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Atinbayeva N, Valent I, Zenk F, Loeser E, Rauer M, Herur S, Quarato P, Pyrowolakis G, Gomez-Auli A, Mittler G, Cecere G, Erhardt S, Tiana G, Zhan Y, Iovino N. Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos. EMBO J 2024; 43:2685-2714. [PMID: 38831123 PMCID: PMC11217351 DOI: 10.1038/s44318-024-00127-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024] Open
Abstract
Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hallmarks of constitutive heterochromatin. Here, we show that H3K9me3 is transmitted from the maternal germline to the next generation. Maternally inherited H3K9me3, and the histone methyltransferases (HMT) depositing it, are required for the organization of constitutive heterochromatin: early embryos lacking H3K9 methylation display de-condensation of pericentromeric regions, centromere-centromere de-clustering, mitotic defects, and nuclear shape irregularities, resulting in embryo lethality. Unexpectedly, quantitative CUT&Tag and 4D microscopy measurements of HP1a coupled with biophysical modeling revealed that H3K9me2/3 is largely dispensable for HP1a recruitment. Instead, the main function of H3K9me2/3 at this developmental stage is to drive HP1a clustering and subsequent heterochromatin compaction. Our results show that HP1a binding to constitutive heterochromatin in the absence of H3K9me2/3 is not sufficient to promote proper embryo development and heterochromatin formation. The loss of H3K9 HMTs and H3K9 methylation alters genome organization and hinders embryonic development.
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Affiliation(s)
- Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085, Freiburg im Breisgau, Germany
| | - Iris Valent
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Fides Zenk
- Brain Mind Institute, School of Life Sciences EPFL, SV3809, 1015, Lausanne, Switzerland
| | - Eva Loeser
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Shwetha Herur
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Giorgos Pyrowolakis
- Centre for Biological signaling studies, University of Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Alejandro Gomez-Auli
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Germano Cecere
- Institute Pasteur, Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, UMR3738, CNRS, 75724, Cedex 15, Paris, France
| | - Sylvia Erhardt
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.
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2
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Chavan A, Isenhart R, Nguyen SC, Kotb NM, Harke J, Sintsova A, Ulukaya G, Uliana F, Ashiono C, Kutay U, Pegoraro G, Rangan P, Joyce EF, Jagannathan M. A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate. Genes Dev 2024; 38:415-435. [PMID: 38866555 PMCID: PMC11216176 DOI: 10.1101/gad.351424.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
The association of genomic loci to the nuclear periphery is proposed to facilitate cell type-specific gene repression and influence cell fate decisions. However, the interplay between gene position and expression remains incompletely understood, in part because the proteins that position genomic loci at the nuclear periphery remain unidentified. Here, we used an Oligopaint-based HiDRO screen targeting ∼1000 genes to discover novel regulators of nuclear architecture in Drosophila cells. We identified the heterochromatin-associated protein Stonewall (Stwl) as a factor promoting perinuclear chromatin positioning. In female germline stem cells (GSCs), Stwl binds and positions chromatin loci, including GSC differentiation genes, at the nuclear periphery. Strikingly, Stwl-dependent perinuclear positioning is associated with transcriptional repression, highlighting a likely mechanism for Stwl's known role in GSC maintenance and ovary homeostasis. Thus, our study identifies perinuclear anchors in Drosophila and demonstrates the importance of gene repression at the nuclear periphery for cell fate.
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Affiliation(s)
- Ankita Chavan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
- Bringing Materials to Life Consortium, ETH Zürich, Zürich 8093, Switzerland
- Life Science Zürich Graduate School, Zürich 8057, Switzerland
| | - Randi Isenhart
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Son C Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Noor M Kotb
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jailynn Harke
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Anna Sintsova
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich 8093, Switzerland
| | - Gulay Ulukaya
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Eric F Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich 8093, Switzerland;
- Bringing Materials to Life Consortium, ETH Zürich, Zürich 8093, Switzerland
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3
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Chavan A, Isenhart R, Nguyen SC, Kotb N, Harke J, Sintsova A, Ulukaya G, Uliana F, Ashiono C, Kutay U, Pegoraro G, Rangan P, Joyce EF, Jagannathan M. A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567611. [PMID: 38014085 PMCID: PMC10680830 DOI: 10.1101/2023.11.17.567611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The association of genomic loci to the nuclear periphery is proposed to facilitate cell-type specific gene repression and influence cell fate decisions. However, the interplay between gene position and expression remains incompletely understood, in part because the proteins that position genomic loci at the nuclear periphery remain unidentified. Here, we used an Oligopaint-based HiDRO screen targeting ~1000 genes to discover novel regulators of nuclear architecture in Drosophila cells. We identified the heterochromatin-associated protein, Stonewall (Stwl), as a factor promoting perinuclear chromatin positioning. In female germline stem cells (GSCs), Stwl binds and positions chromatin loci, including GSC differentiation genes, at the nuclear periphery. Strikingly, Stwl-dependent perinuclear positioning is associated with transcriptional repression, highlighting a likely mechanism for Stwl's known role in GSC maintenance and ovary homeostasis. Thus, our study identifies perinuclear anchors in Drosophila and demonstrates the importance of gene repression at the nuclear periphery for cell fate.
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Affiliation(s)
- Ankita Chavan
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
- Bringing Materials to Life Consortium, ETH Zürich, Switzerland
- Life Science Zurich Graduate School, Zürich, Switzerland
- These authors contributed equally
| | - Randi Isenhart
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- These authors contributed equally
| | - Son C. Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Noor Kotb
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jailynn Harke
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Sintsova
- Institute of Microbiology, Department of Biology, ETH Zürich, Switzerland
| | - Gulay Ulukaya
- Bioinformatics for Next Generation Sequencing (BiNGS) core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - Prashanth Rangan
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric F. Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, ETH Zürich, Switzerland
- Bringing Materials to Life Consortium, ETH Zürich, Switzerland
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4
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Lee GE, Byun J, Lee CJ, Cho YY. Molecular Mechanisms for the Regulation of Nuclear Membrane Integrity. Int J Mol Sci 2023; 24:15497. [PMID: 37895175 PMCID: PMC10607757 DOI: 10.3390/ijms242015497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
The nuclear membrane serves a critical role in protecting the contents of the nucleus and facilitating material and signal exchange between the nucleus and cytoplasm. While extensive research has been dedicated to topics such as nuclear membrane assembly and disassembly during cell division, as well as interactions between nuclear transmembrane proteins and both nucleoskeletal and cytoskeletal components, there has been comparatively less emphasis on exploring the regulation of nuclear morphology through nuclear membrane integrity. In particular, the role of type II integral proteins, which also function as transcription factors, within the nuclear membrane remains an area of research that is yet to be fully explored. The integrity of the nuclear membrane is pivotal not only during cell division but also in the regulation of gene expression and the communication between the nucleus and cytoplasm. Importantly, it plays a significant role in the development of various diseases. This review paper seeks to illuminate the biomolecules responsible for maintaining the integrity of the nuclear membrane. It will delve into the mechanisms that influence nuclear membrane integrity and provide insights into the role of type II membrane protein transcription factors in this context. Understanding these aspects is of utmost importance, as it can offer valuable insights into the intricate processes governing nuclear membrane integrity. Such insights have broad-reaching implications for cellular function and our understanding of disease pathogenesis.
