1
|
Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
2
|
Zhuravlev AV, Zakharov GA, Anufrieva EV, Medvedeva AV, Nikitina EA, Savvateeva-Popova EV. Chromatin Structure and "DNA Sequence View": The Role of Satellite DNA in Ectopic Pairing of the Drosophila X Polytene Chromosome. Int J Mol Sci 2021; 22:8713. [PMID: 34445413 PMCID: PMC8395981 DOI: 10.3390/ijms22168713] [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: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Chromatin 3D structure plays a crucial role in regulation of gene activity. Previous studies have envisioned spatial contact formations between chromatin domains with different epigenetic properties, protein compositions and transcription activity. This leaves specific DNA sequences that affect chromosome interactions. The Drosophila melanogaster polytene chromosomes are involved in non-allelic ectopic pairing. The mutant strain agnts3, a Drosophila model for Williams-Beuren syndrome, has an increased frequency of ectopic contacts (FEC) compared to the wild-type strain Canton-S (CS). Ectopic pairing can be mediated by some specific DNA sequences. In this study, using our Homology Segment Analysis software, we estimated the correlation between FEC and frequency of short matching DNA fragments (FMF) for all sections of the X chromosome of Drosophila CS and agnts3 strains. With fragment lengths of 50 nucleotides (nt), CS showed a specific FEC-FMF correlation for 20% of the sections involved in ectopic contacts. The correlation was unspecific in agnts3, which may indicate the alternative epigenetic mechanisms affecting FEC in the mutant strain. Most of the fragments that specifically contributed to FMF were related to 1.688 or 372-bp middle repeats. Thus, middle repetitive DNA may serve as an organizer of ectopic pairing.
Collapse
Affiliation(s)
- Aleksandr V. Zhuravlev
- Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia; (G.A.Z.); (A.V.M.); (E.A.N.); (E.V.S.-P.)
| | - Gennadii A. Zakharov
- Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia; (G.A.Z.); (A.V.M.); (E.A.N.); (E.V.S.-P.)
- EPAM Systems Inc., Saint Petersburg 197110, Russia
| | - Ekaterina V. Anufrieva
- Faculty of Biology, Herzen State Pedagogical University of Russia, 191186 Saint Petersburg, Russia;
| | - Anna V. Medvedeva
- Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia; (G.A.Z.); (A.V.M.); (E.A.N.); (E.V.S.-P.)
| | - Ekaterina A. Nikitina
- Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia; (G.A.Z.); (A.V.M.); (E.A.N.); (E.V.S.-P.)
- Faculty of Biology, Herzen State Pedagogical University of Russia, 191186 Saint Petersburg, Russia;
| | - Elena V. Savvateeva-Popova
- Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia; (G.A.Z.); (A.V.M.); (E.A.N.); (E.V.S.-P.)
| |
Collapse
|
3
|
Golczyk H, Limanówka A, Uchman-Książek A. Pericentromere clustering in Tradescantia section Rhoeo involves self-associations of AT- and GC-rich heterochromatin fractions, is developmentally regulated, and increases during differentiation. Chromosoma 2020; 129:227-242. [PMID: 32681184 PMCID: PMC7666280 DOI: 10.1007/s00412-020-00740-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Abstract
A spectacular but poorly recognized nuclear repatterning is the association of heterochromatic domains during interphase. Using base-specific fluorescence and extended-depth-of-focus imaging, we show that the association of heterochromatic pericentromeres composed of AT- and GC-rich chromatin occurs on a large scale in cycling meiotic and somatic cells and during development in ring- and bivalent-forming Tradescantia spathacea (section Rhoeo) varieties. The mean number of pericentromere AT-rich domains per root meristem nucleus was ca. half the expected diploid number in both varieties, suggesting chromosome pairing via (peri)centromeric regions. Indeed, regular pairing of AT-rich domains was observed. The AT- and GC-rich associations in differentiated cells contributed to a significant reduction of the mean number of the corresponding foci per nucleus in relation to root meristem. Within the first 10 mm of the root, the pericentromere attraction was in progress, as if it was an active process and involved both AT- and GC-rich associations. Complying with Rabl arrangement, the pericentromeres preferentially located on one nuclear pole, clustered into diverse configurations. Among them, a strikingly regular one with 5-7 ring-arranged pericentromeric AT-rich domains may be potentially engaged in chromosome positioning during mitosis. The fluorescent pattern of pachytene meiocytes and somatic nuclei suggests the existence of a highly prescribed ring/chain type of chromocenter architecture with side-by-side arranged pericentromeric regions. The dynamics of pericentromere associations together with their non-random location within nuclei was compared with nuclear architecture in other organisms, including the widely explored Arabidopsis model.
