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DNA replication in nurse cell polytene chromosomes of Drosophila melanogaster otu mutants. Chromosoma 2014; 124:95-106. [PMID: 25256561 DOI: 10.1007/s00412-014-0487-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 08/19/2014] [Accepted: 09/15/2014] [Indexed: 10/24/2022]
Abstract
Drosophila cell lines are used extensively to study replication timing, yet data about DNA replication in larval and adult tissues are extremely limited. To address this gap, we traced DNA replication in polytene chromosomes from nurse cells of Drosophila melanogaster otu mutants using bromodeoxyuridine incorporation. Importantly, nurse cells are of female germline origin, unlike the classical larval salivary glands, that are somatic. In contrast to salivary gland polytene chromosomes, where replication begins simultaneously across all puffs and interbands, replication in nurse cells is first observed at several specific chromosomal regions. For instance, in the chromosome 2L, these include the regions 31B-E and 37E and proximal parts of 34B and 35B, with the rest of the decondensed chromosomal regions joining replication process a little later. We observed that replication timing of pericentric heterochromatin in nurse cells was shifted from late S phase to early and mid stages. Curiously, chromosome 4 may represent a special domain of the genome, as it replicates on its own schedule which is uncoupled from the rest of the chromosomes. Finally, we report that SUUR protein, an established marker of late replication in salivary gland polytene chromosomes, does not always colocalize with late-replicating regions in nurse cells.
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2
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Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Tóth KF. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 2013; 27:390-9. [PMID: 23392610 DOI: 10.1101/gad.209841.112] [Citation(s) in RCA: 349] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the metazoan germline, piwi proteins and associated piwi-interacting RNAs (piRNAs) provide a defense system against the expression of transposable elements. In the cytoplasm, piRNA sequences guide piwi complexes to destroy complementary transposon transcripts by endonucleolytic cleavage. However, some piwi family members are nuclear, raising the possibility of alternative pathways for piRNA-mediated regulation of gene expression. We found that Drosophila Piwi is recruited to chromatin, colocalizing with RNA polymerase II (Pol II) on polytene chromosomes. Knockdown of Piwi in the germline increases expression of transposable elements that are targeted by piRNAs, whereas protein-coding genes remain largely unaffected. Derepression of transposons upon Piwi depletion correlates with increased occupancy of Pol II on their promoters. Expression of piRNAs that target a reporter construct results in a decrease in Pol II occupancy and an increase in repressive H3K9me3 marks and heterochromatin protein 1 (HP1) on the reporter locus. Our results indicate that Piwi identifies targets complementary to the associated piRNA and induces transcriptional repression by establishing a repressive chromatin state when correct targets are found.
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Affiliation(s)
- Adrien Le Thomas
- California Institute of Technology, Pasadena, California 91125, USA
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Wallace HA, Plata MP, Kang HJ, Ross M, Labrador M. Chromatin insulators specifically associate with different levels of higher-order chromatin organization in Drosophila. Chromosoma 2009; 119:177-94. [PMID: 20033198 DOI: 10.1007/s00412-009-0246-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 10/20/2009] [Accepted: 10/30/2009] [Indexed: 01/08/2023]
Abstract
Chromatin insulators are required for proper temporal and spatial expression of genes in metazoans. Here, we have analyzed the distribution of insulator proteins on the 56F-58A region of chromosome 2R in Drosophila polytene chromosomes to assess the role of chromatin insulators in shaping genome architecture. Data show that the suppressor of Hairy-wing protein [Su(Hw)] is found in three structures differentially associated with insulator proteins: bands, interbands, and multi-gene domains of coexpressed genes. Results show that bands are generally formed by condensation of chromatin that belongs to genes containing one or more Su(Hw) binding sites, whereas, in interbands, Su(Hw) sites appear associated with open chromatin. In addition, clusters of coexpressed genes in this region form bands characterized by the lack of CP190 and BEAF-32 insulator proteins. This pattern correlates with the distribution of specific chromatin marks and is conserved in nurse cells, suggesting that this organization may not be limited to one cell type but represents the basic organization of interphasic chromosomes.
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Affiliation(s)
- Heather A Wallace
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA
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Lei EP, Corces VG. RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 2006; 38:936-41. [PMID: 16862159 DOI: 10.1038/ng1850] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 06/20/2006] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is a conserved silencing mechanism that can act through alteration of chromatin structure. Chromatin insulators promote higher-order nuclear organization, thereby establishing DNA domains subject to distinct transcriptional controls. We present evidence for a functional relationship between RNAi and the gypsy insulator of D. melanogaster. Insulator activity is decreased when Argonaute genes required for RNAi are mutated, and insulator function is improved when the levels of the Rm62 helicase, involved in double-stranded RNA (dsRNA)-mediated silencing and heterochromatin formation, are reduced. Rm62 interacts physically with the DNA-binding insulator protein CP190 in an RNA-dependent manner. Finally, reduction of Rm62 levels results in marked nuclear reorganization of a compromised insulator. These results suggest that the RNAi machinery acts as a modulator of nuclear architecture capable of effecting global changes in gene expression.
