A5091871015- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Nuclear Structure and Function
- Microtubule and mitosis dynamics
- Cancer-related gene regulation
- Chromosomal and Genetic Variations
- Advanced biosensing and bioanalysis techniques
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- Protist diversity and phylogeny
- Invertebrate Immune Response Mechanisms
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Developmental Biology and Gene Regulation
- RNA Interference and Gene Delivery
- Photosynthetic Processes and Mechanisms
- Genetics, Aging, and Longevity in Model Organisms
- Ubiquitin and proteasome pathways
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Cellular Mechanics and Interactions
- DNA and Nucleic Acid Chemistry
- Cancer-related molecular mechanisms research
- Neurobiology and Insect Physiology Research
Siberian Branch of the Russian Academy of Sciences
2014-2024
Russian Academy of Sciences
2008-2023
Institute of Molecular and Cell Biology
2014-2023
Novosibirsk State University
2014-2020
Institute of Cytology and Genetics
2001-2019
Oncode Institute
2012-2018
The Netherlands Cancer Institute
2012-2018
Institute of Chemical Biology and Fundamental Medicine
2009
Highlights•A method for parallel monitoring of thousands reporters integrated in the genome•Genome-wide landscape chromatin position effects mouse embryonic stem cells•Attenuation transcriptional activity lamina-associated domains•• Enhancers and transcription units influence gene expression generally over ∼20 kbSummaryReporter genes into genome are a powerful tool to reveal regulatory elements local context on expression. However, so far such reporter assays have been low throughput. Here,...
Abstract Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it challenging profile Cas9 in endogenous cellular environment. Here we leverage our TRIP technology integrate ~ 1k barcoded reporter genes genomes mouse embryonic stem cells. We target integrated reporters (IRs) using RNA-guided characterize induced mutations by sequencing. report that gRNA-sequence IR explain most variation mutation...
Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due its high sensitivity, it particularly suited study the genome interactions proteins in small tissue samples model organisms such as Drosophila. Here, we report an intein-based approach tune expression level and Dam-fusion Drosophila by addition ligand fly food. This helps suppress possible toxic effects Dam. In addition, describe strategy for genetically controlled specific cell...
Growing evidence suggests that intestinal mucosa homeostasis impacts immunity, metabolism, the Central Nervous System (CNS), and behavior. Here, we investigated effect of monosaccharide fucose on inflammation, microbiota, social behavior in Dextran Sulfate Sodium (DSS)-induced chronic colitis mouse model. Our data show is accompanied by decrease serum tryptophan level depletion specifically tryptophan-producing E. coli Bifidobacterium. These changes are associated with defects male such as a...
Proper control of DNA replication is essential to ensure faithful transmission genetic material and prevent chromosomal aberrations that can drive cancer progression developmental disorders. regulated primarily at the level initiation under strict cell-cycle regulation. Importantly, highly influenced by cues. In Drosophila, specific regions genome are repressed for during differentiation SNF2 domain-containing protein SUUR through an unknown mechanism. We demonstrate recruited active forks...
Piwi in a complex with Piwi-interacting RNAs (piRNAs) triggers transcriptional silencing of transposable elements (TEs) Drosophila ovaries, thus ensuring genome stability. To do this, must scan the nascent transcripts genes and TEs for complementarity to piRNAs. The mechanism this scanning is currently unknown. Here we report DamID-seq mapping multiple chromosomal domains somatic cells ovaries. These significantly overlap genomic regions tethered Nuclear Pore Complexes (NPCs). Accordingly,...
Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of various DNA regulatory elements and their mutant variants. The are based on construction highly diverse plasmid libraries containing two variable fragments, a region interest (a sequence under study; ROI) barcode (BC) used to uniquely tag each ROI, which separated by constant spacer sequence. sequences BC–ROI combinations present in the may be either known priori or not. In latter case, it is necessary...
