1
|
Vizjak P, Kamp D, Hepp N, Scacchetti A, Gonzalez Pisfil M, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. Nat Struct Mol Biol 2024:10.1038/s41594-024-01290-x. [PMID: 38664566 DOI: 10.1038/s41594-024-01290-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/25/2024] [Indexed: 05/07/2024]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with our data. We speculate that monkey-bar mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
Collapse
Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- ViraTherapeutics GmbH, Rum, Austria
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
2
|
Vizjak P, Kamp D, Hepp N, Scacchetti A, Pisfil MG, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569516. [PMID: 38106060 PMCID: PMC10723341 DOI: 10.1101/2023.12.04.569516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. We investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner qualitatively agree with our data. We speculate that 'monkey-bar' mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
Collapse
Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Nicola Hepp
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Epigenetics Institute & Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia (PA), USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| |
Collapse
|
3
|
Karl LA, Galanti L, Bantele SC, Metzner F, Šafarić B, Rajappa L, Foster B, Pires VB, Bansal P, Chacin E, Basquin J, Duderstadt KE, Kurat CF, Bartke T, Hopfner KP, Pfander B. A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler. Life Sci Alliance 2023; 6:e202201790. [PMID: 37468166 PMCID: PMC10355287 DOI: 10.26508/lsa.202201790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Fun30 is the prototype of the Fun30-SMARCAD1-ETL subfamily of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single-subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30Δ mutant. In vitro, Fun30 protein lacking the SAM-key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity and nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome-remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.
Collapse
Affiliation(s)
- Leonhard A Karl
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Susanne Cs Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Barbara Šafarić
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Benjamin Foster
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Vanessa Borges Pires
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Jerôme Basquin
- Crystallization Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
- Physik Department, Technische Universität München, Munich, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| |
Collapse
|
4
|
Martino S, Carollo PS, Barra V. A Glimpse into Chromatin Organization and Nuclear Lamina Contribution in Neuronal Differentiation. Genes (Basel) 2023; 14:genes14051046. [PMID: 37239406 DOI: 10.3390/genes14051046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through the formation of specific regions of active as well as inactive chromatin, allow the coordinated regulation of the genes for each cell fate. In this mini-review, we discuss the current knowledge regarding the regulation of three-dimensional chromatin structure during neuronal differentiation. We also focus on the role the nuclear lamina plays in neurogenesis to ensure the tethering of the chromatin to the nuclear envelope.
Collapse
Affiliation(s)
- Salvatore Martino
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Pietro Salvatore Carollo
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Viviana Barra
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| |
Collapse
|
5
|
Molecular basis of chromatin remodeling by Rhp26, a yeast CSB ortholog. Proc Natl Acad Sci U S A 2019; 116:6120-6129. [PMID: 30867290 DOI: 10.1073/pnas.1818163116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
CSB/ERCC6 belongs to an orphan subfamily of SWI2/SNF2-related chromatin remodelers and plays crucial roles in gene expression, DNA damage repair, and the maintenance of genome integrity. The molecular basis of chromatin remodeling by Cockayne syndrome B protein (CSB) is not well understood. Here we investigate the molecular mechanism of chromatin remodeling by Rhp26, a Schizosaccharomyces pombe CSB ortholog. The molecular basis of chromatin remodeling and nucleosomal epitope recognition by Rhp26 is distinct from that of canonical chromatin remodelers, such as imitation switch protein (ISWI). We reveal that the remodeling activities are bidirectionally regulated by CSB-specific motifs: the N-terminal leucine-latch motif and the C-terminal coupling motif. Rhp26 remodeling activities depend mainly on H4 tails and to a lesser extent on H3 tails, but not on H2A and H2B tails. Rhp26 promotes the disruption of histone cores and the release of free DNA. Finally, we dissected the distinct contributions of two Rhp26 C-terminal regions to chromatin remodeling and DNA damage repair.
Collapse
|
6
|
El-Gammal Z, AlOkda A, El-Badri N. Role of human oocyte-enriched factors in somatic cell reprograming. Mech Ageing Dev 2018; 175:88-99. [PMID: 29890177 DOI: 10.1016/j.mad.2018.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
Abstract
Cellular reprograming paves the way for creating functional patient-specific tissues to eliminate immune rejection responses by applying the same genetic profile. However, the epigenetic memory of a cell remains a challenge facing the current reprograming methods and does not allow transcription factors to bind properly. Because somatic cells can be reprogramed by transferring their nuclear contents into oocytes, introducing specific oocyte factors into differentiated cells is considered a promising approach for mimicking the reprograming process that occurs during fertilization. Mammalian metaphase II oocyte possesses a superior capacity to epigenetically reprogram somatic cell nuclei towards an embryonic stem cell-like state than the current factor-based reprograming approaches. This may be due to the presence of specific factors that are lacking in the current factor-based reprograming approaches. In this review, we focus on studies identifying human oocyte-enriched factors aiming to understand the molecular mechanisms mediating cellular reprograming. We describe the role of oocyte-enriched factors in metabolic switch, chromatin remodelling, and global epigenetic transformation. This is critical for improving the quality of resulting reprogramed cells, which is crucial for therapeutic applications.
Collapse
Affiliation(s)
- Zaynab El-Gammal
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Egypt
| | - Abdelrahman AlOkda
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Egypt.
| |
Collapse
|
7
|
Manning BJ, Yusufzai T. The ATP-dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities. J Biol Chem 2017; 292:11927-11936. [PMID: 28533432 PMCID: PMC5512084 DOI: 10.1074/jbc.m117.779470] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/19/2017] [Indexed: 01/04/2023] Open
Abstract
Proper chromatin regulation is central to genome function and maintenance. The group III chromodomain–helicase–DNA-binding (CHD) family of ATP-dependent chromatin remodeling enzymes, comprising CHD6, CHD7, CHD8, and CHD9, has well-documented roles in transcription regulation, impacting both organism development and disease etiology. These four enzymes are similar in their constituent domains, but they fill surprisingly non-redundant roles in the cell, with deficiencies in individual enzymes leading to dissimilar disease states such as CHARGE syndrome or autism spectrum disorders. The mechanisms explaining their divergent, non-overlapping functions are unclear. In this study, we performed an in-depth biochemical analysis of purified CHD6, CHD7, and CHD8 and discovered distinct differences in chromatin remodeling specificities and activities among them. We report that CHD6 and CHD7 both bind with high affinity to short linker DNA, whereas CHD8 requires longer DNA for binding. As a result, CHD8 slides nucleosomes into positions with more flanking linker DNA than CHD7. Moreover, we found that, although CHD7 and CHD8 slide nucleosomes, CHD6 disrupts nucleosomes in a distinct non-sliding manner. The different activities of these enzymes likely lead to differences in chromatin structure and, thereby, transcriptional control, at the enhancer and promoter loci where these enzymes bind. Overall, our work provides a mechanistic basis for both the non-redundant roles and the diverse mutant disease states of these enzymes in vivo.
