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Savitsky, Mikhail
Publications (7 of 7) Show all publications
Dorafshan, E., Kahn, T. G., Glotov, A., Savitsky, M., Walther, M., Reuter, G. & Schwartz, Y. B. (2019). Ash1 counteracts Polycomb repression independent of histone H3 lysine 36 methylation. EMBO Reports, 20(4), Article ID e46762.
Open this publication in new window or tab >>Ash1 counteracts Polycomb repression independent of histone H3 lysine 36 methylation
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2019 (English)In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 20, no 4, article id e46762Article in journal (Refereed) Published
Abstract [en]

Polycomb repression is critical for metazoan development. Equally important but less studied is the Trithorax system, which safeguards Polycomb target genes from the repression in cells where they have to remain active. It was proposed that the Trithorax system acts via methylation of histone H3 at lysine 4 and lysine 36 (H3K36), thereby inhibiting histone methyltransferase activity of the Polycomb complexes. Here we test this hypothesis by asking whether the Trithorax group protein Ash1 requires H3K36 methylation to counteract Polycomb repression. We show that Ash1 is the only Drosophila H3K36-specific methyltransferase necessary to prevent excessive Polycomb repression of homeotic genes. Unexpectedly, our experiments reveal no correlation between the extent of H3K36 methylation and the resistance to Polycomb repression. Furthermore, we find that complete substitution of the zygotic histone H3 with a variant in which lysine 36 is replaced by arginine does not cause excessive repression of homeotic genes. Our results suggest that the model, where the Trithorax group proteins methylate histone H3 to inhibit the histone methyltransferase activity of the Polycomb complexes, needs revision.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
Ash1, Drosophila, Polycomb, Trithorax
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-158742 (URN)10.15252/embr.201846762 (DOI)000463235300017 ()30833342 (PubMedID)
Available from: 2019-05-20 Created: 2019-05-20 Last updated: 2019-05-20Bibliographically approved
Kravchuk, O., Kim, M., Klepikov, P., Parshikov, A., Georgiev, P. & Savitsky, M. (2017). Transvection in Drosophila: trans-interaction between yellow enhancers and promoter is strongly suppressed by a cis-promoter only in certain genomic regions. Chromosoma, 126(3), 431-441
Open this publication in new window or tab >>Transvection in Drosophila: trans-interaction between yellow enhancers and promoter is strongly suppressed by a cis-promoter only in certain genomic regions
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2017 (English)In: Chromosoma, ISSN 0009-5915, E-ISSN 1432-0886, Vol. 126, no 3, p. 431-441Article in journal (Refereed) Published
Abstract [en]

Transvection is a phenomenon of interallelic communication whereby enhancers of one allele can activate a promoter located on the homologous chromosome. It has been shown for many independent genes that enhancers preferentially act on the cis-linked promoter, but deletion of this promoter allows the enhancers to act in trans. Here, we tested whether this cis-preference in the enhancer-promoter interaction could be reconstituted outside of the natural position of a gene. The yellow gene was chosen as a model system. Transgenic flies were generated that carried the yellow gene modified by the inclusion of the strategically placed recognition sites for the Cre and Flp recombinases. To facilitate transvection, an endogenous Su(Hw) insulator (1A2) or gypsy insulator was placed behind the yellow gene. Independent action of the recombinases produced a pair of derivative alleles, one containing the promoter-driven yellow gene, and the other, the enhancers and promoter that failed to produce a functional yellow protein. As a result, we observed strong transvection in many genomic regions, suggesting that a complete cis-preference of the enhancer-promoter interactions is mainly restricted to genes in their natural loci.

Keywords
Chromatin insulators, Enhancer-promoter communication, Su(Hw), Chromosome pairing, Transcriptional regulation
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-128263 (URN)10.1007/s00412-016-0605-6 (DOI)000401333000008 ()27300555 (PubMedID)
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2018-06-09Bibliographically approved
Savitsky, M., Kim, M., Kravchuk, O. & Schwartz, Y. B. (2016). Distinct Roles of Chromatin Insulator Proteins in Control of the Drosophila Bithorax Complex. Genetics, 202(2), 601-+
Open this publication in new window or tab >>Distinct Roles of Chromatin Insulator Proteins in Control of the Drosophila Bithorax Complex
2016 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, no 2, p. 601-+Article in journal (Refereed) Published
Abstract [en]

Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer-promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and "bridging" proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci; however, their mode of action is poorly understood. Here, we use the Drosophila bithorax complex as a model to investigate the roles of the bridging proteins Cp190 and Mod(mdg4). The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B, which specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly. Looking at effects of CTCF, mod(mdg4), and Cp190 mutations on expression of the bithorax complex genes, we provide the first functional evidence that Mod(mdg4) acts in concert with the DNA binding insulator protein CTCF. We find that Mod(mdg4) and Cp190 are not redundant and may have distinct functional properties. We, for the first time, demonstrate that Cp190 is critical for correct regulation of the bithorax complex and show that Cp190 is required at an exceptionally strong Fub insulator to partition the bithorax complex into two topological domains.

