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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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2
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Tselykh TV, Roos C, Heino TI. The mitochondrial ribosome-specific MrpL55 protein is essential in Drosophila and dynamically required during development. Exp Cell Res 2005; 307:354-66. [PMID: 15894314 DOI: 10.1016/j.yexcr.2005.03.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Revised: 03/22/2005] [Accepted: 03/24/2005] [Indexed: 10/25/2022]
Abstract
We report on the essential Drosophila mRpL55 gene conserved exclusively in metazoans. Null mRpL55 mutants did not grow after hatching, moved slowly and died as first instar larvae. MrpL55 is similar to mammalian MRPL55, a protein that, in a large-scale mass spectrometry study, has been found as a mitoribosome-specific large subunit protein. We showed that MrpL55 was localised to the mitochondrion in S2 cells and tissues and was enriched in cells with a higher protein synthesis activity. The MrpL55 protein contains a KOW-like motif present in proteins with a role in transcriptional anti-termination and regulation of translation. Modulation of mRpL55 expression level is critical for development. Somatic clonal analysis showed that MrpL55 was not required in larval eye imaginal discs but required in pupal discs apparently during the second mitotic wave. Therefore, our results showed that the MrpL55 protein acts dynamically in the cell during development. We propose that MrpL55 is involved in Drosophila mitochondrial biogenesis and G2/M phase cell cycle progression.
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MESH Headings
- Amino Acid Motifs/genetics
- Amino Acid Sequence
- Animals
- Animals, Genetically Modified
- Cell Line
- Cloning, Molecular
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila Proteins/physiology
- Drosophila melanogaster/embryology
- Drosophila melanogaster/growth & development
- Drosophila melanogaster/physiology
- Eye/cytology
- Eye/growth & development
- Female
- Gene Deletion
- Gene Expression/genetics
- Gene Expression Regulation, Developmental
- Humans
- Immunohistochemistry
- Larva/genetics
- Larva/growth & development
- Mitochondria/chemistry
- Mitochondria/metabolism
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Mitochondrial Proteins/physiology
- Molecular Sequence Data
- Mutation
- Nematoda/genetics
- Oogenesis/physiology
- Phenotype
- Protein Structure, Secondary
- RNA, Messenger, Stored/analysis
- RNA, Messenger, Stored/physiology
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/physiology
- Recombination, Genetic/genetics
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/physiology
- Salivary Glands/cytology
- Salivary Glands/metabolism
- Sequence Homology, Amino Acid
- Subcellular Fractions/chemistry
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Affiliation(s)
- Timofey V Tselykh
- Institute of Biotechnology, Developmental Biology Program, University of Helsinki, FIN-00014 Helsinki, Finland.
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3
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Goodrich JS, Clouse KN, Schüpbach T. Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. Development 2004; 131:1949-58. [PMID: 15056611 DOI: 10.1242/dev.01078] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins, hnRNPs, are RNA-binding proteins that play crucial roles in controlling gene expression. In Drosophila oogenesis, the hnRNP Squid (Sqd) functions in the localization and translational regulation of gurken (grk) mRNA. We show that Sqd interacts with Hrb27C, an hnRNP previously implicated in splicing. Like sqd, hrb27C mutants lay eggs with dorsoventral defects and Hrb27C can directly bind to grk RNA. Our data demonstrate a novel role for Hrb27C in promoting grk localization. We also observe a direct physical interaction between Hrb27C and Ovarian tumor (Otu), a cytoplasmic protein implicated in RNA localization. We find that some otu alleles produce dorsalized eggs and it appears that Otu cooperates with Hrb27C and Sqd in the oocyte to mediate proper grk localization. All three mutants share another phenotype, persistent polytene nurse cell chromosomes. Our analyses support dual cooperative roles for Sqd, Hrb27C and Otu during Drosophila oogenesis.