Collapse
Affiliation(s)
- Benjamin J Manning
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215.
| |
Collapse
|
8
|
Hepp MI, Smolle M, Gidi C, Amigo R, Valenzuela N, Arriagada A, Maureira A, Gogol MM, Torrejón M, Workman JL, Gutiérrez JL. Role of Nhp6 and Hmo1 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:316-326. [PMID: 28089519 PMCID: PMC5913752 DOI: 10.1016/j.bbagrm.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/05/2017] [Accepted: 01/07/2017] [Indexed: 10/20/2022]
Abstract
Diverse chromatin modifiers are involved in regulation of gene expression at the level of transcriptional regulation. Among these modifiers are ATP-dependent chromatin remodelers, where the SWI/SNF complex is the founding member. It has been observed that High Mobility Group (HMG) proteins can influence the activity of a number of these chromatin remodelers. In this context, we have previously demonstrated that the yeast HMG proteins Nhp6 and Hmo1 can stimulate SWI/SNF activity. Here, we studied the genome-wide binding patterns of Nhp6, Hmo1 and the SWI/SNF complex, finding that most of gene promoters presenting high occupancy of this complex also display high enrichment of these HMG proteins. Using deletion mutant strains we demonstrate that binding of SWI/SNF is significantly reduced at numerous genomic locations by deletion of NHP6 and/or deletion of HMO1. Moreover, alterations in the nucleosome landscape take place at gene promoters undergoing reduced SWI/SNF binding. Additional analyses show that these effects also correlate with alterations in transcriptional activity. Our results suggest that, besides the ability to stimulate SWI/SNF activity, these HMG proteins are able to assist the loading of this complex onto gene regulatory regions.
Collapse
Affiliation(s)
- Matias I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Michaela Smolle
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Cristian Gidi
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Roberto Amigo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Nicole Valenzuela
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Axel Arriagada
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Alejandro Maureira
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Marcela Torrejón
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - José L Gutiérrez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile.
| |
Collapse
|
9
|
Quan J, Yusufzai T. The tumor suppressor chromodomain helicase DNA-binding protein 5 (CHD5) remodels nucleosomes by unwrapping. J Biol Chem 2015; 289:20717-26. [PMID: 24923445 DOI: 10.1074/jbc.m114.568568] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although mutations or deletions of chromodomain helicase DNA-binding protein 5 (CHD5) have been linked to cancer and implicate CHD5 in tumor suppression, the ATP-dependent activity of CHD5 is currently unknown. In this study, we discovered that CHD5 is a chromatin remodeling factor with a unique enzymatic activity. CHD5 can expose nucleosomal DNA at one or two discrete positions in the nucleosome. The exposure of the nucleosomal DNA by CHD5 is dependent on ATP hydrolysis, but continued ATP hydrolysis is not required to maintain the nucleosomes in their remodeled state. The activity of CHD5 is distinct from other related chromatin remodeling ATPases, such as ACF and BRG1, and does not lead to complete disruption or destabilization of the nucleosome. Rather, CHD5 likely initiates remodeling in a manner similar to that of other remodeling factors but does not significantly reposition the nucleosome. While the related factor CHD4 shows strong ATPase activity, it does not unwrap nucleosomes as efficiently as CHD5. Our findings add to the growing evidence that chromatin remodeling ATPases have diverse roles in modulating chromatin structure.
Collapse
|
10
|
Al-Ani G, Briggs K, Malik SS, Conner M, Azuma Y, Fischer CJ. Quantitative determination of binding of ISWI to nucleosomes and DNA shows allosteric regulation of DNA binding by nucleotides. Biochemistry 2014; 53:4334-45. [PMID: 24898734 PMCID: PMC4100786 DOI: 10.1021/bi500224t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
regulation of chromatin structure is controlled by a family
of molecular motors called chromatin remodelers. The ability of these
enzymes to remodel chromatin structure is dependent on their ability
to couple ATP binding and hydrolysis into the mechanical work that
drives nucleosome repositioning. The necessary first step in determining
how these essential enzymes perform this function is to characterize
both how they bind nucleosomes and how this interaction is regulated
by ATP binding and hydrolysis. With this goal in mind, we monitored
the interaction of the chromatin remodeler ISWI with fluorophore-labeled
nucleosomes and DNA through associated changes in fluorescence anisotropy
of the fluorophore upon binding of ISWI to these substrates. We determined
that one ISWI molecule binds to a 20 bp double-stranded DNA substrate
with an affinity of 18 ± 2 nM. In contrast, two ISWI molecules
can bind to the core nucleosome with short linker DNA with stoichiometric
macroscopic equilibrium constants: 1/β1 = 1.3 ±
0.6 nM, and 1/β2 = 13 ± 7 nM2. Furthermore,
to improve our understanding of the mechanism of DNA translocation
by ISWI, and hence nucleosome repositioning, we determined the effect
of nucleotide analogues on substrate binding by ISWI. While the affinity
of ISWI for the nucleosome substrate with short lengths of flanking
DNA was not affected by the presence of nucleotides, the affinity
of ISWI for the DNA substrate is weakened in the presence of nonhydrolyzable
ATP analogues but not by ADP.
Collapse
Affiliation(s)
- Gada Al-Ani
- Department of Molecular Biosciences, University of Kansas , 2034 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | | | | | | | | | | |
Collapse
|
11
|
Hepp MI, Alarcon V, Dutta A, Workman JL, Gutiérrez JL. Nucleosome remodeling by the SWI/SNF complex is enhanced by yeast high mobility group box (HMGB) proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:764-72. [PMID: 24972368 DOI: 10.1016/j.bbagrm.2014.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 12/01/2022]
Abstract
The regulation of gene expression at the level of transcription involves the concerted action of several proteins and protein complexes committed to dynamically alter the surrounding chromatin environment of a gene being activated or repressed. ATP-dependent chromatin remodeling complexes are key factors in chromatin remodeling, and the SWI/SNF complex is the founding member. While many studies have linked the action of these complexes to specific transcriptional regulation of a large number of genes and much is known about their catalytic activity, less is known about the nuclear elements that can enhance or modulate their activity. A number of studies have found that certain High Mobility Group (HMG) proteins are able to stimulate ATP-dependent chromatin remodeling activity, but their influence on the different biochemical outcomes of this activity is still unknown. In this work we studied the influence of the yeast Nhp6A, Nhp6B and Hmo1 proteins (HMGB family members) on different biochemical outcomes of yeast SWI/SNF remodeling activity. We found that all these HMG proteins stimulate the sliding activity of ySWI/SNF, while transient exposure of nucleosomal DNA and octamer transfer catalyzed by this complex are only stimulated by Hmo1. Consistently, only Hmo1 stimulates SWI/SNF binding to the nucleosome. Additionally, the sliding activity of another chromatin remodeling complex, ISW1a, is only stimulated by Hmo1. Further analyses show that these differential stimulatory effects of Hmo1 are dependent on the presence of its C-terminal tail, which contains a stretch of acidic and basic residues.