Drosophila melanogaster Suppressor of Under-Replication (SuUR) gene encodes a protein that modulates replicative properties heterochromatin in endocycles polytene cells. The SuUR mutation abolishes underreplication intercalary and results partial pericentric heterochromatin. We performed genome-wide mapping SUUR target genes non-polytenic Kc cells by using the DamID approach. show preferentially binds are transcriptionally silent late-replicated. Distinct subsets targets associated with PcG...
Eukaryotic DNA replicates asynchronously, with discrete genomic loci replicating during different stages of S phase.
In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin, as evidenced microscopy observations and DamID mapping of lamina-associated domains (LADs) enriched in dimethylated Lys9 histone H3 (H3K9me2). However, Kc167 culture, only Drosophilla type where LADs have previously been mapped, they are neither H3K9me2-enriched nor overlapped with heterochromatin protein 1a (HP1a). Here, using type-specific we mapped genome-wide LADs, HP1a...
Abstract Background The Drosophila central nervous system (CNS) is a convenient model for the study of molecular mechanisms conserved neurobiological processes. manipulation gene activity in specific cell types and subtypes CNS frequently achieved by employing binary Gal4/UAS system. However, many Gal4 driver lines available from Bloomington Stock Center (BDSC) commonly used neurobiology are still not well characterized. Among these three with driven elav promoter (BDSC #8760, #8765, #458),...
Abstract Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs attached to the nuclear lamina (NL) through lamina-associated (LADs). Here, we identified LADs and at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is commonly used model spermatogonia (SpG) larval mainly filled with spermatocytes (SpCs). We found that initiation SpC-specific transcription correlates promoters’ detachment from NL local spatial...
SUUR (Suppressor of Under-Replication) protein is responsible for late replication and, as a consequence, DNA underreplication intercalary and pericentric heterochromatin in Drosophila melanogaster polytene chromosomes. However, the mechanism by which slows down process not clear. To identify possible partners we performed yeast two-hybrid screen using full-length bait. This identified HP1, well-studied protein, strong interactor. Furthermore, have determined that central region necessary...
Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) identified a set of 12 proteins enriched in regions corresponding to interbands salivary gland polytene chromosomes. Using these data, developed bioinformatic pipeline that partitioned genome into four chromatin types hereby refer as aquamarine, lazurite, malachite ruby.
S2 cells are one of the most widely used Drosophila melanogaster cell lines. A series studies has shown that they particularly suitable for RNAi-based screens aimed at dissection cellular pathways, including those controlling shape and motility, metabolism, host-pathogen interactions. In addition, RNAi in been successfully to identify many new mitotic genes conserved higher eukaryotes, analysis several aspects process. However, no detailed complete description mitosis ultrastructural level...
Graphical abstractAbstractThe Drosophila S2 tissue culture cells are a widely used system for studies on mitosis. particularly sensitive to gene silencing by RNA interference (RNAi), allowing targeted inactivation of mitotic genes. also well suited high-resolution light microscopy analysis mitosis in fixed cells, and can be easily immunostained detect components. In addition, amenable transformation with plasmid encoding fluorescently tagged proteins, vivo their behavior throughout cell...
Expression of the CNDP2 gene is frequently up- or down-regulated in different types human cancers. However, how product this involved cell growth and proliferation poorly understood. Moreover, our knowledge functions orthologs well-established model organisms scarce. In particular, function D. melanogaster ortholog CNDP2, encoded by CG17337 (hereafter referred to as dCNDP2), still unknown. This study was aimed at developing a set genetic molecular tools roles dCNDP2. We generated dCNDP2 null...
The calmodulin-regulated spectrin-associated proteins (CAMSAPs) belong to a conserved protein family, which includes members that bind the polymerizing mcrotubule (MT) minus ends and remain associated with MT lattice formed by end polymerization. Only one of three mammalian CAMSAPs, CAMSAP1, localizes mitotic spindle but its function is unclear. In Drosophila, there only CAMSAP, named Patronin. Previous work has shown Patronin stabilizes non-mitotic MTs required for proper elongation....