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Affiliation(s)
- Jennifer S Goodrich
- Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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4
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Meng X, Wahlström G, Immonen T, Kolmer M, Tirronen M, Predel R, Kalkkinen N, Heino TI, Sariola H, Roos C. The Drosophila hugin gene codes for myostimulatory and ecdysis-modifying neuropeptides. Mech Dev 2002; 117:5-13. [PMID: 12204246 DOI: 10.1016/s0925-4773(02)00175-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In a genomic screen we isolated the Drosophila gene hugin (hug, cytology 87C1-2) by cross-hybridisation to a human glial cell line-derived neurotrophic factor cDNA. Upon cDNA sequence analysis and in vitro expression assays, the hugin gene was found to encode a signal peptide containing proprotein that was further processed in Schneider-2 cells into peptides similar to known neuropeptides. Two of the peptides were similar to FXPRL-amides (pyrokinins) and to the ecdysis-triggering hormone, respectively. The former displayed myostimulatory activity in a bioassay on the cockroach hyperneural muscle preparation, as well as in the Drosophila heart muscle assay. Hugin is expressed during the later half of embryogenesis and during larval stages in a subgroup of neurosecretory cells of the suboesophageal ganglion. Ubiquitous ectopic hugin expression resulted in larval death predominantly at or shortly after ecdysis from second to third instar, suggesting that at least one of the posttranslational cleavage products affects molting of the larva by interfering with the regulation of ecdysis.
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Affiliation(s)
- Xiaojuan Meng
- Developmental Biology Program, Institute of Biotechnology, Viikki Biocenter, PB 56, FIN-00014 University of Helsinki, Finland
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5
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Larsson J, Chen JD, Rasheva V, Rasmuson-Lestander A, Pirrotta V. Painting of fourth, a chromosome-specific protein in Drosophila. Proc Natl Acad Sci U S A 2001; 98:6273-8. [PMID: 11353870 PMCID: PMC33458 DOI: 10.1073/pnas.111581298] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2000] [Indexed: 11/18/2022] Open
Abstract
Chromosome-specific gene regulation is known thus far only as a mechanism to equalize the transcriptional activity of the single male X chromosome with that of the two female X chromosomes. In Drosophila melanogaster, a complex including the five Male-Specific Lethal (MSL) proteins, "paints" the male X chromosome, mediating its hypertranscription. Here, with the molecular cloning of Painting of fourth (Pof), we describe a previously uncharacterized gene encoding a chromosome-specific protein in Drosophila. Unlike the MSL proteins, POF paints an autosome, the fourth chromosome of Drosophila melanogaster. Chromosome translocation analysis shows that the binding depends on an initiation site in the proximal region of chromosome 4 and spreads in cis to involve the entire chromosome. The spreading depends on sequences or structures specific to chromosome 4 and cannot extend to parts of other chromosomes translocated to the fourth. Spreading can also occur in trans to a paired homologue that lacks the initiation region. In the related species Drosophila busckii, POF paints the entire X chromosome exclusively in males, suggesting relationships between the fourth chromosome and the X and between POF complexes and dosage-compensation complexes.
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Affiliation(s)
- J Larsson
- Department of Microbiology, Umeå University, S-901 87 Umeå, Sweden
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6
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Päällysaho S, Huttunen S, Hoikkala A. Identification of X chromosomal restriction fragment length polymorphism markers and their use in a gene localization study in Drosophila virilis and D. littoralis. Genome 2001; 44:242-8. [PMID: 11341735 DOI: 10.1139/g01-006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified six restriction fragment length polymorphism (RFLP) markers based on unique gene sequences on the X chromosome of Drosophila virilis and D. littoralis. The markers were localized by in situ hybridization on larval polytene chromosomes, and the conjugation of the X chromosomes of the two species was studied in salivary glands of interspecific hybrid female larvae. The gene arrangement of D. virilis and D. littoralis appeared to be very different at the proximal end of the X chromosome preventing recombination between RFLP markers located in this area. Simple quantitative trait loci (QTL) analysis showed that five of our marker genes (including nonA and Dmca1A, previously found to affect male courtship song in D. melanogaster) are linked with a gene(s) having a major effect on species differences in the male courtship song between D. virilis and D. littoralis. This shows that the song gene(s) may be located inside a large X-chromosomal inversion in D. littoralis (as previously suggested), but that it may also be located on an area between this inversion and the centromere, close to nonA and Dmca1A. Localization of this gene or gene complex will be continued with the aid of our newly identified RFLP markers by making interspecific crosses between D. virilis group species with more similar X chromosomes.
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Affiliation(s)
- S Päällysaho
- Department of Biology, University of Oulu, Finland.