Collapse
Affiliation(s)
- Matias I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Valentina Alarcon
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Arnob Dutta
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City 64110, MO, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City 64110, MO, USA
| | - José L Gutiérrez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile.
| |
Collapse
|
12
|
DNA methyltransferase 1(DNMT1) induced the expression of suppressors of cytokine signaling3 (Socs3) in a mouse model of asthma. Mol Biol Rep 2014; 41:4413-24. [PMID: 24599782 DOI: 10.1007/s11033-014-3312-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 02/24/2014] [Indexed: 01/21/2023]
Abstract
DNMT1 is the most important methyltransferase enzyme, involved in the regulation of gene expression and appropriate histone modification. It interact with proliferating cell nuclear antigen (PCNA), SNF2 family member ATP-dependent chromatin remodeling enzyme, cyclin dependent kinases inhibitor, E2F1 transcription factor and HDACs to form a repressor complex known as HDAC complexes. The interaction of DNMT1 with numerous protein suppressors of promoters suggests that the enzyme is a crucial element of the transcription suppression complex. Since the mechanism behind over expression of Socs3 in Asthma is unclear, we study the Epigenetic mode of overexpression of Socs3 in terms of methylation/acetylation/inactivation of HDACs/activation of HATs enzymes in a mouse model of asthma. The results show that low expression of DNMT1 might indirectly induce the expression of Socs3 and HAT, and inhibit the expression of HDACs family. Furthermore knockdown of DNMT1 by siRNA induced expression of Socs3 while knock down of Socs3 by siRNA has no effect on DNMT1 expression. Our result suggests that the over expression of Socs3 is due to the inhibition of HDACs complex and hyperacetylation of histones molecule along with down regulation of DNMT1 gene. In depth study on DNMT1 might be useful for the development of therapeutic drug against asthma/allergic diseases.
Collapse
|
13
|
Swygert SG, Peterson CL. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:728-36. [PMID: 24583555 DOI: 10.1016/j.bbagrm.2014.02.013] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 01/08/2023]
Abstract
Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
Collapse
Affiliation(s)
- Sarah G Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
14
|
Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, Hager GL. Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions. Nat Struct Mol Biol 2013; 21:73-81. [PMID: 24317492 PMCID: PMC3947387 DOI: 10.1038/nsmb.2718] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 10/17/2013] [Indexed: 12/24/2022]
Abstract
ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4, and Snf2h. The localization patterns of all three proteins significantly overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome-wide, and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Many regions require the activity of more than one remodeler to regulate accessibility. These findings provide a dynamic view of chromatin organization, and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes.
Collapse
Affiliation(s)
- Stephanie A Morris
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sam John
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Malgorzata Wiench
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
15
|
Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. eLife 2013; 2:e00863. [PMID: 23986862 PMCID: PMC3748710 DOI: 10.7554/elife.00863] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/16/2013] [Indexed: 11/23/2022] Open
Abstract
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.00863.001 In many cells, genomic DNA is wrapped around proteins known as histones to produce particles called nucleosomes. These particles then join together—like beads on a string—to form a highly periodic structure called chromatin. In the nucleus, chromatin is further folded and condensed into chromosomes. However, many important processes, including the replication of DNA and the transcription of genes, require access to the DNA. The cell must therefore be able to disassemble chromatin and remove the histones, and then, once these processes are complete, to reassemble the chromatin. Enzymes known as chromatin assembly factors are responsible for the disassembly and reassembly of chromatin. There are two main types of chromatin assembly factors in eukaryotic cells (i.e., cells with nuclei)—histone chaperones and motor proteins. The histone chaperones escort histones from the cytoplasm, where they are made, to the nucleus. The motor proteins—using energy supplied by ATP molecules—then catalyze the formation of nucleosomes. This involves two activities: the motor proteins assemble nucleosomes by helping the DNA to wrap around the histones, and they also remodel chromatin by altering the positions of nucleosomes along the DNA to ensure that they are periodic—that is, regularly spaced. A conserved motor protein called Chd1 performs chromatin assembly and remodeling in eukaryotic cells. Chd1 works in conjunction with histone chaperones—both are needed for chromatin assembly, and so are DNA, histones and ATP. However, whether or not chromatin assembly and chromatin remodeling by Chd1 are identical or distinct processes is not well understood. Torigoe et al. have now discovered a mutant Chd1 protein that has nucleosome assembly activity (i.e., it can make nucleosomes) but cannot remodel chromatin (i.e., it is unable to move nucleosomes), and thus have demonstrated that these two processes are functionally distinct. Torigoe et al. additionally have found that the mutant Chd1 proteins produce randomly distributed nucleosomes rather than the periodic arrays normally found in chromatin. Further analysis then revealed that the wild-type Chd1 protein, which can remodel chromatin, is able to convert randomly distributed nucleosomes into periodic arrays. These findings have led to a new model for chromatin assembly in which Chd1 initially generates randomly distributed nucleosomes (via its assembly function), and then converts them into periodic arrays of nucleosomes (via its remodeling function). Together, these studies shed light on the mechanisms by which chromatin is created and manipulated in cells. DOI:http://dx.doi.org/10.7554/eLife.00863.002
Collapse
Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology , University of California, San Diego , La Jolla , United States
| | | | | | | | | |
Collapse
|
16
|
Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. eLife 2013. [PMID: 23986862 DOI: 10.7554/elife.00863.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI:http://dx.doi.org/10.7554/eLife.00863.001.
Collapse
Affiliation(s)
- Sharon E Torigoe
- Section of Molecular Biology , University of California, San Diego , La Jolla , United States
| | | | | | | | | |
Collapse
|
17
|
Sinha M, Peterson CL. Chromatin dynamics during repair of chromosomal DNA double-strand breaks. Epigenomics 2012; 1:371-85. [PMID: 20495614 DOI: 10.2217/epi.09.22] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The integrity of a eukaryotic genome is often challenged by DNA double-strand breaks (DSBs). Even a single, unrepaired DSB can be a lethal event, or such unrepaired damage can result in chromosomal instability and loss of genetic information. Furthermore, defects in the pathways that respond to and repair DSBs can lead to the onset of several human pathologic disorders with pleiotropic clinical features, including age-related diseases and cancer. For decades, studies have focused on elucidating the enzymatic mechanisms involved in recognizing, signaling and repairing DSBs within eukaryotic cells. The majority of biochemical and genetic studies have used simple, DNA substrates, whereas only recently efforts have been geared towards understanding how the repair machinery deals with DSBs within chromatin fibers, the nucleoprotein complex that packages DNA within the eukaryotic nucleus. The aim of this review is to discuss our recent understanding of the relationship between chromatin structure and the repair of DSBs by homologous recombination. In particular, we discuss recent studies implicating specialized roles for several, distinct ATP-dependent chromatin remodeling enzymes in facilitating multiple steps within the homologous recombination process.
