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Kolesnikova TD, Klenov MS, Nokhova AR, Lavrov SA, Pokholkova GV, Schubert V, Maltseva SV, Cook KR, Dixon MJ, Zhimulev IF. A Spontaneous Inversion of the X Chromosome Heterochromatin Provides a Tool for Studying the Structure and Activity of the Nucleolus in Drosophila melanogaster. Cells 2022; 11:cells11233872. [PMID: 36497131 PMCID: PMC9736023 DOI: 10.3390/cells11233872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The pericentromeric heterochromatin is largely composed of repetitive sequences, making it difficult to analyze with standard molecular biological methods. At the same time, it carries many functional elements with poorly understood mechanisms of action. The search for new experimental models for the analysis of heterochromatin is an urgent task. In this work, we used the Rif1 mutation, which suppresses the underreplication of all types of repeated sequences, to analyze heterochromatin regions in polytene chromosomes of Drosophila melanogaster. In the Rif1 background, we discovered and described in detail a new inversion, In(1)19EHet, which arose on a chromosome already carrying the In(1)sc8 inversion and transferred a large part of X chromosome heterochromatin, including the nucleolar organizer to a new euchromatic environment. Using nanopore sequencing and FISH, we have identified the eu- and heterochromatin breakpoints of In(1)19EHet. The combination of the new inversion and the Rif1 mutation provides a promising tool for studies of X chromosome heterochromatin structure, nucleolar organization, and the nucleolar dominance phenomenon. In particular, we found that, with the complete polytenization of rDNA repeats, the nucleolus consists of a cloud-like structure corresponding to the classical nucleolus of polytene chromosomes, as well as an unusual intrachromosomal structure containing alternating transcriptionally active and inactive regions.
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Affiliation(s)
- Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| | - Mikhail S. Klenov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Alina R. Nokhova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey A. Lavrov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Seeland, Germany
| | - Svetlana V. Maltseva
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Kevin R. Cook
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael J. Dixon
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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2
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Kolesnikova TD, Kolodyazhnaya AV, Pokholkova GV, Schubert V, Dovgan VV, Romanenko SA, Prokopov DY, Zhimulev IF. Effects of Mutations in the Drosophila melanogaster Rif1 Gene on the Replication and Underreplication of Pericentromeric Heterochromatin in Salivary Gland Polytene Chromosomes. Cells 2020; 9:cells9061501. [PMID: 32575592 PMCID: PMC7349278 DOI: 10.3390/cells9061501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
In Drosophila salivary gland polytene chromosomes, a substantial portion of heterochromatin is underreplicated. The combination of mutations SuURES and Su(var)3-906 results in the polytenization of a substantial fraction of unique and moderately repeated sequences but has almost no effect on satellite DNA replication. The Rap1 interacting factor 1 (Rif) protein is a conserved regulator of replication timing, and in Drosophila, it affects underreplication in polytene chromosomes. We compared the morphology of pericentromeric regions and labeling patterns of in situ hybridization of heterochromatin-specific DNA probes between wild-type salivary gland polytene chromosomes and the chromosomes of Rif1 mutants and SuUR Su(var)3-906 double mutants. We show that, despite general similarities, heterochromatin zones exist that are polytenized only in the Rif1 mutants, and that there are zones that are under specific control of Su(var)3-9. In the Rif1 mutants, we found additional polytenization of the largest blocks of satellite DNA (in particular, satellite 1.688 of chromosome X and simple satellites in chromosomes X and 4) as well as partial polytenization of chromosome Y. Data on pulsed incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into polytene chromosomes indicated that in the Rif1 mutants, just as in the wild type, most of the heterochromatin becomes replicated during the late S phase. Nevertheless, a significantly increased number of heterochromatin replicons was noted. These results suggest that Rif1 regulates the activation probability of heterochromatic origins in the satellite DNA region.