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Affiliation(s)
- Elissa P Lei
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Koryakov DE, Reuter G, Dimitri P, Zhimulev IF. The SuUR gene influences the distribution of heterochromatic proteins HP1 and SU(VAR)3–9 on nurse cell polytene chromosomes of Drosophila melanogaster. Chromosoma 2006; 115:296-310. [PMID: 16607511 DOI: 10.1007/s00412-005-0044-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 12/06/2005] [Accepted: 12/12/2005] [Indexed: 10/24/2022]
Abstract
We have investigated the distribution of three heterochromatic proteins [SUppressor of UnderReplication (SUUR), heterochromatin protein 1 (HP1), and SU(VAR)3-9] in chromosomes of nurse cells (NCs) and have compared the data obtained with the distribution of the same proteins in salivary gland (SG) chromosomes. In NC chromosomes, the SU(VAR)3-9 protein was found in pericentric heterochromatin and at 223 sites on euchromatic arms, while in SG chromosomes, it was mainly restricted to the chromocenter. In NC chromosomes, the HP1 and SUUR proteins bind to 331 and 256 sites, respectively, which are almost twice the number of sites in SG chromosomes. The distribution of the HP1 and SU(VAR)3-9 proteins depends on the SuUR gene. A mutation in this gene results in a dramatic decrease in the amount of SU(VAR)3-9 binding sites in autosomes. In the X chromosome, these sites are relocated in comparison to the SuUR (+), and their total number only varies slightly. HP1 binding sites are redistributed in chromosomes of SuUR mutants, and their overall number did not change as considerably as SU(VAR)3-9. These data together point to an interaction of these three proteins in Drosophila NC chromosomes.
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Deng W, Lin H. Asymmetric germ cell division and oocyte determination during Drosophila oogenesis. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 203:93-138. [PMID: 11131529 DOI: 10.1016/s0074-7696(01)03005-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early oogenesis in Drosophila, with a stereotypic pattern of germ cell division and differentiation, provides an attractive model for studying cell lineage and patterning. Drosophila oogenesis is initiated when a germline stem cell divides asymmetrically to produce a daughter stem cell and a cytoblast. The cystoblast then undergoes four rounds of incomplete mitoses to form a 16-cell cyst, accompanied by the formation of the fusome. Within the cyst, one of the two cells with four intercellular bridges differentiates into an oocyte while the rest become nurse cells. The oocyte then translocates within the cyst to a posterior position, which defines the anterio-posterior axis of the future embryo. Recent studies have shown that the asymmetric germline stem cell division is controlled by somatic signaling involving piwi, fs(1)Yb, and the dpp pathway as well as by intrinsic mechanisms involving pumilio, nanos, arrest, bag-of-marbles, and the spectrosome-the fusome precursor in the stem cells and the cystoblast. The spectrosome in the cystoblast appears to play an important role in polarized fusome growth during cyst formation. The fusome may guide the formation of a polarized microtubule network for the intracyst transport of certain RNAs and proteins to the cystocyte destined to become the oocyte. Genes such as egalitarian, Bicaudal D, stonewall, and encore are important for oocyte determination, while differential adhesion between the oocyte and its surrounding prefollicle cells, as mediated by armadillo, alpha-catenin, shotgun, and the spindle genes, is crucial for oocyte translocation. Early oogenesis shares many parallel features to early spermatogenesis, although distinct differences are also observed at both the phenomenological and mechanistic levels. The study of oogenesis, progressing at an exciting rate, contributes significantly to our understanding of the mechanisms underlying proliferation, differentiation, and patterning.