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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Dej KJ, Spradling AC. The endocycle controls nurse cell polytene chromosome structure during Drosophila oogenesis. Development 1999; 126:293-303. [PMID: 9847243 DOI: 10.1242/dev.126.2.293] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polytene chromosomes exhibit intricate higher order chromatin structure that is easily visualized due to their precisely aligned component strands. However, it remains unclear if the same factors determine chromatin organization in polyploid and diploid cells. We have analyzed one such factor, the cell cycle, by studying changes in Drosophila nurse cell chromosomes throughout the 10 to 12 endocycles of oogenesis. We find that nurse cells undergo three distinct types of endocycle whose parameters are correlated with chromosome behavior. The first four endocycles support complete DNA replication; poorly banded polytene euchromatin progressively condenses during the late S phases to produce blob-like chromosomes. During the unique fifth endocycle, an incomplete late S phase is followed by a mitosis-like state during which the 64C chromosomes dissociate into 32 chromatid pairs held together by unreplicated regions. All the subsequent endocycles lack any late S phase; during these cycles a new polytene chromosome grows from each 2C chromatid pair to generate 32-ploid polytene nuclei. These observations suggest that euchromatin begins to condense during late S phase and that nurse cell polytene chromosome structure is controlled by regulating whether events characteristic of late S and M phase are incorporated or skipped within a given endocycle.
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Affiliation(s)
- K J Dej
- Howard Hughes Medical Institute, Carnegie Institution of Washington, Department of Embryology, Baltimore, MD 21210, USA
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9
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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10
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Zhimulev IF. Polytene chromosomes, heterochromatin, and position effect variegation. ADVANCES IN GENETICS 1997; 37:1-566. [PMID: 9352629 DOI: 10.1016/s0065-2660(08)60341-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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11
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12
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Heino TI, Lahti VP, Tirronen M, Roos C. Polytene chromosomes show normal gene activity but some mRNAs are abnormally accumulated in the pseudonurse cell nuclei of Drosophila melanogaster otu mutants. Chromosoma 1995; 104:44-55. [PMID: 7587594 DOI: 10.1007/bf00352225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Certain mutant alleles of the ovarian tumor (otu) locus give rise to polytene chromosomes in the pseudonurse cells (PNCs). We have previously shown that the banding pattern of these germ line-derived chromosomes is similar to that in the larval salivary gland chromosomes. In this study, we have examined the gene activity of these chromosomes. General gene expression from these chromosomes was studied by uridine autoradiography. The expression of specific genes was monitored by in situ hybridisation to mRNA and also by combining enhancer trap lines with otu mutants. We found that most of the genes studied were expressed in the PNCs as they were in the wild-type nurse cells. Four out of the 12 mRNAs studied accumulated in the nuclei instead of migrating to the cytoplasm. The intensity of accumulation directly correlated with the extent of polytenisation in the PNC nuclei. We suggest that the otu mRNA remains partly attached to the polytene chromosome template after transcription and discuss the effects of this phenomenon on polytenisation of the PNC chromosomes.
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Affiliation(s)
- T I Heino
- Department of Biosciences, Division of Genetics, P.O. Box 56, FIN-00014 University of Helsinki, Finland
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Semeshin VF, Kritikou D, Zacharopoulou A, Zhimulev IF. Electron microscope investigation of polytene chromosomes in the Mediterranean fruit fly Ceratitis capitata. Genome 1995; 38:652-60. [PMID: 7672601 DOI: 10.1139/g95-083] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ultrastructural analyses of polytene chromosomes from male pupal orbital bristle cells and from larval salivary glands of Ceratitis capitata were carried out. It was shown that chromatin complexes corresponding to the X chromosome heterochromatic network are surrounded by material containing ribonucleoprotein (RNP) granules 250-300 A (1 A = 0.1 nm) in diameter. RNP granules of similar size surround the spherical Y chromosome. These data point out the presence of transcriptional activity in both of these chromosomes. The absence of clear structure in chromosomal regions situated between large bands in both types of tissues was observed. These results support the hypothesis of weak synapsis between chromatids or small chromomeres of polytene chromosomes in this species. In addition, we describe a specific puff revealed in both orbital trichogen cells and salivary glands that is morphologically similar to the 93D puff of Drosophila melanogaster.
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Affiliation(s)
- V F Semeshin
- Institute of Cytology and Genetics, Russian Academy, Siberian Branch, Novosibirsk
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14
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Mal'ceva NI, Gyurkovics H, Zhimulev IF. General characteristics of the polytene chromosome from ovarian pseudonurse cells of the Drosophila melanogaster otu11 and fs(2)B mutants. Chromosome Res 1995; 3:191-200. [PMID: 7780663 DOI: 10.1007/bf00710713] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Polytene chromosomes of good cytological quality from pseudonurse cells (PNCs) of fs(2)B and otu11 mutants were obtained, photomaps for otu11 mutants were constructed and the general characteristics of polytene chromosomes from salivary glands (SGs) and PNCs were compared. Three conditions were found to improve the cytological quality of PNC chromosomes: temperature below 18 degrees C, a protein-rich medium and presence of the Y-chromosome. Detailed comparison of the chromosome banding pattern from SGs and PNCs has shown only minor differences between them. The frequency of asynapsis appeared to be 10 times higher for PNC chromosomes. Despite previous reports, features such as breaks and ectopic contacts turned out to be also typical for PNC chromosomes, but with remarkably lower frequencies.
