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Zykova T, Maltseva M, Goncharov F, Boldyreva L, Pokholkova G, Kolesnikova T, Zhimulev I. The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophilamelanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication. Cells 2021; 10:2809. [PMID: 34831030 PMCID: PMC8616060 DOI: 10.3390/cells10112809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Although heterochromatin makes up 40% of the Drosophila melanogaster genome, its organization remains little explored, especially in polytene chromosomes, as it is virtually not represented in them due to underreplication. Two all-new approaches were used in this work: (i) with the use of a newly synthesized Drosophila line that carries three mutations, Rif11, SuURES and Su(var)3-906, suppressing the underreplication of heterochromatic regions, we obtained their fullest representation in polytene chromosomes and described their structure; (ii) 20 DNA fragments with known positions on the physical map as well as molecular genetic features of the genome (gene density, histone marks, heterochromatin proteins, origin recognition complex proteins, replication timing sites and satellite DNAs) were mapped in the newly polytenized heterochromatin using FISH and bioinformatics data. The borders of the heterochromatic regions and variations in their positions on arm 3L have been determined for the first time. The newly polytenized heterochromatic material exhibits two main types of morphology: a banding pattern (locations of genes and short satellites) and reticular chromatin (locations of large blocks of satellite DNA). The locations of the banding and reticular polytene heterochromatin was determined on the physical map.
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Affiliation(s)
- Tatyana Zykova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Mariya Maltseva
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Fedor Goncharov
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Lidia Boldyreva
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Galina Pokholkova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
| | - Tatyana Kolesnikova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
- Laboratory of Structural, Functional and Comparative Genomics Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Igor Zhimulev
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia; (T.Z.); (M.M.); (F.G.); (L.B.); (G.P.); (T.K.)
- Laboratory of Structural, Functional and Comparative Genomics Novosibirsk State University, 630090 Novosibirsk, Russia
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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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Kolesnikova TD. Banding Pattern of Polytene Chromosomes as a Representation of Universal Principles of Chromatin Organization into Topological Domains. BIOCHEMISTRY (MOSCOW) 2018; 83:338-349. [PMID: 29626921 DOI: 10.1134/s0006297918040053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drosophila polytene chromosomes are widely used as a model of eukaryotic interphase chromosomes. The most noticeable feature of polytene chromosome is transverse banding associated with alternation of dense stripes (dark or black bands) and light diffuse areas that encompass alternating less compact gray bands and interbands visible with an electron microscope. In recent years, several approaches have been developed to predict location of morphological structures of polytene chromosomes based on the distribution of proteins on the molecular map of Drosophila genome. Comparison of these structures with the results of analysis of the three-dimensional chromatin organization by the Hi-C method indicates that the morphology of polytene chromosomes represents direct visualization of the interphase nucleus spatial organization into topological domains. Compact black bands correspond to the extended topological domains of inactive chromatin, while interbands are the barriers between the adjacent domains. Here, we discuss the prospects of using polytene chromosomes to study mechanisms of spatial organization of interphase chromosomes, as well as their dynamics and evolution.
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Affiliation(s)
- T D Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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Stadler MR, Haines JE, Eisen MB. Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo. eLife 2017; 6:29550. [PMID: 29148971 PMCID: PMC5739541 DOI: 10.7554/elife.29550] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/13/2017] [Indexed: 11/13/2022] Open
Abstract
High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains.
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Affiliation(s)
- Michael R Stadler
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Jenna E Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Michael B Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States.,Department of Integrative Biology, University of California, Berkeley, CA, United States.,Howard Hughes Medical Institute, Berkeley, CA, United States
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Zhimulev IF, Zykova TY, Goncharov FP, Khoroshko VA, Demakova OV, Semeshin VF, Pokholkova GV, Boldyreva LV, Demidova DS, Babenko VN, Demakov SA, Belyaeva ES. Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster. PLoS One 2014; 9:e101631. [PMID: 25072930 PMCID: PMC4114487 DOI: 10.1371/journal.pone.0101631] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/09/2014] [Indexed: 12/18/2022] Open
Abstract
Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5' ends of housekeeping genes. As a rule, interbands display preferential "head-to-head" orientation of genes. They are enriched for "broad" class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5'-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called "grey" bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.
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Affiliation(s)
- Igor F. Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| | - Tatyana Yu. Zykova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Fyodor P. Goncharov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Varvara A. Khoroshko
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga V. Demakova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valeriy F. Semeshin
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Galina V. Pokholkova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lidiya V. Boldyreva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Darya S. Demidova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir N. Babenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey A. Demakov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena S. Belyaeva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Zhimulev IF, Belyaeva ES, Vatolina TY, Demakov SA. Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA-binding protein occupancy. Bioessays 2012; 34:498-508. [PMID: 22419120 DOI: 10.1002/bies.201100142] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome-wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with "active" chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non-polytene chromosomes.
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Affiliation(s)
- Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia.
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Demakov SA, Vatolina TY, Babenko VN, Semeshin VF, Belyaeva ES, Zhimulev IF. Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. BMC Genomics 2011; 12:566. [PMID: 22093916 PMCID: PMC3240664 DOI: 10.1186/1471-2164-12-566] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/18/2011] [Indexed: 12/20/2022] Open
Abstract
Background Despite many efforts, little is known about distribution and interactions of chromatin proteins which contribute to the specificity of chromomeric organization of interphase chromosomes. To address this issue, we used publicly available datasets from several recent Drosophila genome-wide mapping and annotation projects, in particular, those from modENCODE project, and compared molecular organization of 13 interband regions which were accurately mapped previously. Results Here we demonstrate that in interphase chromosomes of Drosophila cell lines, the interband regions are enriched for a specific set of proteins generally characteristic of the "open" chromatin (RNA polymerase II, CHRIZ (CHRO), BEAF-32, BRE1, dMI-2, GAF, NURF301, WDS and TRX). These regions also display reduced nucleosome density, histone H1 depletion and pronounced enrichment for ORC2, a pre-replication complex component. Within the 13 interband regions analyzed, most were around 3-4 kb long, particularly those where many of said protein features were present. We estimate there are about 3500 regions with similar properties in chromosomes of D. melanogaster cell lines, which fits quite well the number of cytologically observed interbands in salivary gland polytene chromosomes. Conclusions Our observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a universal principle of interphase chromosome organization.
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Affiliation(s)
- Sergey A Demakov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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