Collapse
Affiliation(s)
- Manisha Sinha
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
| | | |
Collapse
|
18
|
Abstract
One of the best studied systems for mammalian chromatin remodeling is transcriptional regulation during T cell development. The variety of these studies have led to important findings in T cell gene regulation and cell fate determination. Importantly, these findings have also advanced our knowledge of the function of remodeling enzymes in mammalian gene regulation. First we briefly present biochemical and cell-free analysis of 3 types of ATP dependent remodeling enzymes (SWI/SNF, Mi2, and ISWI) to construct an intellectual framework to understand how these enzymes might be working. Second, we compare and contrast the function of these enzymes during early (thymic) and late (peripheral) T cell development. Finally, we examine some of the gaps in our present understanding.
Collapse
Affiliation(s)
- Andrea L. Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, USA
| | - Michael J. Pazin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, USA
| |
Collapse
|
19
|
Chambers AL, Downs JA. The RSC and INO80 chromatin-remodeling complexes in DNA double-strand break repair. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:229-61. [PMID: 22749148 DOI: 10.1016/b978-0-12-387665-2.00009-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotes, DNA is packaged into chromatin and is therefore relatively inaccessible to DNA repair enzymes. In order to perform efficient DNA repair, ATP-dependent chromatin-remodeling enzymes are required to alter the chromatin structure near the site of damage to facilitate processing and allow access to repair enzymes. Two of the best-studied remodeling complexes involved in repair are RSC (Remodels the Structure of Chromatin) and INO80 from Saccharomyces cerevisiae, which are both conserved in higher eukaryotes. RSC is very rapidly recruited to breaks and mobilizes nucleosomes to promote phosphorylation of H2A S129 and resection. INO80 enrichment at a break occurs later and is dependent on phospho-S129 H2A. INO80 activity at the break site also facilitates resection. Consequently, both homologous recombination and nonhomologous end-joining are defective in rsc mutants, while subsets of these repair pathways are affected in ino80 mutants.
Collapse
Affiliation(s)
- Anna L Chambers
- MRC Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | | |
Collapse
|
20
|
Mitson M, Kelley LA, Sternberg MJE, Higgs DR, Gibbons RJ. Functional significance of mutations in the Snf2 domain of ATRX. Hum Mol Genet 2011; 20:2603-10. [PMID: 21505078 DOI: 10.1093/hmg/ddr163] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ATRX is a member of the Snf2 family of chromatin-remodelling proteins and is mutated in an X-linked mental retardation syndrome associated with alpha-thalassaemia (ATR-X syndrome). We have carried out an analysis of 21 disease-causing mutations within the Snf2 domain of ATRX by quantifying the expression of the ATRX protein and placing all missense mutations in their structural context by homology modelling. While demonstrating the importance of protein dosage to the development of ATR-X syndrome, we also identified three mutations which primarily affect function rather than protein structure. We show that all three of these mutant proteins are defective in translocating along DNA while one mutant, uniquely for a human disease-causing mutation, partially uncouples adenosine triphosphate (ATP) hydrolysis from DNA binding. Our results highlight important mechanistic aspects in the development of ATR-X syndrome and identify crucial functional residues within the Snf2 domain of ATRX. These findings are important for furthering our understanding of how ATP hydrolysis is harnessed as useful work in chromatin remodelling proteins and the wider family of nucleic acid translocating motors.
Collapse
Affiliation(s)
- Matthew Mitson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
| | | | | | | | | |
Collapse
|
21
|
Liu N, Balliano A, Hayes JJ. Mechanism(s) of SWI/SNF-induced nucleosome mobilization. Chembiochem 2010; 12:196-204. [PMID: 21243709 DOI: 10.1002/cbic.201000455] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Indexed: 11/12/2022]
Abstract
Impediments to DNA access due to assembly of the eukaryotic genome into chromatin are in part overcome by the activity of ATP-dependent chromatin-remodeling complexes. These complexes employ energy derived from ATP hydrolysis to destabilize histone-DNA interactions and alter nucleosome positions, thereby increasing the accessibility of DNA-binding factors to their targets. However, the mechanism by which theses complexes accomplish this task remains unresolved. We review aspects of nucleosome alteration by the SWI/SNF complex, the archetypal remodeling enzyme. We focus on experiments that provide insights into how SWI/SNF induces nucleosome movement along DNA. Numerous biochemical activities have been characterized for this complex, all likely providing clues as to the molecular mechanism of translocation.
Collapse
Affiliation(s)
- Ning Liu
- Department of Biochemistry and Biophysics, University of Rochester, Medical Center, Rochester, NY 14642, USA
| | | | | |
Collapse
|
22
|
Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc Natl Acad Sci U S A 2010; 107:19873-8. [PMID: 20974961 DOI: 10.1073/pnas.1003438107] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin remodeling complexes can translocate nucleosomes along the DNA in an ATP-dependent manner. Here, we studied autofluorescent protein constructs of the human ISWI family members Snf2H, Snf2L, the catalytically inactive Snf2L+13 splice variant, and the accessory Acf1 subunit in living human and mouse cells by fluorescence microscopy/spectroscopy. Except for Snf2L, which was not detected in the U2OS cell line, the endogenous ISWI proteins were abundant at nuclear concentrations between 0.14 and 0.83 μM. A protein interaction analysis showed the association of multimeric Snf2H and Acf1 into a heterotetramer or higher-order ACF complex. During the G1/2 cell cycle phase, Snf2H and Snf2L displayed average residence times <150 ms in the chromatin-bound state. The comparison of active and inactive Snf2H/Snf2L indicated that an immobilized fraction potentially involved in active chromatin remodeling comprised only 1-3%. This fraction was largely increased at replication foci in S phase or at DNA repair sites. To rationalize these findings we propose that ISWI remodelers operate via a "continuous sampling" mechanism: The propensity of nucleosomes to be translocated is continuously tested in transient binding reactions. Most of these encounters are unproductive and efficient remodeling requires an increased binding affinity to chromatin. Due to the relatively high intranuclear remodeler concentrations cellular response times for repositioning a given nucleosome were calculated to be in the range of tens of seconds to minutes.
