Publications by authors named "Anna Fedotova"

14 Publications

  • Page 1 of 1

Structural basis of diversity and homodimerization specificity of zinc-finger-associated domains in Drosophila.

Nucleic Acids Res 2021 02;49(4):2375-2389

Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.

In arthropods, zinc finger-associated domains (ZADs) are found at the N-termini of many DNA-binding proteins with tandem arrays of Cys2-His2 zinc fingers (ZAD-C2H2 proteins). ZAD-C2H2 proteins undergo fast evolutionary lineage-specific expansion and functional diversification. Here, we show that all ZADs from Drosophila melanogaster form homodimers, but only certain ZADs with high homology can also heterodimerize. CG2712, for example, is unable to heterodimerize with its paralog, the previously characterized insulator protein Zw5, with which it shares 46% homology. We obtained a crystal structure of CG2712 protein's ZAD domain that, in spite of a low sequence homology, has similar spatial organization with the only known ZAD structure (from Grauzone protein). Steric clashes prevented the formation of heterodimers between Grauzone and CG2712 ZADs. Using detailed structural analysis, site-directed mutagenesis, and molecular dynamics simulations, we demonstrated that rapid evolutionary acquisition of interaction specificity was mediated by the more energy-favorable formation of homodimers in comparison to heterodimers, and that this specificity was achieved by multiple amino acid substitutions resulting in the formation or breaking of stabilizing interactions. We speculate that specific homodimerization of ZAD-C2H2 proteins is important for their architectural role in genome organization.
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http://dx.doi.org/10.1093/nar/gkab061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7913770PMC
February 2021

Correction to "Second-Harmonic Generation in Resonant Nonlinear Metasurfaces Based on Lithium Niobate".

Nano Lett 2021 Jan 11;21(1):888. Epub 2020 Dec 11.

Institute of Applied Physics, Abbe Center of Photonics, Friedrich Schiller University Jena, 07745 Jena, Germany.

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http://dx.doi.org/10.1021/acs.nanolett.0c04651DOI Listing
January 2021

Second-Harmonic Generation in Resonant Nonlinear Metasurfaces Based on Lithium Niobate.

Nano Lett 2020 Dec 12;20(12):8608-8614. Epub 2020 Nov 12.

Institute of Applied Physics, Abbe Center of Photonics, Friedrich Schiller University Jena, 07745 Jena, Germany.

Lithium niobate is an excellent and widely used material for nonlinear frequency conversion due to its strong optical nonlinearity and broad transparency region. Here, we report the fabrication and experimental investigation of resonant nonlinear metasurfaces for second-harmonic generation based on thin-film lithium niobate. In the fabricated metasurfaces, we observe pronounced Mie-type resonances leading to enhanced second-harmonic generation in the direction normal to the metasurface. We find the largest second-harmonic generation efficiency for the resonance dominated by the electric contributions because its specific field distribution enables the most efficient usage of the largest element of the lithium niobate nonlinear susceptibility tensor. This is confirmed by polarization-resolved second-harmonic measurements, where we study contributions from different elements of the nonlinear susceptibility tensor to the total second-harmonic signal. Our work facilitates establishing lithium niobate as a material for resonant nanophotonics.
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http://dx.doi.org/10.1021/acs.nanolett.0c03290DOI Listing
December 2020

Accurate fetal variant calling in the presence of maternal cell contamination.

Eur J Hum Genet 2020 11 29;28(11):1615-1623. Epub 2020 Jul 29.

Skolkovo Institute of Science and Technology, Skolkovo, Russia.

High-throughput sequencing of fetal DNA is a promising and increasingly common method for the discovery of all (or all coding) genetic variants in the fetus, either as part of prenatal screening or diagnosis, or for genetic diagnosis of spontaneous abortions. In many cases, the fetal DNA (from chorionic villi, amniotic fluid, or abortive tissue) can be contaminated with maternal cells, resulting in the mixture of fetal and maternal DNA. This maternal cell contamination (MCC) undermines the assumption, made by traditional variant callers, that each allele in a heterozygous site is covered, on average, by 50% of the reads, and therefore can lead to erroneous genotype calls. We present a panel of methods for reducing the genotyping error in the presence of MCC. All methods start with the output of GATK HaplotypeCaller on the sequencing data for the (contaminated) fetal sample and both of its parents, and additionally rely on information about the MCC fraction (which itself is readily estimated from the high-throughput sequencing data). The first of these methods uses a Bayesian probabilistic model to correct the fetal genotype calls produced by MCC-unaware HaplotypeCaller. The other two methods "learn" the genotype-correction model from examples. We use simulated contaminated fetal data to train and test the models. Using the test sets, we show that all three methods lead to substantially improved accuracy when compared with the original MCC-unaware HaplotypeCaller calls. We then apply the best-performing method to three chorionic villus samples from spontaneously terminated pregnancies.
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http://dx.doi.org/10.1038/s41431-020-0697-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7576216PMC
November 2020

Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune.