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Affiliation(s)
- Ga-Eun Lee
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Jiin Byun
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Cheol-Jung Lee
- Research Center for Materials Analysis, Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133, Chungcheongnam-do, Republic of Korea
| | - Yong-Yeon Cho
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
- RCD Control and Material Research Institute, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
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Zhang L, Zhang S, Wang R, Sun L. Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants. Int J Mol Sci 2022; 23:ijms23116247. [PMID: 35682924 PMCID: PMC9181106 DOI: 10.3390/ijms23116247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in chromatin remodeling remains unclear. In order to characterize the genome-wide lncRNA expression and their potential interacting factors during this process in Drosophila, we investigated the expression pattern of lncRNAs and mRNAs based on the transcriptome analyses and found significant differences between lncRNAs and mRNAs. Then, we performed TSA-FISH experiments of candidate lncRNAs and their potential interactors that have different functions in Drosophila embryos to determine their expression pattern. In addition, we also analyzed the expression of transposable elements (TEs) and their interactors to explore their expression in ISWI mutants. Our results provide a new perspective for understanding the possible regulatory mechanism of lncRNAs and TEs as well as their targets in chromatin remodeling.
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Meyer-Nava S, Nieto-Caballero VE, Zurita M, Valadez-Graham V. Insights into HP1a-Chromatin Interactions. Cells 2020; 9:E1866. [PMID: 32784937 PMCID: PMC7465937 DOI: 10.3390/cells9081866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Understanding the packaging of DNA into chromatin has become a crucial aspect in the study of gene regulatory mechanisms. Heterochromatin establishment and maintenance dynamics have emerged as some of the main features involved in genome stability, cellular development, and diseases. The most extensively studied heterochromatin protein is HP1a. This protein has two main domains, namely the chromoshadow and the chromodomain, separated by a hinge region. Over the years, several works have taken on the task of identifying HP1a partners using different strategies. In this review, we focus on describing these interactions and the possible complexes and subcomplexes associated with this critical protein. Characterization of these complexes will help us to clearly understand the implications of the interactions of HP1a in heterochromatin maintenance, heterochromatin dynamics, and heterochromatin's direct relationship to gene regulation and chromatin organization.
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Affiliation(s)
| | | | | | - Viviana Valadez-Graham
- Instituto de Biotecnología, Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62210, Mexico; (S.M.-N.); (V.E.N.-C.); (M.Z.)
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Genetic Variation and Potential for Resistance Development to the tTA Overexpression Lethal System in Insects. G3 (BETHESDA, MD.) 2020; 10:1271-1281. [PMID: 32019873 PMCID: PMC7144068 DOI: 10.1534/g3.120.400990] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Release of insect pests carrying the dominant lethal tetracycline transactivator (tTA) overexpression system has been proposed as a means for population suppression. High levels of the tTA transcription factor are thought to be toxic due to either transcriptional squelching or interference with protein ubiquitination. Here we utilized the Drosophila melanogaster Genetic Reference Panel (DGRP) to examine the influence of genetic variation on the efficacy of a female-specific tTA overexpression system. The level of female lethality between DGRP lines varied from 11 to 97% with a broad sense heritability of 0.89. A genome-wide association analysis identified 192 allelic variants associated with high or low lethality (P < 10-5), although none were significant when corrected for multiple testing. 151 of the variants fell within 108 genes that were associated with several biological processes including transcription and protein ubiquitination. In four lines with high female lethality, tTA RNA levels were similar or higher than in the parental tTA overexpression strain. In two lines with low lethality, tTA levels were about two fold lower than in the parental strain. However, in two other lines with low lethality, tTA levels were similar or approximately 30% lower. RNAseq analysis identified genes that were up or downregulated in the four low female lethal lines compared to the four high lethal lines. For example, genes associated with RNA processing and rRNA maturation were significantly upregulated in low lethal lines. Our data suggest that standing genetic variation in an insect population could provide multiple mechanisms for resistance to the tTA overexpression system.
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8
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The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats. Genetics 2019; 210:757-772. [PMID: 30401762 PMCID: PMC6218221 DOI: 10.1534/genetics.118.301146] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/17/2018] [Indexed: 11/18/2022] Open
Abstract
The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the "dot chromosome" because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb "long arm." The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g, low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5' ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.
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Brahmachari V, Kohli S, Gulati P. In praise of mealybugs. J Genet 2018; 97:379-389. [PMID: 29932057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The fascinating chromosomal cycle leading to facultative heterochromatization in the mealybugs has been a challenging system for mechanistic understanding of the phenomenon of genomic imprinting and epigenetics. The elegant cytological dissection of the various processes reported in the literature is equally fascinating for the researchers of current molecular age. Presently, a two way approach is being pursued; continued efforts of utilizing elegant cytology, in combination with the molecular probes to decipher molecular correlates on one hand and on the other, the de novo biochemical/molecular analysis for the identification of the molecular players using genomic tools. The hope is to uncover novel players in genomic imprinting and epigenetic regulation in the mealybug system which shows differential regulation of the entire genome, with 50% of its genome being transcriptionally inactivated in a parental-origin-specific and sex specific manner. In addition to being a model for epigenetic regulation, the mealybugs are being utilized for the analysis of radiation resistance as well as metabolic interactions between the microbiome and the host. The overview presented here is an attempt to bring out some of the work carried out in these directions. We also discuss the areas that remain poorly explored in this system, such as the role/involvement of noncoding RNA in male-specific inactivation and the molecular dissection of heterochromatin, the cytological manifestation of the inactive state of genes and chromosome.
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Affiliation(s)
- Vani Brahmachari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India.
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10
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11
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Deng H, Kerppola TK. Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes. Methods Enzymol 2017; 589:429-455. [PMID: 28336073 DOI: 10.1016/bs.mie.2017.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
We have developed a procedure that enables visualization of the genomic loci that are bound by complexes formed by a specific combination of chromatin-binding proteins. This procedure is based on imaging bimolecular fluorescence complementation (BiFC) complexes on Drosophila polytene chromosomes. BiFC complexes are formed by the facilitated association of two fluorescent protein fragments that are fused to proteins that interact with, or are in close proximity to, each other. The intensity of BiFC complex fluorescence at individual genomic loci is greatly enhanced by the parallel alignment of hundreds of chromatids within the polytene chromosomes. The loci that are bound by the complexes are mapped by comparing the locations of BiFC complex fluorescence with the stereotypical banding patterns of the chromosomes. We describe strategies for the design, expression, and validation of fusion proteins for the analysis of BiFC complex binding on polytene chromosomes. We detail protocols for the preparation of polytene chromosome spreads that have been optimized for the purpose of BiFC complex visualization. Finally, we provide guidance for the interpretation of results from studies of BiFC complex binding on polytene chromosomes and for comparison of the genomic loci that are bound by BiFC complexes with those that are bound by subunits of the corresponding endogenous complexes. The visualization of BiFC complex binding on polytene chromosomes provides a unique method to visualize multiprotein complex binding at specific loci, throughout the genome, in individual cells.