Collapse
|
23
|
Sheu JJC, Guan B, Choi JH, Lin A, Lee CH, Hsiao YT, Wang TL, Tsai FJ, Shih IM. Rsf-1, a chromatin remodeling protein, induces DNA damage and promotes genomic instability. J Biol Chem 2010; 285:38260-9. [PMID: 20923775 DOI: 10.1074/jbc.m110.138735] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Rsf-1 (HBXAP) has been reported as an amplified gene in human cancer, including the highly aggressive ovarian serous carcinoma. Rsf-1 protein interacts with SNF2H to form an ISWI chromatin remodeling complex, RSF. In this study, we investigated the functional role of Rsf-1 by observing phenotypes after expressing it in nontransformed cells. Acute expression of Rsf-1 resulted in DNA damage as evidenced by DNA strand breaks, nuclear γH2AX foci, and activation of the ATM-CHK2-p53-p21 pathway, leading to growth arrest and apoptosis. Deletion mutation and gene knockdown assays revealed that formation of a functional RSF complex with SNF2H was required for Rsf-1 to trigger DNA damage response (DDR). Gene knock-out of TP53 alleles, TP53 mutation, or treatment with an ATM inhibitor abolished up-regulation of p53 and p21 and prevented Rsf-1-induced growth arrest. Chronic induction of Rsf-1 expression resulted in chromosomal aberration and clonal selection for cells with c-myc amplification and CDKN2A/B deletion. Co-culture assays indicated Rsf-1-induced DDR as a selecting barrier that favored outgrowth of cell clones with a TP53 mutation. The above findings suggest that increased Rsf-1 expression and thus excessive RSF activity, which occurs in tumors harboring Rsf-1 amplification, can induce chromosomal instability likely through DDR.
Collapse
Affiliation(s)
- Jim Jinn-Chyuan Sheu
- Department of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Goldman JA, Garlick JD, Kingston RE. Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z. J Biol Chem 2009; 285:4645-51. [PMID: 19940112 DOI: 10.1074/jbc.m109.072348] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
ATP-dependent chromatin remodeling complexes rearrange nucleosomes by altering the position of DNA around the histone octamer. Although chromatin remodelers and the histone variant H2A.Z colocalize on transcriptional control regions, whether H2A.Z directly affects remodeler association or activity is unclear. We determined the relative association of remodelers with H2A.Z chromatin and tested whether replacement of H2A.Z in a nucleosome altered the activity of remodeling enzymes. Many families of remodelers showed increased association with H2A.Z chromatin, but only the ISWI family of chromatin remodelers showed stimulated activity in vitro. An acidic patch on the nucleosome surface, extended by inclusion of H2A.Z in nucleosomes and essential for viability, is required for ISWI stimulation. We conclude that H2A.Z incorporation increases nucleosome remodeling activity of the largest class of mammalian remodelers (ISWI) and that it correlates with increased association of other remodelers to chromatin. This reveals two possible modes for regulation of a remodeler by a histone variant.
Collapse
Affiliation(s)
- Joseph A Goldman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | | | | |
Collapse
|
25
|
Fischer CJ, Yamada K, Fitzgerald DJ. Kinetic mechanism for single-stranded DNA binding and translocation by Saccharomyces cerevisiae Isw2. Biochemistry 2009; 48:2960-8. [PMID: 19203228 DOI: 10.1021/bi8021153] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chromatin remodeling complex Isw2 from Saccharomyces cerevisiae (yIsw2) mobilizes nucleosomes through an ATP-dependent reaction that is coupled to the translocation of the helicase domain of the enzyme along intranucleosomal DNA. In this study, we demonstrate that yIsw2 is capable of translocating along single-stranded DNA in a reaction that is coupled to ATP hydrolysis. We propose that single-stranded DNA translocation by yIsw2 occurs through a series of repeating uniform steps with an overall macroscopic processivity (P) of 0.90 +/- 0.02, corresponding to an average translocation distance of 20 +/- 2 nucleotides before dissociation. This processivity corresponds well to the processivity of nucleosome sliding by yIsw2, thus arguing that single-stranded DNA translocation or tracking may be fundamental to the double-stranded DNA translocation required for effective nucleosome mobilization. Furthermore, we find evidence that a slow initiation process, following DNA binding, may be required to make yIsw2 competent for DNA translocation. We also provide evidence that this slow initiation process may correspond to the second step of a two-step DNA binding mechanism by yIsw2 and a quantitative description of the kinetics of this DNA binding mechanism.
Collapse
Affiliation(s)
- Christopher J Fischer
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Drive, 1082 Malott Hall, Lawrence, Kansas 66045, USA.
| | | | | |
Collapse
|
26
|
van Vugt JJFA, de Jager M, Murawska M, Brehm A, van Noort J, Logie C. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence. PLoS One 2009; 4:e6345. [PMID: 19626125 PMCID: PMC2710519 DOI: 10.1371/journal.pone.0006345] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 06/25/2009] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. METHODOLOGY/PRINCIPAL FINDINGS We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. CONCLUSIONS/SIGNIFICANCE Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.
Collapse
Affiliation(s)
- Joke J. F. A. van Vugt
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, The Netherlands
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Martijn de Jager
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Magdalena Murawska
- Institut für Molekularbiologie und Tumorforschung, University of Marburg, Marburg, Germany
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung, University of Marburg, Marburg, Germany
| | - John van Noort
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Colin Logie
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, The Netherlands
| |
Collapse
|
27
|
Rattner BP, Yusufzai T, Kadonaga JT. HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility. Mol Cell 2009; 34:620-6. [PMID: 19524541 DOI: 10.1016/j.molcel.2009.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/03/2009] [Accepted: 04/10/2009] [Indexed: 12/20/2022]
Abstract
The high-mobility group N (HMGN) proteins are abundant nonhistone chromosomal proteins that bind specifically to nucleosomes at two high-affinity sites. Here we report that purified recombinant human HMGN1 (HMG14) and HMGN2 (HMG17) potently repress ATP-dependent chromatin remodeling by four different molecular motor proteins. In contrast, mutant HMGN proteins with double Ser-to-Glu mutations in their nucleosome-binding domains are unable to inhibit chromatin remodeling. The HMGN-mediated repression of chromatin remodeling is reversible and dynamic. With the ACF chromatin remodeling factor, HMGN2 does not directly inhibit the ATPase activity but rather appears to reduce the affinity of the factor to chromatin. These findings suggest that HMGN proteins serve as a counterbalance to the action of the many ATP-dependent chromatin remodeling activities in the nucleus.
Collapse
Affiliation(s)
- Barbara P Rattner
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0347, USA
| | | | | |
Collapse
|
28
|
Bouazoune K, Miranda TB, Jones PA, Kingston RE. Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF. Nucleic Acids Res 2009; 37:5279-94. [PMID: 19567737 PMCID: PMC2760786 DOI: 10.1093/nar/gkp524] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Chromatin remodeling enzymes use the energy of ATP hydrolysis to alter histone–DNA contacts and regulate DNA-based processes in eukaryotes. Whether different subfamilies of remodeling complexes generate distinct products remains uncertain. We have developed a protocol to analyze nucleosome remodeling on individual products formed in vitro. We used a DNA methyltransferase to examine DNA accessibility throughout nucleosomes that had been remodeled by the ISWI and SWI/SNF families of enzymes. We confirmed that ISWI-family enzymes mainly created patterns of accessibility consistent with canonical nucleosomes. In contrast, SWI/SNF-family enzymes generated widespread DNA accessibility. The protection patterns created by these enzymes were usually located at the extreme ends of the DNA and showed no evidence for stable loop formation on individual molecules. Instead, SWI/SNF family proteins created extensive accessibility by generating heterogeneous products that had fewer histone–DNA contacts than a canonical nucleosome, consistent with models in which a canonical histone octamer has been ‘pushed’ off of the end of the DNA.