Mol Biol Evol 2020 08;37(8):2279-2286

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

The basidiomycete Schizophyllum commune has the highest level of genetic polymorphism known among living organisms. In a previous study, it was also found to have a moderately high per-generation mutation rate of 2×10-8, likely contributing to its high polymorphism. However, this rate has been measured only in an experiment on Petri dishes, and it is unclear how it translates to natural populations. Here, we used an experimental design that measures the rate of accumulation of de novo mutations in a linearly growing mycelium. We show that S. commune accumulates mutations at a rate of 1.24×10-7 substitutions per nucleotide per meter of growth, or ∼2.04×10-11 per nucleotide per cell division. In contrast to what has been observed in a number of species with extensive vegetative growth, this rate does not decline in the course of propagation of a mycelium. As a result, even a moderate per-cell-division mutation rate in S. commune can translate into a very high per-generation mutation rate when the number of cell divisions between consecutive meiosis is large.
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http://dx.doi.org/10.1093/molbev/msaa083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403608PMC
August 2020

The simultaneous interaction of MSL2 with CLAMP and DNA provides redundancy in the initiation of dosage compensation in males.

Development 2019 08 23;146(19). Epub 2019 Aug 23.

Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia

The binding of the male-specific lethal dosage compensation complex (DCC) exclusively to the male X chromosome provides an excellent model system to understand mechanisms of selective recruitment of protein complexes to chromatin. Previous studies showed that the male-specific organizer of the complex, MSL2, and the ubiquitous DNA-binding protein CLAMP are key players in the specificity of X chromosome binding. The CXC domain of MSL2 binds to genomic sites of DCC recruitment Another conserved domain of MSL2, named Clamp-binding domain (CBD) directly interacts with the N-terminal zinc-finger domain of CLAMP. Here, we found that inactivation of CBD or CXC individually only modestly affected recruitment of the DCC to the X chromosome in males. However, combination of these two genetic lesions within the same MSL2 mutant resulted in an increased loss of DCC recruitment to the X chromosome. Thus, proper MSL2 positioning requires an interaction with either CLAMP or DNA to initiate dosage compensation in males.
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http://dx.doi.org/10.1242/dev.179663DOI Listing
August 2019

Improved Protocols of ITS1-Based Metabarcoding and Their Application in the Analysis of Plant-Containing Products.

Genes (Basel) 2019 02 7;10(2). Epub 2019 Feb 7.

Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russia.

Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from the presence of unlabelled components or absence of claimed ones. A promising approach to analyse such products is DNA metabarcoding due to its high resolution and sensitivity. However, this method's application in food analysis requires several methodology optimizations in DNA extraction, amplification and library preparation. In this study, we present such optimizations. The most important methodological outcomes are the following: 1) the DNA extraction method greatly influences amplification success; 2) the main problem for the application of metabarcoding is DNA purity, not integrity or quantity; and 3) the "non-amplifiable" samples can be amplified with polymerases resistant to inhibitors. Using this optimized workflow, we analysed a broad set of plant products (teas, spices and herbal remedies) using two NGS platforms. The analysis revealed the problem of both the presence of extraneous components and the absence of labelled ones. Notably, for teas, no correlation was found between the price and either the absence of labelled components or presence of unlabelled ones; for spices, a negative correlation was found between the price and presence of unlabelled components.
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http://dx.doi.org/10.3390/genes10020122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409534PMC
February 2019

Functional dissection of the developmentally restricted BEN domain chromatin boundary factor Insensitive.

Epigenetics Chromatin 2019 01 3;12(1). Epub 2019 Jan 3.

Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Background: Boundaries in the Drosophila bithorax complex delimit autonomous regulatory domains that activate the parasegment (PS)-specific expression of homeotic genes. The Fab-7 boundary separates the iab-6 and iab-7 regulatory domains that control Abd-B expression in PS11 and PS12. This boundary is composed of multiple functionally redundant elements and has two key activities: it blocks crosstalk between iab-6 and iab-7 and facilitates boundary bypass.

Results: Here, we have used a structure-function approach to elucidate the biochemical properties and the in vivo activities of a conserved BEN domain protein, Insensitive, that is associated with Fab-7. Our biochemical studies indicate that in addition to the C-terminal BEN DNA-binding domain, Insv has two domains that mediate multimerization: one is a coiled-coil domain in the N-terminus, and the other is next to the BEN domain. These multimerization domains enable Insv to bind simultaneously to two canonical 8-bp recognition motifs, as well as to a ~ 100-bp non-canonical recognition sequence. They also mediate the assembly of higher-order multimers in the presence of DNA. Transgenic proteins lacking the N-terminal coiled-coil domain are compromised for boundary function in vivo. We also show that Insv interacts directly with CP190, a protein previously implicated in the boundary functions of several DNA-binding proteins, including Su(Hw) and dCTCF. While CP190 interaction is required for Insv binding to a subset of sites on polytene chromosomes, it has only a minor role in the boundary activity of Insv in the context of Fab-7.

Conclusions: The subdivision of eukaryotic chromosomes into discrete topological domains depends upon the pairing of boundary elements. In flies, pairing interactions are specific and typically orientation dependent. They occur in cis between neighboring heterologous boundaries, and in trans between homologous boundaries. One potential mechanism for ensuring pairing-interaction specificity is the use of sequence-specific DNA-binding proteins that can bind simultaneously with two or more recognition sequences. Our studies indicate that Insv can assemble into a multivalent DNA-binding complex and that the N-terminal Insv multimerization domain is critical for boundary function.
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http://dx.doi.org/10.1186/s13072-018-0249-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317261PMC
January 2019

Fixator-assisted nailing of tibial fractures: New surgical technique and presentation of first 30 cases.

Injury 2019 Feb 10;50(2):515-520. Epub 2018 Nov 10.

F.I. Inozemtsev City Clinical Hospital, 1 Fortunatovskay str., Moscow, 105187, Russia. Electronic address:

Background: Intramedullary nailing is considered a "gold standard" for treatment of tibial shaft fractures. However, some types of fractures are typically considered as "difficult for nailing". This group includes the periarticular fractures, fractures of both bones at the same level, comminuted and segmental fractures of the tibia. Fixator-assisted nailing (FAN) is an effective method treatment of these types of fractures. The main requirements for the ideal reduction device are an ease of its installation and an ability of multiplanar fracture reduction. Fixator-assisted nailing (FAN) with the use of two perpendicular to each other monolateral tubular frames perfectly meets these requirements. In this study we present this new surgical technique and the analysis of first 30 cases.

Methods: A prospective analysis was conducted for 30 patients with "difficult for nailing" tibial fractures treated with fixator-assisted nailing in our institution between September 1, 2017, and March 1, 2018. The duration of surgery and its different stages, the time of fluoroscopy, difficulties encountered during surgery, were analyzed. Clinical and radiological methods were used to evaluated reduction quality.

Results: In all 30 cases the acceptable reduction was achieved. The mean duration of the surgical procedure was 73.7 ± 3 min. The mean duration of fluoroscopy 85.9 ± 4.8 s. In 7 cases we faced with technical difficulties, which were successfully addressed.

Conclusion: The described technique of FAN is an effective method for the treatment of "difficult for nailing" tibial fractures. Future multi-centered studies with a larger number of patients are needed to validate our results.
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http://dx.doi.org/10.1016/j.injury.2018.11.015DOI Listing
February 2019

The BEN Domain Protein Insensitive Binds to the Chromatin Boundary To Establish Proper Segmental Identity in .

Genetics 2018 10 6;210(2):573-585. Epub 2018 Aug 6.