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Affiliation(s)
- Huai Deng
- University of Michigan, Ann Arbor, MI, United States
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12
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5:e16096. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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13
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Fang C, Schmitz L, Ferree PM. An unusually simple HP1 gene set in Hymenopteran insects. Biochem Cell Biol 2015; 93:596-603. [PMID: 26419616 DOI: 10.1139/bcb-2015-0046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The heterochromatin protein 1 (HP1) gene family includes a set of paralogs in higher eukaryotes that serve fundamental roles in heterochromatin structure and maintenance, and other chromatin-related functions. At least 10 full and 16 partial HP1 genes exist among Drosophila species, with multiple gene gains, losses, and sub-functionalizations within this insect group. An important question is whether this diverse set of HP1 genes and their dynamic evolution represent the standard rule in eukaryotic groups. Here we have begun to address this question by bio-informatically identifying the HP1 family genes in representative species of the insect order Hymenoptera, which includes all ants, bees, wasps, and sawflies. Compared to Drosophila species, Hymenopterans have a much simpler set of HP1 genes, including one full and two partial HP1s. All 3 genes appear to have been present in the common ancestor of the Hymenopterans and they derive from a Drosophila HP1B-like gene. In ants, a partial HP1 gene containing only a chromoshadow domain harbors amino acid changes at highly conserved sites within the PxVxL recognition region, suggesting that this gene has undergone sub-functionalization. In the jewel wasp Nasonia vitripennis, the full HP1 and partial chromoshadow-only HP1 are expressed in both germ line and somatic tissues. However, the partial chromodomain-only HP1 is expressed exclusively in the ovary and testis, suggesting that it may have a specialized chromatin role during gametogenesis. Our findings demonstrate that the HP1 gene family is much simpler and evolutionarily less dynamic within the Hymenopterans compared to the much younger Drosophila group, a pattern that may reflect major differences in the range of chromatin-related functions present in these and perhaps other insect groups.
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Affiliation(s)
- C Fang
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - L Schmitz
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - P M Ferree
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
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14
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Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI. Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes Dev 2014; 28:1445-60. [PMID: 24990964 PMCID: PMC4083088 DOI: 10.1101/gad.241950.114] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Heterochromatin protein 1 (HP1a) plays conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Using BioTAP-XL mass spectrometry and sequencing across multiple life stages of Drosophila, Alekseyenko et al. identify HP1a chromatin-associated protein and RNA interactions. They discover 13 novel candidates among the top interactions. Furthermore, HP1a selectively associates with a broad set of RNAs transcribed from repetitive regions. The validation of several novel HP1a protein interactors reveals new HP1a links to chromatin organization and function. Heterochromatin protein 1 (HP1a) has conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Here we identify chromatin-associated protein and RNA interactions of HP1a by BioTAP-XL mass spectrometry and sequencing from Drosophila S2 cells, embryos, larvae, and adults. Our results reveal an extensive list of known and novel HP1a-interacting proteins, of which we selected three for validation. A strong novel interactor, dADD1 (Drosophila ADD1) (CG8290), is highly enriched in heterochromatin, harbors an ADD domain similar to human ATRX, displays selective binding to H3K9me2 and H3K9me3, and is a classic genetic suppressor of position-effect variegation. Unexpectedly, a second hit, HIPP1 (HP1 and insulator partner protein-1) (CG3680), is strongly connected to CP190-related complexes localized at putative insulator sequences throughout the genome in addition to its colocalization with HP1a in heterochromatin. A third interactor, the histone methyltransferase MES-4, is also enriched in heterochromatin. In addition to these protein–protein interactions, we found that HP1a selectively associated with a broad set of RNAs transcribed from repetitive regions. We propose that this rich network of previously undiscovered interactions will define how HP1a complexes perform their diverse functions in cells and developing organisms.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrey A Gorchakov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Institute of Molecular and Cellular Biology, Novosibirsk 630090, Russia
| | - Barry M Zee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA; Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Cipressa F, Di Giorgio ML, Cenci G. A simple approach for multicolor immunofluorescence staining in different Drosophila cell types. J Cell Physiol 2013; 229:683-7. [PMID: 24170430 DOI: 10.1002/jcp.24506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/24/2013] [Indexed: 11/09/2022]
Abstract
Multicolor immunostaining analysis is often a desirable tool in cell biology for most researchers. Nonetheless, this is not an easy task and often not affordable by many laboratories as it might require expensive instrumentation and sophisticated analysis software. Here, we describe a simple protocol for performing sequential immunostainings on two different Drosophila specimens. Our strategy relies on an efficient and reproducible method for removal primary antibodies and/or fluorophore-conjugated secondary antibodies that does not affect antigene integrity. We show that alternation of multiple rounds of antibody incubation and removal on the same slide, followed by registration of the same DAPI-stained image, provides a simple framework for the sequential detection of several antigens in the same cell. Given that the sample fixation procedures used for Drosophila tissues are compatible with most specimen processing protocols, we can envisage that the multicolor immunostaining strategy presented here can be also adapted to different samples including mammalian tissues and/or cells.
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Affiliation(s)
- Francesca Cipressa
- Dipartimento di Biologia e Biotecnologie "C. Darwin", SAPIENZA Università di Roma, Roma, Italy
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16
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Elgin SCR, Reuter G. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol 2013; 5:a017780. [PMID: 23906716 DOI: 10.1101/cshperspect.a017780] [Citation(s) in RCA: 319] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Position-effect variegation (PEV) results when a gene normally in euchromatin is juxtaposed with heterochromatin by rearrangement or transposition. When heterochromatin packaging spreads across the heterochromatin/euchromatin border, it causes transcriptional silencing in a stochastic pattern. PEV is intensely studied in Drosophila using the white gene. Screens for dominant mutations that suppress or enhance white variegation have identified many conserved epigenetic factors, including the histone H3 lysine 9 methyltransferase SU(VAR)3-9. Heterochromatin protein HP1a binds H3K9me2/3 and interacts with SU(VAR)3-9, creating a core memory system. Genetic, molecular, and biochemical analysis of PEV in Drosophila has contributed many key findings concerning establishment and maintenance of heterochromatin with concomitant gene silencing.