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Affiliation(s)
- Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| | - Alexandra V. Kolodyazhnaya
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Galina V. Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland, Germany;
| | - Viktoria V. Dovgan
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
| | - Dmitry Yu. Prokopov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
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3
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Sidorenko DS, Sidorenko IA, Zykova TY, Goncharov FP, Larsson J, Zhimulev IF. Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila melanogaster. Chromosoma 2019; 128:97-117. [PMID: 31041520 PMCID: PMC6536484 DOI: 10.1007/s00412-019-00703-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 01/09/2019] [Accepted: 04/02/2019] [Indexed: 12/24/2022]
Abstract
The fourth chromosome smallest in the genome of Drosophila melanogaster differs from other chromosomes in many ways. It has high repeat density in conditions of a large number of active genes. Gray bands represent a significant part of this polytene chromosome. Specific proteins including HP1a, POF, and dSETDB1 establish the epigenetic state of this unique chromatin domain. In order to compare maps of localization of genes, bands, and chromatin types of the fourth chromosome, we performed FISH analysis of 38 probes chosen according to the model of four chromatin types. It allowed clarifying the dot chromosome cytological map consisting of 16 loose gray bands, 11 dense black bands, and 26 interbands. We described the relation between chromatin states and bands. Open aquamarine chromatin mostly corresponds to interbands and it contains 5'UTRs of housekeeping genes. Their coding parts are embedded in gray bands substantially composed of lazurite chromatin of intermediate compaction. Polygenic black bands contain most of dense ruby chromatin, and also some malachite and lazurite. Having an accurate map of the fourth chromosome bands and its correspondence to physical map, we found that DNase I hypersensitivity sites, ORC2 protein, and P-elements are mainly located in open aquamarine chromatin, while element 1360, characteristic of the fourth chromosome, occupies band chromatin types. POF and HP1a proteins providing special organization of this chromosome are mostly located in aquamarine and lazurite chromatin. In general, band organization of the fourth chromosome shares the features of the whole Drosophila genome.
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Affiliation(s)
- Darya S Sidorenko
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8/2, Novosibirsk, Russia, 630090
| | - Ivan A Sidorenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana Yu Zykova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8/2, Novosibirsk, Russia, 630090
| | - Fedor P Goncharov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8/2, Novosibirsk, Russia, 630090
| | - Jan Larsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8/2, Novosibirsk, Russia, 630090. .,Laboratory of structural, functional and comparative genomics of the Novosibirsk State University, Novosibirsk, Russia.
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Sidorenko DS, Zykova TY, Khoroshko VA, Pokholkova GV, Demakov SA, Larsson J, Belyaeva ES, Zhimulev IF. Polytene chromosomes reflect functional organization of the Drosophila genome. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. Each region of polytene chromosomes has a unique banding pattern. Using the model of four chromatin types that reveals domains of varying compaction degrees, we were able to correlate the physical and cytological maps of some polytene chromosome regions and to show the main properties of genetic and molecular organization of bands and interbands, that we describe in this review. On the molecular map of the genome, the interbands correspond to decompacted aquamarine chromatin and 5’ ends of ubiquitously active genes. Gray bands contain lazurite and malachite chromatin, intermediate in the level of compaction, and, mainly, coding parts of genes. Dense black transcriptionally inactive bands are enriched in ruby chromatin. Localization of several dozens of interbands on the genome molecular map allowed us to study in detail their architecture according to the data of whole genome projects. The distribution of proteins and regulatory elements of the genome in the promoter regions of genes localized in the interbands shows that these parts of interbands are probably responsible for the formation of open chromatin that is visualized in polytene chromosomes as interbands. Thus, the permanent genetic activity of interbands and gray bands and the inactivity of genes in black bands are the basis of the universal banding pattern in the chromosomes of all Drosophila tissues. The smallest fourth chromosome of Drosophila with an atypical protein composition of chromatin is a special case. Using the model of four chromatin states and fluorescent in situ hybridization, its cytological map was refined and the genomic coordinates of all bands and interbands were determined. It was shown that, in spite of the peculiarities of this chromosome, its band organization in general corresponds to the rest of the genome. Extremely long genes of different Drosophila chromosomes do not fit the common scheme, since they can occupy a series of alternating bands and interbands (up to nine chromosomal structures) formed by parts of these genes.