Collapse
Affiliation(s)
- Hieronim Golczyk
- Department of Molecular Biology, Institute of Biological Sciences, John Paul II Catholic University of Lublin, Konstantynów 1i, 20-708, Lublin, Poland.
| | - Arleta Limanówka
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
| | - Anna Uchman-Książek
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
| |
Collapse
|
4
|
Hjelmen CE, Holmes VR, Burrus CG, Piron E, Mynes M, Garrett MA, Blackmon H, Johnston JS. Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA. Evolution 2020; 74:1423-1436. [PMID: 32438451 DOI: 10.1111/evo.14022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/05/2020] [Accepted: 05/17/2020] [Indexed: 12/11/2022]
Abstract
Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus and leverage these data to propose a model for estimating the rate at which additional DNA is accumulated as heterochromatin and euchromatin and also predict the minimum genome size for Drosophila. According to comparative phylogenetic approaches, the rates of change of heterochromatin differ strikingly between Drosophila subgenera. Although these subgenera differ in karyotype, there were no differences by chromosome number, suggesting other structural changes may influence accumulation of heterochromatin. Measurements were taken for both sexes, allowing the visualization of genome size and heterochromatin changes for the hypothetical path of XY sex chromosome differentiation. Additionally, the model presented here estimates a minimum genome size in Sophophora remarkably close to the smallest insect genome measured to date, in a species over 200 million years diverged from Drosophila.
Collapse
Affiliation(s)
- Carl E Hjelmen
- Department of Biology, Texas A&M University, College Station, Texas.,Department of Entomology, Texas A&M University, College Station, Texas
| | | | - Crystal G Burrus
- Department of Biology, Texas A&M University, College Station, Texas
| | - Elizabeth Piron
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Melissa Mynes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Margaret A Garrett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas
| | | |
Collapse
|
5
|
Dialynas G, Delabaere L, Chiolo I. Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes. Exp Biol Med (Maywood) 2019; 244:1362-1371. [PMID: 31364400 PMCID: PMC6880141 DOI: 10.1177/1535370219862282] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022] Open
Abstract
Repairing DNA double-strand breaks is particularly challenging in pericentromeric heterochromatin, where the abundance of repeated sequences exacerbates the risk of ectopic recombination. In Drosophila Kc cells, accurate homologous recombination repair of heterochromatic double-strand breaks relies on the relocalization of repair sites to the nuclear periphery before Rad51 recruitment and strand invasion. This movement is driven by Arp2/3-dependent nuclear actin filaments and myosins’ ability to walk along them. Conserved mechanisms enable the relocalization of heterochromatic repair sites in mouse cells, and defects in these pathways lead to massive ectopic recombination in heterochromatin and chromosome rearrangements. In Drosophila polytene chromosomes, extensive DNA movement is blocked by a stiff structure of chromosome bundles. Repair pathways in this context are poorly characterized, and whether heterochromatic double-strand breaks relocalize in these cells is unknown. Here, we show that damage in heterochromatin results in relaxation of the heterochromatic chromocenter, consistent with a dynamic response. Arp2/3, the Arp2/3 activator Scar, and the myosin activator Unc45, are required for heterochromatin stability in polytene cells, suggesting that relocalization enables heterochromatin repair also in this tissue. Together, these studies reveal critical roles for actin polymerization and myosin motors in heterochromatin repair and genome stability across different organisms and tissue types.