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Affiliation(s)
- Sarah C R Elgin
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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17
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Mendez DL, Mandt RE, Elgin SCR. Heterochromatin Protein 1a (HP1a) partner specificity is determined by critical amino acids in the chromo shadow domain and C-terminal extension. J Biol Chem 2013; 288:22315-23. [PMID: 23793104 DOI: 10.1074/jbc.m113.468413] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Drosophila melanogaster Heterochromatin Protein 1a (HP1a) is an essential protein critical for heterochromatin assembly and regulation. Its chromo shadow domain (CSD) homodimerizes, a requirement for binding protein partners that contain a PXVXL motif. How does HP1a select among its many different PXVXL-containing partners? HP1a binds tightly to Heterochromatin Protein 2 (HP2), but weakly to PIWI. We investigated differences in homodimerization and the impact of the C-terminal extension (CTE) by contrasting HP1a to its paralogue, HP1b. HP1a and HP1b differ in the dimerization interface, with HP1a having an Arg at position 188 rather than Glu. We find that while this substitution reduces the dimerization constant, it does not impact the binding surface as demonstrated by unchanged partner binding affinities. However, the CTE (only 4 residues in HP1a as compared with 87 residues in HP1b) is critical; the charged residues in HP1a are necessary for tight peptide binding. Examining a panel of amino acid substitutions in the HP1a CSD, we find that Leu-165 in HP1a interacts with HP2 but not PIWI, supporting the conclusion that different sites in the binding surface provide discrimination for partner selection. Partner sequence is also critical for affinity, as the remaining difference in binding between HP2 and PIWI polypeptides is eliminated by swapping the PXVXL motifs between the two. Taken together, these studies indicate that the binding surface of the HP1a CSD plus its short CTE provide the needed discrimination among HP1a's partners, and that the CTE is important for differentiating the interactions of the Drosophila HP1 paralogs.
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Affiliation(s)
- Deanna L Mendez
- Department of Biology, Washington University, Saint Louis, Missouri 63130, USA
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18
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Mendez DL, Kim D, Chruszcz M, Stephens GE, Minor W, Khorasanizadeh S, Elgin SCR. The HP1a disordered C terminus and chromo shadow domain cooperate to select target peptide partners. Chembiochem 2011; 12:1084-96. [PMID: 21472955 DOI: 10.1002/cbic.201000598] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Indexed: 11/09/2022]
Abstract
Drosophila melanogaster heterochromatin protein 1a (HP1a) is essential for compacted heterochromatin structure and the associated gene silencing. Its chromo shadow domain (CSD) is well known for binding to peptides that contain a PXVXL motif. Heterochromatin protein 2 (HP2) is a non-histone chromosomal protein that associates with HP1a in the pericentric heterochromatin, telomeres, and the fourth chromosome. Using NMR spectroscopy, fluorescence polarization, and site-directed mutagenesis, we identified an LCVKI motif in HP2 that binds to the HP1a CSD. The binding affinity of the HP2 fragment is approximately two orders of magnitude higher than that of peptides from PIWI (with a PRVKV motif), AF10 (with a PLVVL motif), or CG15356 (with LYPLL and LSIVA motifs). To delineate differential interactions of the HP1a CSD, we characterized its structure, backbone dynamics, and dimerization constant. We found that the dimerization constant is bracketed by the affinities of HP2 and PIWI, which dock to the same HP1a homodimer surface. This suggests that HP2, but not PIWI, interaction can drive the homodimerization of HP1a. Interestingly, the integrity of the disordered C-terminal extension (CTE) of HP1a is essential for discriminatory binding, whereas swapping the PXVXL motifs does not confer specificity. Serine phosphorylation at the peptide binding surface of the CSD is thought to regulate heterochromatin assembly. Glutamic acid substitution at these sites destabilizes HP1a dimers, but improves the interaction with both binding partners. Our studies underscore the importance of CSD dimerization and cooperation with the CTE in forming distinct complexes of HP1a.
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Affiliation(s)
- Deanna L Mendez
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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19
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Drosophila RISC component VIG and its homolog Vig2 impact heterochromatin formation. PLoS One 2009; 4:e6182. [PMID: 19584931 PMCID: PMC2703606 DOI: 10.1371/journal.pone.0006182] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 05/29/2009] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin formation plays an important role in gene regulation and the maintenance of genome integrity. Here we present results from a study of the D. melanogaster gene vig, encoding an RNAi complex component and its homolog vig2 (CG11844) that support their involvement in heterochromatin formation and/or maintenance. Protein null mutations vig(EP812) and vig2(PL470) act as modifiers of Position Effect Variegation (PEV). VIG and Vig2 are present in polytene chromosomes and partially overlap with HP1. Quantitative immunoblots show depletion of HP1 and HP2 (large isoform) in isolated nuclei from the vig(EP812) mutant. The vig2(PL470) mutant strain demonstrates a decreased level of H3K9me2. Pull-down experiments using antibodies specific to HP1 recovered both VIG and Vig2. The association between HP1 and both VIG and Vig2 proteins depends on an RNA component. The above data and the developmental profiles of the two genes suggest that Vig2 may be involved in heterochromatin targeting and establishment early in development, while VIG may have a role in stabilizing HP1/HP2 chromatin binding during later stages.
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20
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Riddle NC, Shaffer CD, Elgin SCR. A lot about a little dot - lessons learned from Drosophila melanogaster chromosome 4. Biochem Cell Biol 2009; 87:229-41. [PMID: 19234537 DOI: 10.1139/o08-119] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome 4 is associated with heterochromatic marks, such as heterochromatin protein 1 and histone 3 lysine 9 methylation. Chromosome 4 is also marked by POF (painting-of-fourth), a chromosome 4-specific chromosomal protein, and utilizes a dedicated histone methyltransferase, EGG. Studies of chromosome 4 have helped to shape our understanding of heterochromatin domains and their establishment and maintenance. In this review, we provide a synthesis of the work to date and an outlook to the future.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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21
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Epigenetic marks for chromosome imprinting during spermatogenesis in coccids. Chromosoma 2009; 118:501-12. [DOI: 10.1007/s00412-009-0214-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 03/20/2009] [Accepted: 04/18/2009] [Indexed: 11/26/2022]
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22
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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.
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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
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23
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Girton JR, Johansen KM. Chromatin structure and the regulation of gene expression: the lessons of PEV in Drosophila. ADVANCES IN GENETICS 2008; 61:1-43. [PMID: 18282501 DOI: 10.1016/s0065-2660(07)00001-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Position-effect variegation (PEV) was discovered in 1930 in a study of X-ray-induced chromosomal rearrangements. Rearrangements that place euchromatic genes adjacent to a region of centromeric heterochromatin give a variegated phenotype that results from the inactivation of genes by heterochromatin spreading from the breakpoint. PEV can also result from P element insertions that place euchromatic genes into heterochromatic regions and rearrangements that position euchromatic chromosomal regions into heterochromatic nuclear compartments. More than 75 years of studies of PEV have revealed that PEV is a complex phenomenon that results from fundamental differences in the structure and function of heterochromatin and euchromatin with respect to gene expression. Molecular analysis of PEV began with the discovery that PEV phenotypes are altered by suppressor and enhancer mutations of a large number of modifier genes whose products are structural components of heterochromatin, enzymes that modify heterochromatic proteins, or are nuclear structural components. Analysis of these gene products has led to our current understanding that formation of heterochromatin involves specific modifications of histones leading to the binding of particular sets of heterochromatic proteins, and that this process may be the mechanism for repressing gene expression in PEV. Other modifier genes produce products whose function is part of an active mechanism of generation of euchromatin that resists heterochromatization. Current studies of PEV are focusing on defining the complex patterns of modifier gene activity and the sequence of events that leads to the dynamic interplay between heterochromatin and euchromatin.