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Affiliation(s)
| | | | | | | | | | - J. Larsson
- Department of Molecular Biology, Umea University
| | | | - I. F. Zhimulev
- Institute of Molecular and Cellular Biology, SB RAS; 3 Laboratory of Structural, Functional and Comparative Genomics of the Novosibirsk State University
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5
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Munden A, Rong Z, Sun A, Gangula R, Mallal S, Nordman JT. Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila. eLife 2018; 7:e39140. [PMID: 30277458 PMCID: PMC6185109 DOI: 10.7554/elife.39140] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Control of DNA copy number is essential to maintain genome stability and ensure proper cell and tissue function. In Drosophila polyploid cells, the SNF2-domain-containing SUUR protein inhibits replication fork progression within specific regions of the genome to promote DNA underreplication. While dissecting the function of SUUR's SNF2 domain, we identified an interaction between SUUR and Rif1. Rif1 has many roles in DNA metabolism and regulates the replication timing program. We demonstrate that repression of DNA replication is dependent on Rif1. Rif1 localizes to active replication forks in a partially SUUR-dependent manner and directly regulates replication fork progression. Importantly, SUUR associates with replication forks in the absence of Rif1, indicating that Rif1 acts downstream of SUUR to inhibit fork progression. Our findings uncover an unrecognized function of the Rif1 protein as a regulator of replication fork progression.
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Affiliation(s)
- Alexander Munden
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Zhan Rong
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Amanda Sun
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Rama Gangula
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
| | - Simon Mallal
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
- Department of Pathology, Microbiology and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
| | - Jared T Nordman
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
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6
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McElroy KA, Jung YL, Zee BM, Wang CI, Park PJ, Kuroda MI. upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks. G3 (BETHESDA, MD.) 2017; 7:625-635. [PMID: 28064188 PMCID: PMC5295607 DOI: 10.1534/g3.116.037788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022]
Abstract
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications (PTMs) of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by, these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here, we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells that are mutant for upSET We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone PTM quantification. To test whether this finding was consistent in the whole organism, we deleted the upSET coding sequence using CRISPR/Cas-9, which we found to be lethal in both sexes in flies. We were able to rescue this lethality using a tagged upSET transgene, and found that UpSET protein localizes to transcriptional start sites (TSS) of active genes throughout the genome. Misregulated heterochromatin is apparent by suppressed position effect variegation of the wm4 allele in heterozygous upSET-deleted flies. Using nascent-RNA sequencing in the upSET-mutant S2 lines, we show that this result applies to heterochromatin genes generally. Our findings support a critical role for UpSET in maintaining heterochromatin, perhaps by delimiting the active chromatin environment.
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Affiliation(s)
- Kyle A McElroy
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Youngsook L Jung
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115
| | - Barry M Zee
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Charlotte I Wang
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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7
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Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 2015; 25:445-58. [PMID: 25589440 PMCID: PMC4352887 DOI: 10.1101/gr.185579.114] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Drosophila melanogaster plays an important role in molecular,
genetic, and genomic studies of heredity, development, metabolism, behavior, and
human disease. The initial reference genome sequence reported more than a decade ago
had a profound impact on progress in Drosophila research, and
improving the accuracy and completeness of this sequence continues to be important to
further progress. We previously described improvement of the 117-Mb sequence in the
euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a
whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here,
we report an improved reference sequence of the single-copy and middle-repetitive
regions of the genome, produced using cytogenetic mapping to mitotic and polytene
chromosomes, clone-based finishing and BAC fingerprint verification, ordering of
scaffolds by alignment to cDNA sequences, incorporation of other map and sequence
data, and validation by whole-genome optical restriction mapping. These data
substantially improve the accuracy and completeness of the reference sequence and the
order and orientation of sequence scaffolds into chromosome arm assemblies.