Collapse
Affiliation(s)
- George Dialynas
- Department of Molecular and Computational Biology,
University
of Southern California, Los Angeles
90089, USA
| | - Laetitia Delabaere
- Department of Molecular and Computational Biology,
University
of Southern California, Los Angeles
90089, USA
| | - Irene Chiolo
- Department of Molecular and Computational Biology,
University
of Southern California, Los Angeles
90089, USA
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- T D Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| |
Collapse
|
7
|
Khoroshko VA, Levitsky VG, Zykova TY, Antonenko OV, Belyaeva ES, Zhimulev IF. Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes. PLoS One 2016; 11:e0157147. [PMID: 27300486 PMCID: PMC4907538 DOI: 10.1371/journal.pone.0157147] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/25/2016] [Indexed: 12/28/2022] Open
Abstract
Late-replicating domains (intercalary heterochromatin) in the Drosophila genome display a number of features suggesting their organization is quite unique. Typically, they are quite large and encompass clusters of functionally unrelated tissue-specific genes. They correspond to the topologically associating domains and conserved microsynteny blocks. Our study aims at exploring further details of molecular organization of intercalary heterochromatin and has uncovered surprising heterogeneity of chromatin composition in these regions. Using the 4HMM model developed in our group earlier, intercalary heterochromatin regions were found to host chromatin fragments with a particular epigenetic profile. Aquamarine chromatin fragments (spanning 0.67% of late-replicating regions) are characterized as a class of sequences that appear heterogeneous in terms of their decompactization. These fragments are enriched with enhancer sequences and binding sites for insulator proteins. They likely mark the chromatin state that is related to the binding of cis-regulatory proteins. Malachite chromatin fragments (11% of late-replicating regions) appear to function as universal transitional regions between two contrasting chromatin states. Namely, they invariably delimit intercalary heterochromatin regions from the adjacent active chromatin of interbands. Malachite fragments also flank aquamarine fragments embedded in the repressed chromatin of late-replicating regions. Significant enrichment of insulator proteins CP190, SU(HW), and MOD2.2 was observed in malachite chromatin. Neither aquamarine nor malachite chromatin types appear to correlate with the positions of highly conserved non-coding elements (HCNE) that are typically replete in intercalary heterochromatin. Malachite chromatin found on the flanks of intercalary heterochromatin regions tends to replicate earlier than the malachite chromatin embedded in intercalary heterochromatin. In other words, there exists a gradient of replication progressing from the flanks of intercalary heterochromatin regions center-wise. The peculiar organization and features of replication in large late-replicating regions are discussed as possible factors shaping the evolutionary stability of intercalary heterochromatin.
Collapse
Affiliation(s)
| | - Viktor G. Levitsky
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Tatyana Yu. Zykova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | | | - Elena S. Belyaeva
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
8
|
Andreyenkova NG, Kolesnikova TD, Makunin IV, Pokholkova GV, Boldyreva LV, Zykova TY, Zhimulev IF, Belyaeva ES. Late replication domains are evolutionary conserved in the Drosophila genome. PLoS One 2013; 8:e83319. [PMID: 24391753 PMCID: PMC3877026 DOI: 10.1371/journal.pone.0083319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022] Open
Abstract
Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.
Collapse
Affiliation(s)
- Natalya G. Andreyenkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor V. Makunin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Research Computing Centre, The University of Queensland, Brisbane, St Lucia, QLD, Australia
| | - Galina V. Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lidiya V. Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana Yu. Zykova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Elena S. Belyaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
9
|
Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin. Chromosoma 2012; 121:573-83. [PMID: 23015267 DOI: 10.1007/s00412-012-0382-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/12/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
Abstract
In salivary gland polytene chromosomes of Drosophila melanogaster, the regions of intercalary heterochromatin are characterized by late replication, under-replication, and genetic silencing. Using Gal4/UAS system, we induced transcription of sequences adjacent to transgene insertions in the band 11A6-9. This activation resulted in a loss of "silent" and appearance of "active" epigenetic marks, recruitment of RNA polymerase II, and formation of a puff. The activated region is now early replicating and shows increased level of DNA polytenization. Notably, all these changes are restricted to the area around the inserts, whereas the rest of the band remains inactive and late replicating. Although only a short area near the insertion site is transcribed, it results in an "open" chromatin conformation in a much broader region. We conclude that regions of intercalary heterochromatin do not form stand-alone units of late replication and under-replication. Every part of such regions can be activated and polytenized independently of other parts.