Department of Molecular Biology, Princeton University, New Jersey 08544

Boundaries (insulators) in the bithorax complex (BX-C) delimit autonomous regulatory domains that orchestrate the parasegment (PS)-specific expression of the BX-C homeotic genes. The boundary separates the and regulatory domains, which control Abd-B expression in PS11 and PS12, respectively. This boundary is composed of multiple functionally redundant elements and has two key functions: it blocks cross talk between and and facilitates boundary bypass. Here, we show that two BEN domain protein complexes, Insensitive and Elba, bind to multiple sequences located in the nuclease hypersensitive regions. Two of these sequences are recognized by both Insv and Elba and correspond to a CCAATTGG palindrome. Elba also binds to a related CCAATAAG sequence, while Insv does not. However, the third Insv recognition sequences is ∼100 bp in length and contains the CCAATAAG sequence at one end. Both Insv and Elba are assembled into large complexes (∼420 and ∼265-290 kDa, respectively) in nuclear extracts. Using a sensitized genetic background, we show that the Insv protein is required for boundary function and that PS11 identity is not properly established in mutants. This is the first demonstration that a BEN domain protein is important for the functioning of an endogenous fly boundary.
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http://dx.doi.org/10.1534/genetics.118.301259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6216583PMC
October 2018

High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution.

Plant J 2017 Jul 12;91(2):278-291. Epub 2017 Jun 12.

A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.

Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.
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http://dx.doi.org/10.1111/tpj.13563DOI Listing
July 2017

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila.

Nucleic Acids Res 2016 09 2;44(15):7228-41. Epub 2016 May 2.

Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia

According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to promoters near the TSS and extensively colocalize with cohesin and condensin complexes. ZIPIC, Pita and Zw5 are structurally similar in containing the N-terminal zinc finger-associated domain (ZAD) and different numbers of C2H2-type zinc fingers at the C-terminus. Here we have shown that the ZAD domains of ZIPIC, Pita and Zw5 form homodimers. In Drosophila transgenic lines, these proteins are able to support long-distance interaction between GAL4 activator and the reporter gene promoter. However, no functional interaction between binding sites for different proteins has been revealed, suggesting that such interactions are highly specific. ZIPIC facilitates long-distance stimulation of the reporter gene by GAL4 activator in yeast model system. Many of the genomic binding sites of ZIPIC, Pita and Zw5 are located at the boundaries of topologically associated domains (TADs). Thus, ZAD-containing zinc-finger proteins can be attributed to the class of architectural proteins.
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http://dx.doi.org/10.1093/nar/gkw371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009728PMC
September 2016

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin.

Genome Res 2015 Jan 23;25(1):89-99. Epub 2014 Oct 23.

Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia

Insulators are multiprotein-DNA complexes that regulate the nuclear architecture. The Drosophila CP190 protein is a cofactor for the DNA-binding insulator proteins Su(Hw), CTCF, and BEAF-32. The fact that CP190 has been found at genomic sites devoid of either of the known insulator factors has until now been unexplained. We have identified two DNA-binding zinc-finger proteins, Pita, and a new factor named ZIPIC, that interact with CP190 in vivo and in vitro at specific interaction domains. Genomic binding sites for these proteins are clustered with CP190 as well as with CTCF and BEAF-32. Model binding sites for Pita or ZIPIC demonstrate a partial enhancer-blocking activity and protect gene expression from PRE-mediated silencing. The function of the CTCF-bound MCP insulator sequence requires binding of Pita. These results identify two new insulator proteins and emphasize the unifying function of CP190, which can be recruited by many DNA-binding insulator proteins.
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http://dx.doi.org/10.1101/gr.174169.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317163PMC
January 2015

New properties of Drosophila scs and scs' insulators.

PLoS One 2013 24;8(4):e62690. Epub 2013 Apr 24.

Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.

Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. The first insulators to be identified were scs and scs', which flank the domain including two heat shock 70 genes. Zw5 and BEAF bind to scs and scs', respectively, and are responsible for the interaction between these insulators. Using the regulatory regions of yellow and white reporter genes, we have found that the interaction between scs and scs' improves the enhancer-blocking activity of the weak scs' insulator. The sequences of scs and scs' insulators include the promoters of genes that are strongly active in S2 cells but not in the eyes, in which the enhancer-blocking activity of these insulators has been extensively examined. Only the promoter of the Cad87A gene located at the end of the scs insulator drives white expression in the eyes, and the white enhancer can slightly stimulate this promoter. The scs insulator contains polyadenylation signals that may be important for preventing transcription through the insulator. As shown previously, scs and scs' can insulate transcription of the white transgene from the enhancing effects of the surrounding genome, a phenomenon known as the chromosomal position effect (CPE). 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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062690PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634774PMC
December 2013