Representation of the Y chromosome and other heterochromatic regions
is particularly improved. The new 143.9-Mb reference sequence, designated Release 6,
effectively exhausts clone-based technologies for mapping and sequencing. Highly
repeat-rich regions, including large satellite blocks and functional elements such as
the ribosomal RNA genes and the centromeres, are largely inaccessible to current
sequencing and assembly methods and remain poorly represented. Further significant
improvements will require sequencing technologies that do not depend on molecular
cloning and that produce very long reads.
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Affiliation(s)
- Roger A Hoskins
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
| | - Joseph W Carlson
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H Wan
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Soo Park
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ivonne Mendez
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel E Galle
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Benjamin W Booth
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Barret D Pfeiffer
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Reed A George
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Robert Svirskas
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Jacqueline Schein
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Maria Carmela Accardo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Elisabetta Damia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - María Méndez-Lago
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Beatriz de Pablos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Olga V Demakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Lidiya V Boldyreva
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Marco Marra
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - A Bernardo Carvalho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, CEP 21944-970, Rio de Janeiro, Brazil
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" and Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, 00185 Roma, Italy
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Gerald M Rubin
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Gary H Karpen
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Susan E Celniker
- Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
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8
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Tethering of SUUR and HP1 proteins results in delayed replication of euchromatic regions in Drosophila melanogaster polytene chromosomes. Chromosoma 2014; 124:209-20. [PMID: 25398563 DOI: 10.1007/s00412-014-0491-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/14/2014] [Accepted: 10/28/2014] [Indexed: 12/19/2022]
Abstract
We analyze how artificial targeting of Suppressor of Under-Replication (SUUR) and HP1 proteins affects DNA replication in the "open," euchromatic regions. Normally these regions replicate early in the S phase and display no binding of either SUUR or HP1. These proteins were expressed as fusions with DNA-binding domain of GAL4 and recruited to multimerized UAS integrated in three euchromatic sites of the polytene X chromosome: 3B, 8D, and 18B. Using PCNA staining as a marker of ongoing replication, we showed that targeting of SUUR(GAL4DBD) and HP1(GAL4DBD) results in delayed replication of appropriate euchromatic regions. Specifically, replication at these regions starts early, much like in the absence of the fusion proteins; however, replication completion is significantly delayed. Notably, delayed replication was insufficient to induce underreplication. Recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on expression of a mini-white reporter, found near UAS. Whereas SUUR(GAL4DBD) had no measurable influence on mini-white expression, HP1(GAL4DBD) targeting silenced mini-white, even in the absence of functional SU(VAR)3-9. Furthermore, recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on the protein composition of target regions. HP1(GAL4DBD) but not SUUR(GAL4DBD) could displace an open chromatin marker, CHRIZ, from the tethering sites.
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9
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Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster. Chromosoma 2013; 123:253-64. [DOI: 10.1007/s00412-013-0445-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 08/09/2013] [Accepted: 11/18/2013] [Indexed: 12/30/2022]
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10
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Kolesnikova TD, Posukh OV, Andreyeva EN, Bebyakina DS, Ivankin AV, Zhimulev IF. Drosophila SUUR protein associates with PCNA and binds chromatin in a cell cycle-dependent manner. Chromosoma 2012; 122:55-66. [DOI: 10.1007/s00412-012-0390-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/25/2012] [Accepted: 10/22/2012] [Indexed: 01/06/2023]
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11
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Kwon SH, Workman JL. The changing faces of HP1: From heterochromatin formation and gene silencing to euchromatic gene expression: HP1 acts as a positive regulator of transcription. Bioessays 2011; 33:280-9. [PMID: 21271610 DOI: 10.1002/bies.201000138] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Heterochromatin protein 1 (HP1) is a positive regulator of active transcription in euchromatin. HP1 was first identified in Drosophila melanogaster as a major component of heterochromatin. Most eukaryotes have at least three isoforms of HP1, which are conserved in overall structure but localize differentially to heterochromatin and euchromatin. Although initial studies revealed a key role for HP1 in heterochromatin formation and gene silencing, recent progress has shed light on additional roles for HP1 in processes such as euchromatic gene expression. Recent studies have highlighted the importance of HP1-mediated gene regulation in euchromatin. Here, we focus on recent advances in understanding the role of HP1 in active transcription in euchromatin and how modification and localization of HP1 can regulate distinct functions for this protein in different contexts.