Collapse
|
10
|
Late replication domains in polytene and non-polytene cells of Drosophila melanogaster. PLoS One 2012; 7:e30035. [PMID: 22253867 PMCID: PMC3254639 DOI: 10.1371/journal.pone.0030035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 12/08/2011] [Indexed: 12/20/2022] Open
Abstract
In D. melanogaster polytene chromosomes, intercalary heterochromatin (IH) appears as large dense bands scattered in euchromatin and comprises clusters of repressed genes. IH displays distinctly low gene density, indicative of their particular regulation. Genes embedded in IH replicate late in the S phase and become underreplicated. We asked whether localization and organization of these late-replicating domains is conserved in a distinct cell type. Using published comprehensive genome-wide chromatin annotation datasets (modENCODE and others), we compared IH organization in salivary gland cells and in a Kc cell line. We first established the borders of 60 IH regions on a molecular map, these regions containing underreplicated material and encompassing ∼12% of Drosophila genome. We showed that in Kc cells repressed chromatin constituted 97% of the sequences that corresponded to IH bands. This chromatin is depleted for ORC-2 binding and largely replicates late. Differences in replication timing between the cell types analyzed are local and affect only sub-regions but never whole IH bands. As a rule such differentially replicating sub-regions display open chromatin organization, which apparently results from cell-type specific gene expression of underlying genes. We conclude that repressed chromatin organization of IH is generally conserved in polytene and non-polytene cells. Yet, IH domains do not function as transcription- and replication-regulatory units, because differences in transcription and replication between cell types are not domain-wide, rather they are restricted to small “islands” embedded in these domains. IH regions can thus be defined as a special class of domains with low gene density, which have narrow temporal expression patterns, and so displaying relatively conserved organization.
Collapse
|
11
|
Drosopoulou E, Nestel D, Nakou I, Kounatidis I, Papadopoulos NT, Bourtzis K, Mavragani-Tsipidou P. Cytogenetic analysis of the Ethiopian fruit fly Dacus ciliatus (Diptera: Tephritidae). Genetica 2011; 139:723-32. [PMID: 21505759 DOI: 10.1007/s10709-011-9575-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 04/02/2011] [Indexed: 11/25/2022]
Abstract
The Ethiopian fruit fly, Dacus ciliatus, is an important pest of cucurbits, which recently invaded the Middle East. The genetics and cytogenetics of D. ciliatus have been scarcely studied. Such information is, however, an essential basis for understanding the biology of insect pests, as well as for the design of modern control strategies. We report here the mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of this species. The mitotic metaphase complement consists of six pairs of chromosomes, including one pair of heteromorphic sex (XX/XY) chromosomes. The heterogametic sex is ascribed to the male. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes (10 polytene arms), which correspond to the five autosomes of the mitotic nuclei, and a heterochromatic mass corresponding to the sex chromosomes. Banding patterns, as well as the most characteristic features and prominent landmarks of each polytene chromosome are presented and discussed. Chromosomal homologies between D. ciliatus and Bactrocera oleae are proposed by comparing chromosome banding patterns and by in situ hybridization of the hsp70 gene.
Collapse
Affiliation(s)
- E Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki (AUTH), 54124 Thessaloniki, Greece
| | | | | | | | | | | | | |
Collapse
|
12
|
Sharakhova MV, George P, Brusentsova IV, Leman SC, Bailey JA, Smith CD, Sharakhov IV. Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics 2010; 11:459. [PMID: 20684766 PMCID: PMC3091655 DOI: 10.1186/1471-2164-11-459] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 08/04/2010] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized. RESULTS To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin. CONCLUSIONS Our results demonstrate that Anopheles polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the An. gambiae heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.
Collapse
|
13
|
Smith MB, Weiler KS. Drosophila D1 overexpression induces ectopic pairing of polytene chromosomes and is deleterious to development. Chromosoma 2010; 119:287-309. [PMID: 20127347 DOI: 10.1007/s00412-010-0257-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 12/24/2009] [Accepted: 01/06/2010] [Indexed: 11/30/2022]
Abstract
Eukaryotic genomes function in the context of chromatin, but the roles of most nonhistone chromosomal proteins are far from understood. The D1 protein of Drosophila is an example of a chromosomal protein that has been fairly well characterized biochemically, but has nevertheless eluded functional description. To this end, we have undertaken a gain-of-function genetical analysis of D1, utilizing the GAL4-UAS system. We determined that ubiquitous overexpression of D1 using the Act5C- or tubP-GAL4 drivers was lethal to the organism during larval growth. We also ectopically expressed D1 in a tissue-limited manner using other GAL4 drivers. In general, ectopic D1 was observed to inhibit differentiation and/or development. We observed effects on pattern formation of the adult eye, bristle morphogenesis, and spermatogenesis. These phenotypes may be the consequence of misregulation of D1 target genes. A surprising result was obtained when D1 was overexpressed in the third instar salivary gland. The polytene chromosomes exhibited numerous ectopic associations such that spreading of the chromosome arms was precluded. We mapped the sites of ectopic pairing along the polytene chromosome arms, and found a correlation with sites of intercalary heterochromatin. We speculate that these sites comprise the natural targets of D1 protein activity and that D1 is involved in the ectopic pairing observed for wild-type chromosomes. Together, our data suggest that D1 may influence multiple biochemical activities within the nucleus.
