLSX 38 kb)

Table (database)

10.6084/m9.figshare.c.3613415_d7

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Search for genetic bases of species differences between Lake Baikal coregonid fishes: whitefish, C. baicalensis, and omul, C. migratorius

Advances in Limnology (2012)

Oksana S. Bychenko Л. В. Суханова Tatyana Azhikina Eliyahu Sverdlov

10.1127/advlim/63/2012/177

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Features of Stress-Induced Changes of HSP70 Expression in Populations of Immunocompetent Cells

Heat shock proteins (2018)