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Affiliation(s)
- So Hee Kwon
- Stowers Institute for Medical Research, Kansas City, MO, USA
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The SUUR protein is involved in binding of SU(VAR)3-9 and methylation of H3K9 and H3K27 in chromosomes of Drosophila melanogaster. Chromosome Res 2011; 19:235-49. [PMID: 21340745 DOI: 10.1007/s10577-011-9193-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 01/30/2011] [Accepted: 02/02/2011] [Indexed: 10/25/2022]
Abstract
In the present work, we found that the SUUR protein is required for the SU(VAR)3-9 enzyme to bind to the salivary gland polytene chromosomes. The SuUR mutation results in loss of SU(VAR)3-9 on the chromosomes, whereas artificial expression of the SuUR gene restores its binding. The SUUR protein is also involved in methylation of the residues H3K9 and H3K27. However, mono-, di-, and tri-methylated forms of H3K9 and H3K27 behave differently in various chromosomal domains in response to the SuUR mutation. Euchromatin and chromosome 4 are almost completely deprived of mono-, di-, and tri-methylation of H3K9. In the chromocenter, mono-methylation is reduced, di-methylation shows no noticeable changes, and tri-methylation is lost. Furthermore, mono- and di-methylation of H3K27 are not influenced by the SuUR mutation, whereas tri-methylation is lost in the chromocenter. Artificial expression of the SuUR gene on the SuUR (-) background restores the pattern of methylated residues characteristic for the wild type.
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Kokoza EB, Kolesnikova TD, Zykov IA, Belyaeva ES, Zhimulev IF. Reversible decondensation of heterochromatin regions of Drosophila melanogaster polytene chromosomes during ectopic expression of the SuUR gene. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2009; 426:244-6. [PMID: 19650328 DOI: 10.1134/s0012496609030156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- E B Kokoza
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, ul. Akademika Lavrent'eva 10, Novosibirsk, 630090 Russia
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14
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Andreyeva EN, Kolesnikova TD, Belyaeva ES, Glaser RL, Zhimulev IF. Local DNA underreplication correlates with accumulation of phosphorylated H2Av in the Drosophila melanogaster polytene chromosomes. Chromosome Res 2008; 16:851-62. [PMID: 18704724 DOI: 10.1007/s10577-008-1244-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/05/2008] [Accepted: 06/05/2008] [Indexed: 12/29/2022]
Abstract
DNA in Drosophila melanogaster polytene chromosomes is known to be locally underreplicated in both pericentric and intercalary heterochromatin. When the SuUR gene is mutant, complete and partial suppression of underreplication are observed in intercalary and pericentric heterochromatin, respectively; in contrast, overexpression of SuUR results in stronger underreplication. Using antibodies against phosphorylated histone H2Av and flies with different levels of SuUR expression, we demonstrated a clear correlation between the extent of underreplication in specific chromosome regions and the accumulation of H2Av phosphorylated at S137 (gamma-H2AX) at the same sites. Phosphorylated H2Av is a well-established marker of DNA double-stranded breaks (DSB). Our data thus argue that DNA underreplication leads to DSBs and that DSBs accumulate as salivary gland cells progress throughout repeated endocycles. We speculate that ligation of free double-stranded DNA termini causes the formation of ectopic contacts between the underreplicated regions in heterochromatin.