Collapse
Affiliation(s)
- Marissa B Smith
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | | |
Collapse
|
14
|
Kolesnikova TD, Demakov SA, Ivankin AV, Andreenkova NG, Zhimulev IF. The mutation of the Suppressor of Underreplication gene does not affect the replication fork rate in the Drosophila melanogaster salivary gland polytene chromosomes. DOKL BIOCHEM BIOPHYS 2009; 427:175-8. [PMID: 19817130 DOI: 10.1134/s1607672909040024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- T D Kolesnikova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy ofSciences, pr Akademika Lavrent'eva 10, Novosibirsk 630090, Russia
| | | | | | | | | |
Collapse
|
15
|
Dulev S, de Renty C, Mehta R, Minkov I, Schwob E, Strunnikov A. Essential global role of CDC14 in DNA synthesis revealed by chromosome underreplication unrecognized by checkpoints in cdc14 mutants. Proc Natl Acad Sci U S A 2009; 106:14466-71. [PMID: 19666479 PMCID: PMC2723162 DOI: 10.1073/pnas.0900190106] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Indexed: 12/27/2022] Open
Abstract
The CDC14 family of multifunctional evolutionarily conserved phosphatases includes major regulators of mitosis in eukaryotes and of DNA damage response in humans. The CDC14 function is also crucial for accurate chromosome segregation, which is exemplified by its absolute requirement in yeast for the anaphase segregation of nucleolar organizers; however the nature of this essential pathway is not understood. Upon investigation of the rDNA nondisjunction phenomenon, it was found that cdc14 mutants fail to complete replication of this locus. Moreover, other late-replicating genomic regions (10% of the genome) are also underreplicated in cdc14 mutants undergoing anaphase. This selective genome-wide replication defect is due to dosage insufficiency of replication factors in the nucleus, which stems from two defects, both contingent on the reduced CDC14 function in the preceding mitosis. First, a constitutive nuclear import defect results in a drastic dosage decrease for those replication proteins that are regulated by nuclear transport. Particularly, essential RPA subunits display both lower mRNA and protein levels, as well as abnormal cytoplasmic localization. Second, the reduced transcription of MBF and SBF-controlled genes in G1 leads to the reduction in protein levels of many proteins involved in DNA replication. The failure to complete replication of late replicons is the primary reason for chromosome nondisjunction upon CDC14 dysfunction. As the genome-wide slow-down of DNA replication does not trigger checkpoints [Lengronne A, Schwob E (2002) Mol Cell 9:1067-1078], CDC14 mutations pose an overwhelming challenge to genome stability, both generating chromosome damage and undermining the checkpoint control mechanisms.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Anaphase/genetics
- Blotting, Western
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Nucleus/metabolism
- Chromatin Immunoprecipitation
- Chromosome Segregation
- Chromosomes, Fungal/genetics
- DNA Damage
- DNA Replication
- DNA, Fungal/biosynthesis
- DNA, Fungal/genetics
- DNA, Ribosomal/genetics
- G1 Phase/genetics
- Genes, Essential/genetics
- Genes, Essential/physiology
- Genome, Fungal/genetics
- Genome-Wide Association Study
- Models, Biological
- Mutation
- Protein Binding
- Protein Tyrosine Phosphatases/genetics
- Protein Tyrosine Phosphatases/metabolism
- Replication Protein A/genetics
- Replication Protein A/metabolism
- S Phase/genetics
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
Collapse
Affiliation(s)
- Stanimir Dulev
- National Institutes of Health, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892
- University of Plovdiv, Plovdiv 4000, Bulgaria
| | - Christelle de Renty
- Institute of Molecular Genetics, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, University Montpellier 2, 34293, France; and
| | - Rajvi Mehta
- National Institutes of Health, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892
| | - Ivan Minkov
- University of Plovdiv, Plovdiv 4000, Bulgaria
| | - Etienne Schwob
- Institute of Molecular Genetics, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, University Montpellier 2, 34293, France; and
| | - Alexander Strunnikov