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Affiliation(s)
- N I Mal'ceva
- Laboratory of Molecular Cytogenetics, Siberian Division of Russian Academy of Sciences, Novosibirsk
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Tissue-specific expression of the diazepam-binding inhibitor in Drosophila melanogaster: cloning, structure, and localization of the gene. Mol Cell Biol 1994. [PMID: 7935415 DOI: 10.1128/mcb.14.10.6983] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diazepam-binding inhibitor (DBI; also called acyl coenzyme A-binding protein or endozepine) is a 10-kDa polypeptide found in organisms ranging from yeasts to mammals. It has been shown that DBI and its processing products are involved in various specific biological processes such as GABAA/benzodiazepine receptor modulation, acyl coenzyme A metabolism, steroidogenesis, and insulin secretion. We have cloned and sequenced the Drosophila melanogaster gene and cDNA encoding DBI. The Drosophila DBI gene encodes a protein of 86 amino acids that shows 51 to 56% identity with previously known DBI proteins. The gene is composed of one noncoding 5' and two coding exons and is localized on the chromosomal map at position 65E. Several transcription initiation sites were detected by RNase protection and primer extension experiments. Computer analysis of the promoter region revealed features typical of housekeeping genes, such as the lack of TATA and CCAAT elements. However, in its low GC content and lack of a CpG island, the region resembles promoters of tissue-specific genes. Northern (RNA) analysis revealed that the expression of the DBI gene occurred from the larval stage onwards throughout the adult stage. In adult flies, DBI mRNA and immunoreactivity were detected in the cardia, part of the Malpighian tubules, the fat body, and gametes of both sexes. Developmentally regulated expression, disappearing during metamorphosis, was detected in the larval and pupal brains. No expression was detected in the adult nervous system. On the basis of the expression of DBI in some but not all tissues with high energy consumption, we propose that in D. melanogaster, DBI is involved in energy metabolism in a manner that depends on the substrate used for energy production.
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Kolmer M, Roos C, Tirronen M, Myöhänen S, Alho H. Tissue-specific expression of the diazepam-binding inhibitor in Drosophila melanogaster: cloning, structure, and localization of the gene. Mol Cell Biol 1994; 14:6983-95. [PMID: 7935415 PMCID: PMC359229 DOI: 10.1128/mcb.14.10.6983-6995.1994] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The diazepam-binding inhibitor (DBI; also called acyl coenzyme A-binding protein or endozepine) is a 10-kDa polypeptide found in organisms ranging from yeasts to mammals. It has been shown that DBI and its processing products are involved in various specific biological processes such as GABAA/benzodiazepine receptor modulation, acyl coenzyme A metabolism, steroidogenesis, and insulin secretion. We have cloned and sequenced the Drosophila melanogaster gene and cDNA encoding DBI. The Drosophila DBI gene encodes a protein of 86 amino acids that shows 51 to 56% identity with previously known DBI proteins. The gene is composed of one noncoding 5' and two coding exons and is localized on the chromosomal map at position 65E. Several transcription initiation sites were detected by RNase protection and primer extension experiments. Computer analysis of the promoter region revealed features typical of housekeeping genes, such as the lack of TATA and CCAAT elements. However, in its low GC content and lack of a CpG island, the region resembles promoters of tissue-specific genes. Northern (RNA) analysis revealed that the expression of the DBI gene occurred from the larval stage onwards throughout the adult stage. In adult flies, DBI mRNA and immunoreactivity were detected in the cardia, part of the Malpighian tubules, the fat body, and gametes of both sexes. Developmentally regulated expression, disappearing during metamorphosis, was detected in the larval and pupal brains. No expression was detected in the adult nervous system. On the basis of the expression of DBI in some but not all tissues with high energy consumption, we propose that in D. melanogaster, DBI is involved in energy metabolism in a manner that depends on the substrate used for energy production.
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Affiliation(s)
- M Kolmer
- Department of Biomedical Sciences, University of Tampere, Finland
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