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Affiliation(s)
- E N Andreyeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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15
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Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 2008; 177:1277-90. [PMID: 18039867 DOI: 10.1534/genetics.107.075069] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although "whole"-genome sequences, such as those now available for 12 Drosophila species, provide information about euchromatic DNA content, they cannot give an accurate estimate of genome sizes that include heterochromatin or repetitive DNA content. Moreover, genome sequences typically represent only one strain or isolate of a single species that does not reflect intraspecies variation. To more accurately estimate whole-genome DNA content and compare these estimates to newly assembled genomes, we used flow cytometry to measure the 2C genome values, relative to Drosophila melanogaster. We estimated genome sizes for the 12 sequenced Drosophila species as well as 91 different strains of 38 species of Drosophilidae. Significant differences in intra- and interspecific 2C genome values exist within the Drosophilidae. Furthermore, by measuring polyploid 16C ovarian follicle cell underreplication we estimated the amount of satellite DNA in each of these species. We found a strong correlation between genome size and amount of satellite underreplication. Addition and loss of heterochromatin satellite repeat elements appear to have made major contributions to the large differences in genome size observed in the Drosophilidae.
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Andreyeva EN, Kolesnikova TD, Demakova OV, Mendez-Lago M, Pokholkova GV, Belyaeva ES, Rossi F, Dimitri P, Villasante A, Zhimulev IF. High-resolution analysis of Drosophila heterochromatin organization using SuUR Su(var)3-9 double mutants. Proc Natl Acad Sci U S A 2007; 104:12819-24. [PMID: 17640911 PMCID: PMC1937550 DOI: 10.1073/pnas.0704690104] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural and functional analyses of heterochromatin are essential to understanding how heterochromatic genes are regulated and how centromeric chromatin is formed. Because the repetitive nature of heterochromatin hampers its genome analysis, new approaches need to be developed. Here, we describe how, in double mutants for Su(var)3-9 and SuUR genes encoding two structural proteins of heterochromatin, new banded heterochromatic segments appear in all polytene chromosomes due to the strong suppression of under-replication in pericentric regions. FISH on salivary gland polytene chromosomes from these double mutant larvae allows high resolution of heterochromatin mapping. In addition, immunostaining experiments with a set of antibodies against euchromatic and heterochromatic proteins reveal their unusual combinations in the newly appeared segments: binding patterns for HP1 and HP2 are coincident, but both are distinct from H3diMetK9 and H4triMetK20. In several regions, partial overlapping staining is observed for the proteins characteristic of active chromatin RNA Pol II, H3triMetK4, Z4, and JIL1, the boundary protein BEAF, and the heterochromatin-enriched proteins HP1, HP2, and SU(VAR)3-7. The exact cytological position of the centromere of chromosome 3 was visualized on salivary gland polytene chromosomes by using the centromeric dodeca satellite and the centromeric protein CID. This region is enriched in H3diMetK9 and H4triMetK20 but is devoid of other proteins analyzed.
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Affiliation(s)
- Eugenia N. Andreyeva
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Tatyana D. Kolesnikova
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga V. Demakova
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Maria Mendez-Lago
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autonóma de Madrid, Cantoblanco, 28049 Madrid, Spain; and
| | - Galina V. Pokholkova
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S. Belyaeva
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Fabrizio Rossi
- Istituto Pasteur–Fondazione Cenci Bolognetti and Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Via dei Sardi, 70, 00185 Rome, Italy
| | - Patrizio Dimitri
- Istituto Pasteur–Fondazione Cenci Bolognetti and Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Via dei Sardi, 70, 00185 Rome, Italy
| | - Alfredo Villasante
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autonóma de Madrid, Cantoblanco, 28049 Madrid, Spain; and
| | - Igor F. Zhimulev
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- To whom correspondence should be addressed at:
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 10, Novosibirsk 630090, Russia. E-mail:
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