- National Institutes of Health, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892
| |
Collapse
|
16
|
Andreyenkova NG, Kokoza EB, Semeshin VF, Belyaeva ES, Demakov SA, Pindyurin AV, Andreyeva EN, Volkova EI, Zhimulev IF. Localization and characteristics of DNA underreplication zone in the 75C region of intercalary heterochromatin in Drosophila melanogaster polytene chromosomes. Chromosoma 2009; 118:747-61. [PMID: 19685068 DOI: 10.1007/s00412-009-0232-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/16/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
Abstract
In Drosophila polytene chromosomes, regions of intercalary heterochromatin are scattered throughout the euchromatic arms. Here, we present data on the first fine analysis of the individual intercalary heterochromatin region, 75C1-2, located in the 3L chromosome. By using electron microscopy, we demonstrated that this region appears as three closely adjacent condensed bands. Mapping of the region on the physical map by means of the chromosomal rearrangements with known breakpoints showed that the length of the region is about 445 kb. Although it seems that the SUUR protein binds to the whole 75C1-2 region, the proximal part of the region is fully polytenized, so the DNA underreplication zone is asymmetric and located in the distal half of the region. Finally, we speculate that intercalary heterochromatin regions of Drosophila polytene chromosomes are organized into three different types with respect to the localization of the underreplication zone.
Collapse
Affiliation(s)
- Natalya G Andreyenkova
- Department of Molecular and Cellular Biology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Batista MRD, Ananina G, Azeredo-Espin AML, Klaczko LB. Photographic map of the polytene chromosomes of Cochliomyia hominivorax. MEDICAL AND VETERINARY ENTOMOLOGY 2009; 23 Suppl 1:92-97. [PMID: 19335835 DOI: 10.1111/j.1365-2915.2008.00775.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) is one of the most important myiasis-causing flies and is responsible for severe economic losses to the livestock industry throughout the Neotropical region. A polytene chromosome map is an invaluable tool for the genetic analysis and manipulation of any species because it allows the integration of physical and genetic maps. Cochliomyia hominivorax has a diploid number of 12 chromosomes (2n = 12): five pairs of autosomes and one pair of sex chromosomes (XX/XY), which do not polytenize. We created a new photomap of the polytene chromosomes of C. hominivorax describing its five autosomes (chromosomes 2-6). Pupal trichogen cells, which have chromosomes with a high degree of polytenization, were used to elaborate this map. The photomap was made by comparing 20 different nuclei and choosing, for each chromosome segment, the region with the highest resolution. Thus, we present a new photomap of the five autosomes of this species, with a total resolution of 1450 bands.
Collapse
Affiliation(s)
- M R D Batista
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP, Campinas, São Paulo, Brazil
| | | | | | | |
Collapse
|
18
|
Kounatidis I, Papadopoulos N, Bourtzis K, Mavragani-Tsipidou P. Genetic and cytogenetic analysis of the fruit fly Rhagoletis cerasi (Diptera: Tephritidae). Genome 2008; 51:479-91. [PMID: 18545272 DOI: 10.1139/g08-032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The European cherry fruit fly, Rhagoletis cerasi, is a major agricultural pest for which biological, genetic, and cytogenetic information is limited. We report here a cytogenetic analysis of 4 natural Greek populations of R. cerasi, all of them infected with the endosymbiotic bacterium Wolbachia pipientis. The mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of this pest species are presented here. The mitotic metaphase complement consists of 6 pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement has shown a total of 5 long chromosomes (10 polytene arms) that correspond to the 5 autosomes of the mitotic nuclei and a heterochromatic mass corresponding to the sex chromosomes. The most prominent landmarks of each polytene chromosome, the "weak points", and the unusual asynapsis of homologous pairs of polytene chromosomes at certain regions of the polytene elements are also presented and discussed.