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Affiliation(s)
- Jack R Girton
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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24
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Andreyeva EN, Kolesnikova TD, Demakova OV, Mendez-Lago M, Pokholkova GV, Belyaeva ES, Rossi F, Dimitri P, Villasante A, Zhimulev IF. High-resolution analysis of Drosophila heterochromatin organization using SuUR Su(var)3-9 double mutants. Proc Natl Acad Sci U S A 2007; 104:12819-24. [PMID: 17640911 PMCID: PMC1937550 DOI: 10.1073/pnas.0704690104] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural and functional analyses of heterochromatin are essential to understanding how heterochromatic genes are regulated and how centromeric chromatin is formed. Because the repetitive nature of heterochromatin hampers its genome analysis, new approaches need to be developed. Here, we describe how, in double mutants for Su(var)3-9 and SuUR genes encoding two structural proteins of heterochromatin, new banded heterochromatic segments appear in all polytene chromosomes due to the strong suppression of under-replication in pericentric regions. FISH on salivary gland polytene chromosomes from these double mutant larvae allows high resolution of heterochromatin mapping. In addition, immunostaining experiments with a set of antibodies against euchromatic and heterochromatic proteins reveal their unusual combinations in the newly appeared segments: binding patterns for HP1 and HP2 are coincident, but both are distinct from H3diMetK9 and H4triMetK20. In several regions, partial overlapping staining is observed for the proteins characteristic of active chromatin RNA Pol II, H3triMetK4, Z4, and JIL1, the boundary protein BEAF, and the heterochromatin-enriched proteins HP1, HP2, and SU(VAR)3-7. The exact cytological position of the centromere of chromosome 3 was visualized on salivary gland polytene chromosomes by using the centromeric dodeca satellite and the centromeric protein CID. This region is enriched in H3diMetK9 and H4triMetK20 but is devoid of other proteins analyzed.
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Affiliation(s)
- Eugenia N. Andreyeva
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Tatyana D. Kolesnikova
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga V. Demakova
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Maria Mendez-Lago
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autonóma de Madrid, Cantoblanco, 28049 Madrid, Spain; and
| | - Galina V. Pokholkova
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S. Belyaeva
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Fabrizio Rossi
- Istituto Pasteur–Fondazione Cenci Bolognetti and Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Via dei Sardi, 70, 00185 Rome, Italy
| | - Patrizio Dimitri
- Istituto Pasteur–Fondazione Cenci Bolognetti and Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Via dei Sardi, 70, 00185 Rome, Italy
| | - Alfredo Villasante
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autonóma de Madrid, Cantoblanco, 28049 Madrid, Spain; and
| | - Igor F. Zhimulev
- *Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- To whom correspondence should be addressed at:
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentyev Avenue 10, Novosibirsk 630090, Russia. E-mail:
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25
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Abstract
Transcription in heterochromatin seems to be an oxymoron--surely the 'silenced' form of chromatin should not be transcribed. But there have been frequent reports of low-level transcription in heterochromatic regions, and several hundred genes are found in these regions in Drosophila. Most strikingly, recent investigations implicate RNA interference mechanisms in targeting and maintaining heterochromatin, and these mechanisms are inherently dependent on transcription. Silencing of chromatin might involve trans-acting sources of the crucial small RNAs that carry out RNA interference, but in some cases, transcription of the region to be silenced seems to be required--an apparent contradiction.
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Affiliation(s)
- Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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26
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Stephens GE, Xiao H, Lankenau DH, Wu C, Elgin SCR. Heterochromatin protein 2 interacts with Nap-1 and NURF: a link between heterochromatin-induced gene silencing and the chromatin remodeling machinery in Drosophila. Biochemistry 2007; 45:14990-9. [PMID: 17154536 PMCID: PMC2534143 DOI: 10.1021/bi060983y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterochromatin protein 2 (HP2) is a nonhistone chromosomal protein from Drosophila melanogaster that binds to heterochromatin protein 1 (HP1) and has been implicated in heterochromatin-induced gene silencing. Heretofore, HP1 has been the only known binding partner of HP2, a large protein devoid of sequence motifs other than a pair of AT hooks. In an effort to identify proteins that interact with HP2 and assign functions to its various domains, nuclear proteins were fractionated under nondenaturing conditions. On separation of nuclear proteins, nucleosome assembly protein 1 (Nap-1) has an overlapping elution profile with HP2 (assayed by Western blot) and has been identified by mass spectrometry in fractions with HP2. Upon probing fractions in which HP2 and Nap-1 are both present, we find that the nucleosome remodeling factor (NURF), an ISWI-dependent chromatin remodeling complex, is also present. Results from coimmunoprecipitation experiments suggest that HP2 interacts with Nap-1 as well as with NURF; NURF appears to interact directly with both HP2 and Nap-1. Three distinct domains within HP2 mediate the interaction with NURF, allowing us to assign NURF binding domains in addition to the AT hooks and HP1 binding domains already mapped in HP2. Mutations in Nap-1 are shown to suppress position effect variegation, suggesting that Nap-1 functions to help to assemble chromatin into a closed form, as does HP2. On the basis of these interactions, we speculate that HP2 may cooperate with these factors in the remodeling of chromatin for silencing.
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Affiliation(s)
- Gena E. Stephens
- Department of Biology, Washington University, CB-1229, St. Louis, MO 63130
- Correspondence to be sent to: Gena E. Stephens, Telephone: 314-935-6837, Fax: 314-935-5125, E-mail:
| | - Hua Xiao
- Laboratory of Molecular Cell Biology, National Cancer Institute, Building 37, Room 6068, National Institutes of Health, Bethesda, Maryland 20892
| | - Dirk-H. Lankenau
- University of Heidelberg, Institute of Zoology, Im Neuenheimer Feld 230, D-69120 Heidelberg, Germany
| | - Carl Wu
- Laboratory of Molecular Cell Biology, National Cancer Institute, Building 37, Room 6068, National Institutes of Health, Bethesda, Maryland 20892
| | - Sarah C. R. Elgin
- Department of Biology, Washington University, CB-1229, St. Louis, MO 63130
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27
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Volpi S, Bongiorni S, Prantera G. HP2-like protein: a new piece of the facultative heterochromatin puzzle. Chromosoma 2007; 116:249-58. [PMID: 17297601 DOI: 10.1007/s00412-007-0095-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/04/2007] [Accepted: 01/08/2007] [Indexed: 11/28/2022]
Abstract
In Drosophila melanogaster, the two chromosomal proteins HP1 and HP2 colocalize on heterochromatic and euchromatic sites in polytene chromosomes. Mutations in the HP2 gene act as dominant suppressors of position effect variegation, demonstrating a role for HP2 in the formation or maintenance of heterochromatin. In this paper, we investigated whether a putative homolog of the D. melanogaster HP2 is involved in the facultative heterochromatinization process in mealybugs. Using an antibody raised against the Drosophila HP2, we identified in the mealybug Planococcus citri a cross-reactive epitope, which we refer to as HP2-like. We investigated the HP2-like pattern during the male embryo development where the entire paternal haploid chromosome set becomes heterochromatic. The HP2 antibody heavily decorates the chromocenters, where it localizes with HP1, and marks the chromatin before it acquires the full cytological characteristics of the male-specific heterochromatin. In euchromatic chromosomes, HP2-like is mainly concentrated at telomeric sites. The interplay between HP2-like and HP1-like was studied by dsRNA interference experiments. Extinguishing HP1-like expression by RNAi does not prevent the association of HP2-like with facultative heterochromatin, implying that HP2-like binds to chromatin in a HP1-independent manner. Our results confirm and extend the structural and functional conservation of proteins involved in heterochromatin assembly.