Collapse
Affiliation(s)
- Karim Bouazoune
- Department of Molecular Biology & Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | | | | | | |
Collapse
|
29
|
Somers J, Owen-Hughes T. Mutations to the histone H3 alpha N region selectively alter the outcome of ATP-dependent nucleosome-remodelling reactions. Nucleic Acids Res 2009; 37:2504-13. [PMID: 19264807 PMCID: PMC2677872 DOI: 10.1093/nar/gkp114] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mutational analysis of the histone H3 N-terminal region has shown it to play an important role both in chromatin function in vivo and nucleosome dynamics in vitro. Here we use a library of mutations in the H3 N-terminal region to investigate the contribution of this region to the action of the ATP-dependent remodelling enzymes Chd1, RSC and SWI/SNF. All of the enzymes were affected differently by the mutations with Chd1 being affected the least and RSC being most sensitive. In addition to affecting the rate of remodelling by RSC, some mutations prevented RSC from moving nucleosomes to locations in which DNA was unravelled. These observations illustrate that the mechanisms by which different ATP-dependent remodelling enzymes act are sensitive to different features of nucleosome structure. They also show how alterations to histones can affect the products generated as a result of ATP-dependent remodelling reactions.
Collapse
Affiliation(s)
- Joanna Somers
- Wellcome Trust Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | |
Collapse
|
30
|
Ishii H, Du H, Zhang Z, Henderson A, Sen R, Pazin MJ. Mi2beta shows chromatin enzyme specificity by erasing a DNase I-hypersensitive site established by ACF. J Biol Chem 2009; 284:7533-41. [PMID: 19158090 DOI: 10.1074/jbc.m807617200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ATP-dependent chromatin-remodeling enzymes are linked to changes in gene expression; however, it is not clear how the multiple remodeling enzymes found in eukaryotes differ in function and work together. In this report, we demonstrate that the ATP-dependent remodeling enzymes ACF and Mi2beta can direct consecutive, opposing chromatin-remodeling events, when recruited to chromatin by different transcription factors. In a cell-free system based on the immunoglobulin heavy chain gene enhancer, we show that TFE3 induces a DNase I-hypersensitive site in an ATP-dependent reaction that requires ACF following transcription factor binding to chromatin. In a second step, PU.1 directs Mi2beta to erase an established DNase I-hypersensitive site, in an ATP-dependent reaction subsequent to PU.1 binding to chromatin, whereas ACF will not support erasure. Erasure occurred without displacing the transcription factor that initiated the site. Other tested enzymes were unable to erase the DNase I-hypersensitive site. Establishing and erasing the DNase I-hypersensitive site required transcriptional activation domains from TFE3 and PU.1, respectively. Together, these results provide important new mechanistic insight into the combinatorial control of chromatin structure.
Collapse
Affiliation(s)
- Haruhiko Ishii
- Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| | | | | | | | | | | |
Collapse
|
31
|
Papait R, Pistore C, Grazini U, Babbio F, Cogliati S, Pecoraro D, Brino L, Morand AL, Dechampesme AM, Spada F, Leonhardt H, McBlane F, Oudet P, Bonapace IM. The PHD domain of Np95 (mUHRF1) is involved in large-scale reorganization of pericentromeric heterochromatin. Mol Biol Cell 2008; 19:3554-63. [PMID: 18508923 DOI: 10.1091/mbc.e07-10-1059] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Heterochromatic chromosomal regions undergo large-scale reorganization and progressively aggregate, forming chromocenters. These are dynamic structures that rapidly adapt to various stimuli that influence gene expression patterns, cell cycle progression, and differentiation. Np95-ICBP90 (m- and h-UHRF1) is a histone-binding protein expressed only in proliferating cells. During pericentromeric heterochromatin (PH) replication, Np95 specifically relocalizes to chromocenters where it highly concentrates in the replication factories that correspond to less compacted DNA. Np95 recruits HDAC and DNMT1 to PH and depletion of Np95 impairs PH replication. Here we show that Np95 causes large-scale modifications of chromocenters independently from the H3:K9 and H4:K20 trimethylation pathways, from the expression levels of HP1, from DNA methylation and from the cell cycle. The PHD domain is essential to induce this effect. The PHD domain is also required in vitro to increase access of a restriction enzyme to DNA packaged into nucleosomal arrays. We propose that the PHD domain of Np95-ICBP90 contributes to the opening and/or stabilization of dense chromocenter structures to support the recruitment of modifying enzymes, like HDAC and DNMT1, required for the replication and formation of PH.
Collapse
Affiliation(s)
- Roberto Papait
- Department of Structural and Functional Biology, University of Insubria, 21052 Busto Arsizio (VA), Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
dCHD3, a novel ATP-dependent chromatin remodeler associated with sites of active transcription. Mol Cell Biol 2008; 28:2745-57. [PMID: 18250149 DOI: 10.1128/mcb.01839-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
ATP-dependent chromatin remodelers of the CHD family play important roles during differentiation and development. Three CHD proteins, dMi-2, dChd1, and Kismet, have been described for Drosophila melanogaster. Here, we study dCHD3, a novel member of the CHD family. dCHD3 is related in sequence to dMi-2 but lacks several domains implicated in dMi-2 function. We demonstrate that dCHD3 is a nuclear protein and that expression is tightly regulated during fly development. Recombinant dCHD3 remodels mono- and polynucleosomes in an ATP-dependent manner in vitro. Its chromodomains are critical for nucleosome binding and remodeling. Unlike dMi-2, dCHD3 exists as a monomer. Nevertheless, both proteins colocalize with RNA polymerase II to actively transcribed regions on polytene chromosomes, suggesting that both remodelers participate in the process of transcription.
Collapse
|
33
|
Maier VK, Chioda M, Rhodes D, Becker PB. ACF catalyses chromatosome movements in chromatin fibres. EMBO J 2007; 27:817-26. [PMID: 17962805 DOI: 10.1038/sj.emboj.7601902] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 10/04/2007] [Indexed: 12/18/2022] Open
Abstract
Nucleosome-remodelling factors containing the ATPase ISWI, such as ACF, render DNA in chromatin accessible by promoting the sliding of histone octamers. Although the ATP-dependent repositioning of mononucleosomes is readily observable in vitro, it is unclear to which extent nucleosomes can be moved in physiological chromatin, where neighbouring nucleosomes, linker histones and the folding of the nucleosomal array restrict mobility. We assembled arrays consisting of 12 nucleosomes or 12 chromatosomes (nucleosomes plus linker histone) from defined components and subjected them to remodelling by ACF or the ATPase CHD1. Both factors increased the access to DNA in nucleosome arrays. ACF, but not CHD1, catalysed profound movements of nucleosomes throughout the array, suggesting different remodelling mechanisms. Linker histones inhibited remodelling by CHD1. Surprisingly, ACF catalysed significant repositioning of entire chromatosomes in chromatin containing saturating levels of linker histone H1. H1 inhibited the ATP-dependent generation of DNA accessibility by only about 50%. This first demonstration of catalysed chromatosome movements suggests that the bulk of interphase euchromatin may be rendered dynamic by dedicated nucleosome-remodelling factors.