Keywords
HOX genes, chromatin, chromatin insulators, Drosophila, gene regulation
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-118794 (URN)10.1534/genetics.115.179309 (DOI)000371304600021 ()26715665 (PubMedID)
Available from: 2016-04-11 Created: 2016-04-04 Last updated: 2018-06-07Bibliographically approved
Kravchuk, O. I., Mikhailov, V. S. & Savitsky, M. (2015). A simple and efficient method of inducing targeted deletions in the drosophila genome. Russian journal of genetics, 51(11), 1144-1148
Open this publication in new window or tab >>A simple and efficient method of inducing targeted deletions in the drosophila genome
2015 (English)In: Russian journal of genetics, ISSN 1022-7954, E-ISSN 1608-3369, Vol. 51, no 11, p. 1144-1148Article in journal (Refereed) Published
Abstract [en]

Deletion mutagenesis is one of the most efficient approaches to studying gene function. However, conventional methods of inducing targeted mutations in the drosophila genome are timeand labor-consuming. This work proposes a new, simple, and effective method of producing drosophila mutants with gene deletions. The method involves the insertion of I-SceI and I-CreI recognition sites and a fragment homologous to the target sequence into the chromosome region of interest by means of an attB-containing construct, the induction of double-strand DNA breaks by the appropriate meganuclease, and their repair by homologous recombination. The procedure results in a deletion extending from the attP-site to the target locus. A cassette was designed to enable single-step construct production for the deletion of any given genomic region. A set of markers facilitates the selection of recombination events. The efficacy of the proposed technique was confirmed by the induction of a 47-kb deletion containing the qtc gene.

Keywords
Drosophila, method of deletion mutagenesis, double-strand DNA break repair
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-113442 (URN)10.1134/S1022795415110101 (DOI)000365129000012 ()
Available from: 2015-12-18 Created: 2015-12-18 Last updated: 2018-06-07Bibliographically approved
Schwartz, Y. B., Linder-Basso, D., Kharchenko, P. V., Tolstorukov, M. Y., Kim, M., Li, H.-B., . . . Pirrotta, V. (2012). Nature and function of insulator protein binding sites in the Drosophila genome. Genome Research, 22, 2188-2198
Open this publication in new window or tab >>Nature and function of insulator protein binding sites in the Drosophila genome
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2012 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 22, p. 2188-2198Article in journal (Refereed) Published
Abstract [en]

Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes.

National Category
Cell and Molecular Biology Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-58142 (URN)10.1101/gr.138156.112 (DOI)22767387 (PubMedID)
Available from: 2012-08-27 Created: 2012-08-27 Last updated: 2018-06-08Bibliographically approved
Dorafshan, E., Kahn, T. G., Glotov, A., Savitsky, M., Walther, M., Reuter, G. & Schwartz, Y. B.Does Ash1 counteract Polycomb repression by methylating H3K36?.
Open this publication in new window or tab >>Does Ash1 counteract Polycomb repression by methylating H3K36?
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Polycomb repression is critical to maintain cell type specific genome expression programs in a wide range of multicellular animals. Equally important but less studied is the Trithorax group system, which safeguards Polycomb target genes from the repression in cells where they have to remain active. Based on in vitro studies it was proposed that the Trithorax group system acts via methylation of histone H3 at Lysine 4 (H3K4) and Lysine 36 (H3K36) thereby inhibiting histone methyltransferase activity of the Polycomb complexes. This hypothesis is yet to be comprehensively tested in vivo. Here we used the power of the Drosophila model to investigate how the Trithorax group protein Ash1 and the H3K36 methylation counteract Polycomb repression. We show, for the first time, that Ash1 is the only Drosophila H3K36-specific methyltransferase required to prevent excessive Polycomb repression of homeotic genes. Unexpectedly, our experiments revealed no correlation between the extent of H3K36 methylation and the resistance to Polycomb repression. Furthermore, we find that complete substitution of the zygotic histone H3 with a variant in which Lysine 36 is replaced by Arginine does not cause excessive repression of Drosophila homeotic genes. Together with earlier studies, our results suggest that the model, where the Trithorax group proteins methylate histone H3 to inhibit the histone methyltransferase activity of the Polycomb complexes, may need to be reevaluated.

Keywords
Polycomb, H3K36 methylation, HOX genes, Trithorax, Ash1, Drosophila
National Category
Genetics Developmental Biology
Research subject
Molecular Biology; Genetics
Identifiers
urn:nbn:se:umu:diva-153350 (URN)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Kempe Foundations
Available from: 2018-11-19 Created: 2018-11-19 Last updated: 2018-11-20
Dorafshan, E., Kahn, T. G., Glotov, A., Savitsky, M. & Schwartz, Y. B.Functional dissection of Drosophila Ash1 domains.
Open this publication in new window or tab >>Functional dissection of Drosophila Ash1 domains
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(English)Manuscript (preprint) (Other academic)
Keywords
Ash1, Ash1 domains, PHD, SET, BAH, AT hooks, novel alleles
National Category
Genetics
Research subject
Molecular Biology; Genetics
Identifiers
urn:nbn:se:umu:diva-153352 (URN)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationThe Kempe Foundations
Available from: 2018-11-19 Created: 2018-11-19 Last updated: 2018-11-20
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