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Affiliation(s)
- Silvia Volpi
- Dipartimento di Agrobiologia e Agrochimica, Università della Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy
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28
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Greil F, de Wit E, Bussemaker HJ, van Steensel B. HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. EMBO J 2007; 26:741-51. [PMID: 17255947 PMCID: PMC1794385 DOI: 10.1038/sj.emboj.7601527] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 11/23/2006] [Indexed: 01/08/2023] Open
Abstract
Heterochromatin is important for the maintenance of genome stability and regulation of gene expression; yet our knowledge of heterochromatin structure and function is incomplete. We identified four novel Drosophila heterochromatin proteins (HPs). Three of these proteins (HP3, HP4 and HP5) interact directly with HP1, whereas HP6 in turn binds to each of these three proteins. Immunofluorescence microscopy and genome-wide mapping of in vivo binding sites shows that all four proteins are components of heterochromatin. Depletion of HP1 causes redistribution of all four proteins, indicating that HP1 is essential for their heterochromatic targeting. Finally, mutants of HP4 and HP5 are dominant suppressors of position effect variegation, demonstrating their importance in heterochromatic gene silencing. These results indicate that HP1 acts as a docking platform for several mediator proteins that contribute to heterochromatin function.
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Affiliation(s)
- Frauke Greil
- Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elzo de Wit
- Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Harmen J Bussemaker
- Department of Biological Sciences and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Bas van Steensel
- Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX Amsterdam, The Netherlands. Tel.: +31 20 512 2040; Fax: +31 20 669 1383; E-mail:
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29
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Haynes KA, Gracheva E, Elgin SCR. A Distinct type of heterochromatin within Drosophila melanogaster chromosome 4. Genetics 2006; 175:1539-42. [PMID: 17194780 PMCID: PMC1840055 DOI: 10.1534/genetics.106.066407] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Studies of transcriptional gene silencing in Drosophila melanogaster suggest that most of chromosome 4 resembles pericentric heterochromatin. However, some modifiers of position-effect variegation, including chromosome 4 dosage and loss of SU(VAR)3-9, have different effects on silencing in pericentric vs. distal arm chromosome 4 heterochromatin, distinguishing these two heterochromatin types.
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Affiliation(s)
- Karmella A Haynes
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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30
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Demakova OV, Pokholkova GV, Kolesnikova TD, Demakov SA, Andreyeva EN, Belyaeva ES, Zhimulev IF. The SU(VAR)3-9/HP1 complex differentially regulates the compaction state and degree of underreplication of X chromosome pericentric heterochromatin in Drosophila melanogaster. Genetics 2006; 175:609-20. [PMID: 17151257 PMCID: PMC1800617 DOI: 10.1534/genetics.106.062133] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In polytene chromosomes of Drosophila melanogaster, regions of pericentric heterochromatin coalesce to form a compact chromocenter and are highly underreplicated. Focusing on study of X chromosome heterochromatin, we demonstrate that loss of either SU(VAR)3-9 histone methyltransferase activity or HP1 protein differentially affects the compaction of different pericentric regions. Using a set of inversions breaking X chromosome heterochromatin in the background of the Su(var)3-9 mutations, we show that distal heterochromatin (blocks h26-h29) is the only one within the chromocenter to form a big "puff"-like structure. The "puffed" heterochromatin has not only unique morphology but also very special protein composition as well: (i) it does not bind proteins specific for active chromatin and should therefore be referred to as a pseudopuff and (ii) it strongly associates with heterochromatin-specific proteins SU(VAR)3-7 and SUUR, despite the fact that HP1 and HP2 are depleted particularly from this polytene structure. The pseudopuff completes replication earlier than when it is compacted as heterochromatin, and underreplication of some DNA sequences within the pseudopuff is strongly suppressed. So, we show that pericentric heterochromatin is heterogeneous in its requirement for SU(VAR)3-9 with respect to the establishment of the condensed state, time of replication, and DNA polytenization.
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Affiliation(s)
- Olga V Demakova
- Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
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31
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Shaffer CD, Cenci G, Thompson B, Stephens GE, Slawson EE, Adu-Wusu K, Gatti M, Elgin SCR. The large isoform of Drosophila melanogaster heterochromatin protein 2 plays a critical role in gene silencing and chromosome structure. Genetics 2006; 174:1189-204. [PMID: 16980400 PMCID: PMC1667101 DOI: 10.1534/genetics.106.057604] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster heterochromatin protein 2 (HP2) interacts with heterochromatin protein 1 (HP1). In polytene chromosomes, HP2 and HP1 colocalize at the chromocenter, telomeres, and the small fourth chromosome. We show here that HP2 is present in the arms as well as the centromeric regions of mitotic chromosomes. We also demonstrate that Su(var)2-HP2 exhibits a dosage-dependent modification of variegation of a yellow reporter transgene, indicating a structural role in heterochromatin formation. We have isolated and characterized 14 new mutations in the Su(var)2-HP2 gene. Using wm4h, many (but not all) mutant alleles show dominant Su(var) activity. Su(var)2-HP2 mutant larvae show a wide variety of mitotic abnormalities, but not the telomere fusion seen in larvae deficient for HP1. The Su(var)2-HP2 gene codes for two isoforms: HP2-L (approximately 365 kDa) and HP2-S (approximately 175 kDa), lacking exons 5 and 6. In general, mutations that affect only the larger isoform result in more pronounced defects than do mutations common to both isoforms. This suggests that an imbalance between large and small isoforms is particularly deleterious. These results indicate a role for HP2 in the structural organization of chromosomes and in heterochromatin-induced gene silencing and show that the larger isoform plays a critical role in these processes.