Collapse
Affiliation(s)
- Verena K Maier
- Molekularbiologie, Adolf-Butenandt Institut, Ludwig Maximilian Universität, Munich, Germany
| | | | | | | |
Collapse
|
34
|
Fischer CJ, Saha A, Cairns BR. Kinetic model for the ATP-dependent translocation of Saccharomyces cerevisiae RSC along double-stranded DNA. Biochemistry 2007; 46:12416-26. [PMID: 17918861 PMCID: PMC2810488 DOI: 10.1021/bi700930n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chromatin remodeling complex RSC from Saccharomyces cerevisiae is a DNA translocase that moves with directionality along double-stranded DNA in a reaction that is coupled to ATP hydrolysis. To better understand how this basic molecular motor functions, a novel method of analysis has been developed to study the kinetics of RSC translocation along double-stranded DNA. The data provided are consistent with RSC translocation occurring through a series of repeating uniform steps with an overall processivity of P = 0.949 +/- 0.003; this processivity corresponds to an average translocation distance of 20 +/- 1 base pairs (bp) before dissociation. Interestingly, a slow initiation process, following DNA binding, is required to make RSC competent for DNA translocation. These results are further discussed in the context of previously published studies of RSC and other DNA translocases.
Collapse
Affiliation(s)
- Christopher J Fischer
- Department of Physics and Astronomy, 1082 Malott Hall, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | | | | |
Collapse
|
35
|
van Vugt JJFA, Ranes M, Campsteijn C, Logie C. The ins and outs of ATP-dependent chromatin remodeling in budding yeast: biophysical and proteomic perspectives. ACTA ACUST UNITED AC 2007; 1769:153-71. [PMID: 17395283 DOI: 10.1016/j.bbaexp.2007.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 01/22/2007] [Accepted: 01/29/2007] [Indexed: 11/30/2022]
Abstract
ATP-dependent chromatin remodeling is performed by multi-subunit protein complexes. Over the last years, the identity of these factors has been unveiled in yeast and many parallels have been drawn with animal and plant systems, indicating that sophisticated chromatin transactions evolved prior to their divergence. Here we review current knowledge pertaining to the molecular mode of action of ATP-dependent chromatin remodeling, from single molecule studies to genome-wide genetic and proteomic studies. We focus on the budding yeast versions of SWI/SNF, RSC, DDM1, ISWI, CHD1, INO80 and SWR1.
Collapse
Affiliation(s)
- Joke J F A van Vugt
- Department of Molecular Biology, NCMLS, Radboud University, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | | | | | | |
Collapse
|
36
|
Shur I, Solomon R, Benayahu D. Dynamic interactions of chromatin-related mesenchymal modulator, a chromodomain helicase-DNA-binding protein, with promoters in osteoprogenitors. Stem Cells 2007; 24:1288-93. [PMID: 16705189 DOI: 10.1634/stemcells.2005-0300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The newly identified protein chromatin-related mesenchymal modulator (CReMM) is expressed by marrow stromal progenitors in vivo and ex vivo. CReMM belongs to a recently identified subgroup of chromodomain helicase-DNA-binding proteins composed of multiple domains including chromodomains, SNF2/ATPase, helicase-C domain, SANT, and A/T-hook-DNA binding domain. Chromatin immunoprecipitation assay was applied to follow the dynamics of CReMM binding to A/T-rich regions on promoters of genes that play a role in osteoblast maturation. CReMM interaction with BMP4 and biglycan promoters in the marrow stromal cells was challenged with transforming growth factor-beta. Treatment with 17beta-estradiol enhanced the binding to estrogen receptor and abolished binding to the prolactin receptor promoters; CReMM interaction with osteocalcin promoter was identified constantly. CReMM binding to the analyzed endogenous promoters suggests its direct role in the transcriptional program activated during osteogenic cell differentiation, which may be a useful tool for following the molecular mechanism of the "stemness" of mesenchymal cells.
Collapse
Affiliation(s)
- Irena Shur
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Israel
| | | | | |
Collapse
|
37
|
Abstract
MOTIVATION Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors. RESULTS The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable. AVAILABILITY http://www.jncasr.ac.in/cremofac/
Collapse
Affiliation(s)
- Agrawal Shipra
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | | | | |
Collapse
|
38
|
Domanskyi A, Virtanen K, Palvimo J, Jänne O. Biochemical characterization of androgen receptor-interacting protein 4. Biochem J 2006; 393:789-95. [PMID: 16212558 PMCID: PMC1360732 DOI: 10.1042/bj20050823] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
ARIP4 [AR (androgen receptor)-interacting protein 4] is a member of the SNF2-like family of proteins. Its sequence similarity to known proteins is restricted to the centrally located SNF2 ATPase domain. ARIP4 is an active ATPase, and dsDNA (double-stranded DNA) and ssDNA (single-stranded DNA) enhance its catalytic activity. We show in the present study that ARIP4 interacts with AR and binds to DNA and mononucleosomes. The N-terminal region of ARIP4 mediates interaction with AR. Kinetic parameters of the ARIP4 ATPase are similar to those of BRG-1 and SNF2h, two members of the SNF2-like protein family, but the specific activity of ARIP4 protein purified to >90% homogeneity is approximately ten times lower, being 120 molecules of ATP hydrolysed by an ARIP4 molecule per min in contrast with approx. 1000 ATP molecules hydrolysed per min by ATP-dependent chromatin remodellers. Unlike other members of the SNF2 family, ARIP4 does not appear to form large protein complexes in vivo or remodel mononucleosomes in vitro. ARIP4 is covalently modified by sumoylation, and mutation of six potential SUMO (small ubiquitin-related modifier) attachment sites abolished the ability of ARIP4 to bind DNA, hydrolyse ATP and activate AR function. We conclude that, similar to its closest homologues in the SNF2-like protein family, ATRX (alpha-thalassemia, mental retardation, X-linked) and Rad54, ARIP4 does not seem to be a classical chromatin remodelling protein.