Collapse
Affiliation(s)
- Ilias Kounatidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | | | | | | |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- E N Andreyeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | | | | | | | | |
Collapse
|
20
|
Volkova EI, Belyakin SN, Belyaeva ES, Zhimulev IF. Distribution of induced chromosome rearrangement breakpoints along the chromosome length and the problem of intercalary heterochromatin in Drosophila melanogaster. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408060033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Belyaeva ES, Andreyeva EN, Belyakin SN, Volkova EI, Zhimulev IF. Intercalary heterochromatin in polytene chromosomes of Drosophila melanogaster. Chromosoma 2008; 117:411-8. [PMID: 18491121 DOI: 10.1007/s00412-008-0163-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 03/06/2008] [Accepted: 04/10/2008] [Indexed: 01/06/2023]
Abstract
Intercalary heterochromatin consists of extended chromosomal domains which are interspersed throughout the euchromatin and contain silent genetic material. These domains comprise either clusters of functionally unrelated genes or tandem gene duplications and possibly stretches of noncoding sequences. Strong repression of genetic activity means that intercalary heterochromatin displays properties that are normally attributable to classic pericentric heterochromatin: high compaction, late replication and underreplication in polytene chromosomes, and the presence of heterochromatin-specific proteins. Late replication and underreplication occurs when the suppressor of underreplication protein is present in intercalary heterochromatic regions. Intercalary heterochromatin underreplication in polytene chromosomes results in free double-stranded ends of DNA molecules; ligation of these free ends is the most likely mechanism for ectopic pairing between intercalary heterochromatic and pericentric heterochromatic regions. No support has been found for the view that the frequency of chromosome aberrations is elevated in intercalary heterochromatin.
Collapse
Affiliation(s)
- E S Belyaeva
- Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | | | | | | | | |
Collapse
|
22
|
Pindyurin AV, Boldyreva LV, Shloma VV, Kolesnikova TD, Pokholkova GV, Andreyeva EN, Kozhevnikova EN, Ivanoschuk IG, Zarutskaya EA, Demakov SA, Gorchakov AA, Belyaeva ES, Zhimulev IF. Interaction between theDrosophilaheterochromatin proteins SUUR and HP1. J Cell Sci 2008; 121:1693-703. [DOI: 10.1242/jcs.018655] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
SUUR (Suppressor of Under-Replication) protein is responsible for late replication and, as a consequence, for DNA underreplication of intercalary and pericentric heterochromatin in Drosophila melanogaster polytene chromosomes. However, the mechanism by which SUUR slows down the replication process is not clear. To identify possible partners for SUUR we performed a yeast two-hybrid screen using full-length SUUR as bait. This identified HP1, the well-studied heterochromatin protein, as a strong SUUR interactor. Furthermore, we have determined that the central region of SUUR is necessary and sufficient for interaction with the C-terminal part of HP1, which contains the hinge and chromoshadow domains. In addition, recruitment of SUUR to ectopic HP1 sites on chromosomes provides evidence for their association in vivo. Indeed, we found that the distributions of SUUR and HP1 on polytene chromosomes are interdependent: both absence and overexpression of HP1 prevent SUUR from chromosomal binding, whereas SUUR overexpression causes redistribution of HP1 to numerous sites occupied by SUUR. Finally, HP1 binds to intercalary heterochromatin when histone methyltransferase activity of SU(VAR)3-9 is increased. We propose that interaction with HP1 is crucial for the association of SUUR with chromatin.
Collapse
Affiliation(s)
- Alexey V. Pindyurin
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Lidiya V. Boldyreva
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Victor V. Shloma
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Tatiana D. Kolesnikova
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Galina V. Pokholkova
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Evgeniya N. Andreyeva
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena N. Kozhevnikova
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Igor G. Ivanoschuk
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ekaterina A. Zarutskaya
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergey A. Demakov
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Andrey A. Gorchakov
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S. Belyaeva
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Igor F. Zhimulev
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk 630090, Russia
| |
Collapse
|
23
|
Kolesnikova TD, Andreeva EN, Pindyurin AV, Ananko NG, Belyakin SN, Shloma VV, Yurlova AA, Makunin IV, Pokholkova GV, Volkova EI, Zarutskaya EA, Kokoza EB, Semeshin VF, Belyaeva ES, Zhimulev IF. Contribution of the SuUR gene to the organization of epigenetically repressed regions of Drosophila melanogaster chromosomes. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406080011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|