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Blattes R, Monod C, Susbielle G, Cuvier O, Wu JH, Hsieh TS, Laemmli UK, Käs E. Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide. EMBO J 2006; 25:2397-408. [PMID: 16675949 PMCID: PMC1478169 DOI: 10.1038/sj.emboj.7601125] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 04/11/2006] [Indexed: 11/09/2022] Open
Abstract
The functions of DNA satellites of centric heterochromatin are difficult to assess with classical molecular biology tools. Using a chemical approach, we demonstrate that synthetic polyamides that specifically target AT-rich satellite repeats of Drosophila melanogaster can be used to study the function of these sequences. The P9 polyamide, which binds the X-chromosome 1.688 g/cm3 satellite III (SAT III), displaces the D1 protein. This displacement in turn results in a selective loss of HP1 and topoisomerase II from SAT III, while these proteins remain bound to the adjacent rDNA repeats and to other regions not targeted by P9. Conversely, targeting of (AAGAG)n satellite V repeats by the P31 polyamide results in the displacement of HP1 from these sequences, indicating that HP1 interactions with chromatin are sensitive to DNA-binding ligands. P9 fed to larvae suppresses the position-effect variegation phenotype of white-mottled adult flies. We propose that this effect is due to displacement of the heterochromatin proteins D1, HP1 and topoisomerase II from SAT III, hence resulting in stochastic chromatin opening and desilencing of the nearby white gene.
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Affiliation(s)
- Roxane Blattes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Caroline Monod
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Guillaume Susbielle
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Olivier Cuvier
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier Cedex, France
| | - Jian-hong Wu
- Department of Biochemistry, Nanaline H Duke Building, Duke University Medical Center, Durham, NC, USA
| | - Tao-shih Hsieh
- Department of Biochemistry, Nanaline H Duke Building, Duke University Medical Center, Durham, NC, USA
| | - Ulrich K Laemmli
- Département de Biologie Moléculaire, Université de Genève, Sciences II, Geneva, Switzerland
| | - Emmanuel Käs
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
- LBME, UMR5099, IBCG, 118 route de Narbonne, 31062 Toulouse Cedex 9, France. Tel.: +33 561 335959; Fax: +33 561 335886; E-mail:
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33
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Andreyeva EN, Belyaeva ES, Semeshin VF, Pokholkova GV, Zhimulev IF. Three distinct chromatin domains in telomere ends of polytene chromosomes in Drosophila melanogaster Tel mutants. J Cell Sci 2005; 118:5465-77. [PMID: 16278293 DOI: 10.1242/jcs.02654] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Drosophila melanogaster telomeric DNA is known to comprise two domains: the terminal tract of retrotransposons (HeT-A, TART and TAHRE) and telomere-associated sequences (TAS). Chromosome tips are capped by a protein complex, which is assembled on the chromosome ends independently of the underlying terminal DNA sequences. To investigate the properties of these domains in salivary gland polytene chromosomes, we made use of Tel mutants. Telomeres in this background are elongated owing to the amplification of a block of terminal retroelements. Supercompact heterochromatin is absent from the telomeres of polytene chromosomes: electron microscopy analysis identifies the telomeric cap and the tract of retroelements as a reticular material, having no discernible banding pattern, whereas TAS repeats appear as faint bands. According to the pattern of bound proteins, the cap, tract of retroelements and TAS constitute distinct and non-overlapping domains in telomeres. SUUR, HP2, SU(VAR)3-7 and H3Me3K27 localize to the cap region, as has been demonstrated for HP1. All these proteins are also found in pericentric heterochromatin. The tract of retroelements is associated with proteins characteristic for both heterochromatin (H3Me3K9) and euchromatin (H3Me3K4, JIL-1, Z4). The TAS region is enriched for H3Me3K27. PC and E(Z) are detected both in TAS and many intercalary heterochromatin regions. Telomeres complete replication earlier than heterochromatic regions. The frequency of telomeric associations in salivary gland polytene chromosomes does not depend on the SuUR gene dosage, rather it appears to be defined by the telomere length.
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Affiliation(s)
- Evgenia N Andreyeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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34
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Stephens GE, Slawson EE, Craig CA, Elgin SCR. Interaction of heterochromatin protein 2 with HP1 defines a novel HP1-binding domain. Biochemistry 2005; 44:13394-403. [PMID: 16201764 PMCID: PMC2534139 DOI: 10.1021/bi051006+] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heterochromatin Protein 2 (HP2) is a nonhistone chromosomal protein from Drosophila melanogaster localized principally in the pericentric heterochromatin, telomeres, and fourth chromosome, all regions associated with HP1. Mutations in HP2 can suppress position effect variegation, indicating a role in gene silencing and heterochromatin formation [Shaffer, C. D. et al. (2002) Proc. Natl. Acad. Sci.U.S.A. 99, 14332-14337]. In vitro coimmunoprecipitation experiments with various peptides from HP2 have identified a single HP1-binding domain. Conserved domains in HP2, including those within the HP1-binding region, have been identified by recovering and sequencing Su(var)2-HP2 from D. willistoni and D. virilis, as well as examining available sequence data from D. pseudoobscura. A PxVxL motif, shown to be an HP1-binding domain in many HP1-interacting proteins, is observed but is not well-conserved in location and sequence and does not mediate HP2 binding to HP1. The sole HP1-binding domain is composed of two conserved regions of 12 and 16 amino acids separated by 19 amino acids. Site-directed mutagenesis within the two conserved regions has shown that the 16 amino acid domain is critical for HP1 binding. This constitutes a novel domain for HP1 interaction, providing a critical link for heterochromatin formation in Drosophila.
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Affiliation(s)
- Gena E Stephens
- Department of Biology, Washington University, CB-1229, St. Louis, Missouri 63130, USA.
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35
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Nikolenko JV, Shidlovskii YV, Lebedeva LA, Krasnov AN, Georgieva SG, Nabirochkina EN. Transcriptional Coactivator SAYP Can Suppress Transcription in Heterochromatin. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Shidlovskii YV, Krasnov AN, Nikolenko JV, Lebedeva LA, Kopantseva M, Ermolaeva MA, Ilyin YV, Nabirochkina EN, Georgiev PG, Georgieva SG. A novel multidomain transcription coactivator SAYP can also repress transcription in heterochromatin. EMBO J 2005; 24:97-107. [PMID: 15616585 PMCID: PMC544920 DOI: 10.1038/sj.emboj.7600508] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Accepted: 11/15/2004] [Indexed: 11/08/2022] Open
Abstract
Enhancers of yellow (e(y)) is a group of genetically and functionally related genes for proteins involved in transcriptional regulation. The e(y)3 gene of Drosophila considered here encodes a ubiquitous nuclear protein that has homologues in other metazoan species. The protein encoded by e(y)3, named Supporter of Activation of Yellow Protein (SAYP), contains an AT-hook, two PHD fingers, and a novel evolutionarily conserved domain with a transcriptional coactivator function. Mutants expressing a truncated SAYP devoid of the conserved domain die at a midembryonic stage, which suggests a crucial part for SAYP during early development. SAYP binds to numerous sites of transcriptionally active euchromatin on polytene chromosomes and coactivates transcription of euchromatin genes. Unexpectedly, SAYP is also abundant in the heterochromatin regions of the fourth chromosome and in the chromocenter, and represses the transcription of euchromatin genes translocated to heterochromatin; its PHD fingers are essential to heterochromatic silencing. Thus, SAYP plays a dual role in transcription regulation in euchromatic and heterochromatic regions.