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Affiliation(s)
- W Deng
- Department of Cell Biology, Duke University Medical School Durham, North Carolina 27710, USA
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Makarova KS, Aravind L, Koonin EV. A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem Sci 2000; 25:50-2. [PMID: 10664582 DOI: 10.1016/s0968-0004(99)01530-3] [Citation(s) in RCA: 218] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- K S Makarova
- Dept of Pathology, F.E. Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799, USA
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Sahut-Barnola I, Pauli D. The Drosophila gene stand still encodes a germline chromatin-associated protein that controls the transcription of the ovarian tumor gene. Development 1999; 126:1917-26. [PMID: 10101125 DOI: 10.1242/dev.126.9.1917] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Drosophila gene stand still (stil) encodes a novel protein required for survival, sexual identity and differentiation of female germ cells. Using specific antibodies, we show that the Stil protein accumulates in the nucleus of all female germ cells throughout development, and is transiently expressed during early stages of male germline differentiation. Changes of Stil subnuclear localization during oogenesis suggest an association with chromatin. Several mutant alleles, which are point mutations in the Stil N-terminal domain, encode proteins that no longer co-localized with chromatin. We find that Stil binds to many sites on polytene chromosomes with strong preference for decondensed chromatin. This localization is very similar to that of RNA polymerase II. We show that Stil is required for high levels of transcription of the ovarian tumor gene in germ cells. Expression of ovarian tumor in somatic cells can be induced by ectopic expression of Stil. Finally, we find that transient ubiquitous somatic expression of Stil results in lethality of the fly at all stages of development.
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Affiliation(s)
- I Sahut-Barnola
- Department of Zoology and Animal Biology, University of Geneva, 1211 Geneva 4, Switzerland
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Perrin L, Demakova O, Fanti L, Kallenbach S, Saingery S, Mal'ceva NI, Pimpinelli S, Zhimulev I, Pradel J. Dynamics of the sub-nuclear distribution of Modulo and the regulation of position-effect variegation by nucleolus in Drosophila. J Cell Sci 1998; 111 ( Pt 18):2753-61. [PMID: 9718368 DOI: 10.1242/jcs.111.18.2753] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
modulo belongs to the class of Drosophila genes named ‘suppressor of position-effect variegation’, suggesting the involvement of the encoded protein in chromatin compaction/relaxation processes. Using complementary procedures of cell fractionation, immunolocalisation on mitotic and polytene chromosomes and cross-linking/immunoprecipitation of genomic DNA targets, we have analysed the sub-nuclear distribution of Modulo. While actually associated to condensed chromatin and heterochromatin sites, the protein is also abundantly found at nucleolus. From a comparison of Modulo pattern on chromosomes of different cell types and mutant lines, we propose a model in which the nucleolus balances the Modulo protein available for chromatin compaction and PEV modification. At a molecular level, repetitive elements instead of rDNA constitute Modulo DNA targets, indicating that the protein directly contacts DNA in heterochromatin but not at the nucleolus. Consistent with a role for Modulo in nucleolus activity and protein synthesis capacity, somatic clones homozygous for a null mutation express a cell-autonomous phenotype consisting of growth alteration and short slender bristles, characteristic traits of Minute mutations, which are known to affect ribosome biogenesis. The results provide evidence suggesting that Modulo participates in distinct molecular networks in the nucleolus and heterochromatin and has distinct functions in the two compartments.
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Affiliation(s)
- L Perrin
- Laboratoire de Génétique et de Physiologie du Développement, Institut de Biologie du Développement de Marseille, CNRS/INSERM/Université de la Méditerranée/AP de Marseille, Campus de Luminy Case 907. 13288 Marseille cedex 9, France
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Belyaeva ES, Zhimulev IF, Volkova EI, Alekseyenko AA, Moshkin YM, Koryakov DE. Su(UR)ES: a gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proc Natl Acad Sci U S A 1998; 95:7532-7. [PMID: 9636184 PMCID: PMC22673 DOI: 10.1073/pnas.95.13.7532] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A genetic locus suppressing DNA underreplication in intercalary heterochromatin (IH) and pericentric heterochromatin (PH) of the polytene chromosomes of Drosophila melanogaster salivary glands, has been described. Found in the In(1)scV2 strain, the mutation, designated as Su(UR)ES, was located on chromosome 3L at position 34. 8 and cytologically mapped to region 68A3-B4. A cytological phenotype was observed in the salivary gland chromosomes of larvae homozygous and hemizygous for Su(UR)ES: (i) in the IH regions, that normally are incompletely polytenized and so they often break to form "weak points," underreplication is suppressed, breaks and ectopic contacts disappear; (ii) the degree of polytenization in PH grows higher. That is why the regions in chromosome arm basements, normally beta-heterochromatic, acquire a distinct banding pattern, i. e., become euchromatic by morphological criteria; (iii) an additional bulk of polytenized material arises between the arms of chromosome 3 to form a fragment with a typical banding pattern. Chromosome 2 PH reveals additional alpha-heterochromatin. Su(UR)ES does not affect the viability, fertility, or morphological characters of the imago, and has semidominant expression in the heterozygote and distinct maternal effect. The results obtained provide evidence that the processes leading to DNA underreplication in IH and PH are affected by the same genetic mechanism.
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Affiliation(s)
- E S Belyaeva
- Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
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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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