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Affiliation(s)
| | - Aleksey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Russia
- Centre for Medical Studies, University of Oslo, Moscow, Russia
| | | | | | | | | | - Yurij V Ilyin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Russia
| | - Elena N Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, Russia
- Centre for Medical Studies, University of Oslo, Moscow, Russia
| | | | - Sofia G Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Russia
- Centre for Medical Studies, University of Oslo, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Russia
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37
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Abstract
We focus here on the intercalary heterochromatin (IH) of Drosophila melanogaster and, in particular, its molecular properties. In the polytene chromosomes of Drosophila, IH is represented by a reproducible set of dense bands scattered along the euchromatic arms. IH contains mainly unique DNA sequences, and shares certain features with other heterochromatin types such as pericentric, telomeric, and PEV-induced heterochromatin, the inactive mammalian X-chromosome and the heterochromatized male chromosome set in coccids. These features are transcriptional silencing, chromatin compactness, late DNA replication, underrreplication or elimination in somatic cells, and formation of the heterochromatin state in early embryogenesis. Post-translational modification of histones and the specific nonhistone protein complexes are shown to participate in the establishment and maintenance of silencing for all heterochromatin types. Many IH regions contain binding sites for HP1 and/or Pc-G proteins and all the regions are sites of heterochromatin-associated SuUR protein. Some IH regions are known to contain homeotic genes. Summarizing these data, we suggest that IH regions comprise stable inactivated genes, whose silencing is developmentally programmed.
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Affiliation(s)
- Igor F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Russia
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38
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Adkins NL, Watts M, Georgel PT. To the 30-nm chromatin fiber and beyond. ACTA ACUST UNITED AC 2004; 1677:12-23. [PMID: 15020041 DOI: 10.1016/j.bbaexp.2003.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Revised: 09/25/2003] [Accepted: 09/25/2003] [Indexed: 10/26/2022]
Abstract
Chromatin fibers are intrinsically dynamic macromolecular complexes whose biological functions are intimately linked with their structure and interactions with chromatin-associated proteins (CAPs). Three-dimensional architectural transitions between or within the two co-existing chromatin types referred to as euchromatin and heterochromatin have been associated with activation or repression of nuclear functions. The presence of specific subsets of chromosomal proteins co-existing with the different chromatin conformations suggests a functional significance for their co-localization. The major points of emphasis of this review will assess the structure, function and recently documented exchanges amongst various members of the CAP family.
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Affiliation(s)
- Nicholas L Adkins
- Department of Biological Sciences, College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV 25701, USA
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39
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Pal-Bhadra M, Leibovitch BA, Gandhi SG, Chikka MR, Rao M, Bhadra U, Birchler JA, Elgin SCR. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 2004; 303:669-72. [PMID: 14752161 DOI: 10.1126/science.1092653] [Citation(s) in RCA: 541] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genes normally resident in euchromatic domains are silenced when packaged into heterochromatin, as exemplified in Drosophila melanogaster by position effect variegation (PEV). Loss-of-function mutations resulting in suppression of PEV have identified critical components of heterochromatin, including proteins HP1, HP2, and histone H3 lysine 9 methyltransferase. Here, we demonstrate that this silencing is dependent on the RNA interference machinery, using tandem mini-white arrays and white transgenes in heterochromatin to show loss of silencing as a result of mutations in piwi, aubergine, or spindle-E (homeless), which encode RNAi components. These mutations result in reduction of H3 Lys9 methylation and delocalization of HP1 and HP2, most dramatically in spindle-E mutants.
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Affiliation(s)
- Manika Pal-Bhadra
- Division of Biological Sciences, 117 Tucker Hall, University of Missouri, Columbia, MO 65211, USA
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40
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Zhimulev IF, Belyaeva ES, Semeshin VF, Koryakov DE, Demakov SA, Demakova OV, Pokholkova GV, Andreyeva EN. Polytene Chromosomes: 70 Years of Genetic Research. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 241:203-75. [PMID: 15548421 DOI: 10.1016/s0074-7696(04)41004-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Polytene chromosomes were described in 1881 and since 1934 they have served as an outstanding model for a variety of genetic experiments. Using the polytene chromosomes, numerous biological phenomena were discovered. First the polytene chromosomes served as a model of the interphase chromosomes in general. In polytene chromosomes, condensed (bands), decondensed (interbands), genetically active (puffs), and silent (pericentric and intercalary heterochromatin as well as regions subject to position effect variegation) regions were found and their features were described in detail. Analysis of the general organization of replication and transcription at the cytological level has become possible using polytene chromosomes. In studies of sequential puff formation it was found for the first time that the steroid hormone (ecdysone) exerts its action through gene activation, and that the process of gene activation upon ecdysone proceeds as a cascade. Namely on the polytene chromosomes a new phenomenon of cellular stress response (heat shock) was discovered. Subsequently chromatin boundaries (insulators) were discovered to flank the heat shock puffs. Major progress in solving the problems of dosage compensation and position effect variegation phenomena was mainly related to studies on polytene chromosomes. This review summarizes the current status of studies of polytene chromosomes and of various phenomena described using this successful model.
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia
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41
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Abstract
The information contained within the linear sequence of bases (the genome) must be faithfully replicated in each cell cycle, with a balance of constancy and variation taking place over the course of evolution. Recently, it has become clear that additional information important for genetic regulation is contained within the chromatin proteins associated with DNA (the epigenome). Epigenetic information also must be faithfully duplicated in each cell cycle, with a balance of constancy and variation taking place during the course of development to achieve differentiation while maintaining identity within cell lineages. Both the genome and the epigenome are synthesized at the replication fork, so the events occurring during S-phase provide a critical window of opportunity for eliciting change or maintaining existing genetic states. Cells discriminate between different states of chromatin through the activities of proteins that selectively modify the structure of chromatin. Several recent studies report the localization of certain chromatin modifying proteins to replication forks at specific times during S-phase. Since transcriptionally active and inactive chromosome domains generally replicate at different times during S-phase, this spatiotemporal regulation of chromatin assembly proteins may be an integral part of epigenetic inheritance.
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Affiliation(s)
- Adrian J McNairn
- Department of Biochemistry and Molecular Biology, S.U.N.Y. Syracuse, NY 13210, USA
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42
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Jaskelioff M, Peterson CL. Chromatin and transcription: histones continue to make their marks. Nat Cell Biol 2003; 5:395-9. [PMID: 12724776 DOI: 10.1038/ncb0503-395] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mariela Jaskelioff
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St, Worcester, MA 01605, USA
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43
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Stephens GE, Craig CA, Li Y, Wallrath LL, Elgin SCR. Immunofluorescent staining of polytene chromosomes: exploiting genetic tools. Methods Enzymol 2003; 376:372-93. [PMID: 14975319 DOI: 10.1016/s0076-6879(03)76025-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gena E Stephens
- Biology Department, Washington University in St. Louis, Missouri 63130, USA
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