Collapse
Affiliation(s)
- Andrii Domanskyi
- *Biomedicum Helsinki, Institute of Biomedicine (Physiology), University of Helsinki, FI-00014 Helsinki, Finland
| | - Katja T. Virtanen
- *Biomedicum Helsinki, Institute of Biomedicine (Physiology), University of Helsinki, FI-00014 Helsinki, Finland
| | - Jorma J. Palvimo
- *Biomedicum Helsinki, Institute of Biomedicine (Physiology), University of Helsinki, FI-00014 Helsinki, Finland
- †Department of Medical Biochemistry, University of Kuopio, FI-70211 Kuopio, Finland
| | - Olli A. Jänne
- *Biomedicum Helsinki, Institute of Biomedicine (Physiology), University of Helsinki, FI-00014 Helsinki, Finland
- ‡Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, FI-00290 Helsinki, Finland
- To whom correspondence should be addressed, at Biomedicum Helsinki, Institute of Biomedicine (Physiology), P.O. Box 63 (Haartmaninkatu 8), FI-00014 Helsinki, Finland (email )
| |
Collapse
|
39
|
Surapureddi S, Viswakarma N, Yu S, Guo D, Rao MS, Reddy JK. PRIC320, a transcription coactivator, isolated from peroxisome proliferator-binding protein complex. Biochem Biophys Res Commun 2006; 343:535-43. [PMID: 16554032 DOI: 10.1016/j.bbrc.2006.02.160] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 02/20/2006] [Indexed: 11/17/2022]
Abstract
Ciprofibrate, a potent peroxisome proliferator, induces pleiotropic responses in liver by activating peroxisome proliferator-activated receptor alpha (PPARalpha), a nuclear receptor. Transcriptional regulation by liganded nuclear receptors involves the participation of coregulators that form multiprotein complexes possibly to achieve cell and gene specific transcription. SDS-PAGE and matrix-assisted laser desorption/ionization reflection time-of-flight mass spectrometric analyses of ciprofibrate-binding proteins from liver nuclear extracts obtained using ciprofibrate-Sepharose affinity matrix resulted in the identification of a new high molecular weight nuclear receptor coactivator, which we designated PRIC320. The full-length human cDNA encoding this protein has an open-reading frame that codes for a 320kDa protein containing 2882 amino acids. PRIC320 contains five LXXLL signature motifs that mediate interaction with nuclear receptors. PRIC320 binds avidly to nuclear receptors PPARalpha, CAR, ERalpha, and RXR, but only minimally with PPARgamma. PRIC320 also interacts with transcription cofactors CBP, PRIP, and PBP. Immunoprecipitation-immunoblotting as well as cellular localization studies confirmed the interaction between PPARalpha and PRIC320. PRIC320 acts as a transcription coactivator by stimulating PPARalpha-mediated transcription. We conclude that ciprofibrate, a PPARalpha ligand, binds a multiprotein complex and PRIC320 cloned from this complex functions as a nuclear receptor coactivator.
Collapse
Affiliation(s)
- Sailesh Surapureddi
- The Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | | | | | | | | |
Collapse
|
40
|
Thiriet C, Hayes JJ. Histone dynamics during transcription: exchange of H2A/H2B dimers and H3/H4 tetramers during pol II elongation. Results Probl Cell Differ 2006; 41:77-90. [PMID: 16909891 DOI: 10.1007/400_009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chromatin within eukaryotic cell nuclei accommodates many complex activities that require at least partial disassembly and reassembly of nucleosomes. This disassembly/reassembly is thought to be somewhat localized when associated with processes such as site-specific DNA repair but likely occurs over extended regions during processive processes such as DNA replication or transcription. Here we review data addressing the effect of transcription elongation on nucleosome disassembly/reassembly, specifically focusing on the issue of transcription-dependent exchange of H2A/H2B dimers and H3/H4 tetramers. We suggest a model whereby passage of a polymerase through a nucleosome induces displacement of H2A/H2B dimers with a much higher probability than displacement of H3/H4 tetramers such that the extent of tetramer replacement is relatively low and proportional to polymerase density on any particular gene.
Collapse
Affiliation(s)
- Christophe Thiriet
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Box 712, Rochester, NY 14625, USA
| | | |
Collapse
|
41
|
Johnson CN, Adkins NL, Georgel P. Chromatin remodeling complexes: ATP-dependent machines in action. Biochem Cell Biol 2005; 83:405-17. [PMID: 16094444 DOI: 10.1139/o05-115] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Since the initial characterization of chromatin remodeling as an ATP-dependent process, many studies have given us insight into how nucleosome-remodeling complexes can affect various nuclear functions. However, the multistep DNA-histone remodeling process has not been completely elucidated. Although new studies are published on a nearly weekly basis, the nature and roles of interactions of the individual SWI/SNF- and ISWI-based remodeling complexes and DNA, core histones, and other chromatin-associated proteins are not fully understood. In addition, the potential changes associated with ATP recruitment and its subsequent hydrolysis have not been fully characterized. This review explores possible mechanisms by which chromatin-remodeling complexes are recruited to specific loci, use ATP hydrolysis to achieve actual remodeling through disruption of DNA-histone interactions, and are released from their chromatin template. We propose possible roles for ATP hydrolysis in a chromatin-release/target-scanning process that offer an alternative to or complement the often overlooked function of delivering the energy required for sliding or dislodging specific subsets of core histones.
Collapse
Affiliation(s)
- Cotteka N Johnson
- Division of Biological Sciences, Marshall University, Huntington, WV 25755, USA
| | | | | |
Collapse
|
42
|
Shur I, Benayahu D. Characterization and functional analysis of CReMM, a novel chromodomain helicase DNA-binding protein. J Mol Biol 2005; 352:646-55. [PMID: 16095617 DOI: 10.1016/j.jmb.2005.06.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 06/12/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
The present study describes a newly identified protein named CReMM (chromatin-related mesenchymal modulator). The protein was studied by bioinformatic means and classified as a member of the third subfamily of chromodomain helicase DNA-binding proteins (CHD). In silico translation defined CReMM as a multiple domains protein including two chromodomains, SNF2/ATPase, helicase C domain and an A/T-DNA-binding domain (DBD). Predicted extensive post-translation phosphorylation on serine and tyrosine residues was demonstrated by Western blot in the presence and in the absence of phosphatase inhibitors using specific antibodies. Immunoprecipitated CReMM disclosed a DNA-dependent ATPase activity quantified by colorimetric assay. Electrophoresis mobility-shift assay (EMSA) validated that CReMM binds to A/T-rich DNA. CReMM is expressed in mesenchymal progenitors, as shown in vitro and in vivo. CReMM protein structural motifs and proven biochemical activities highlight its role in chromatin remodeling. Further delineation of the function of this protein will provide information about its dynamics in transcriptional regulation of mesenchymal cells.
Collapse
Affiliation(s)
- I Shur
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Israel
| | | |
Collapse
|
43
|
Svedruzić ZM, Wang C, Kosmoski JV, Smerdon MJ. Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface. J Biol Chem 2005; 280:40051-7. [PMID: 16210312 DOI: 10.1074/jbc.m509478200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclobutane-thymine dimers (CTDs), the most common DNA lesion induced by UV radiation, cause 30 degrees bending and 9 degrees unwinding of the DNA helix. We prepared site-specific CTDs within a short sequence bracketed by strong nucleosome-positioning sequences. The rotational setting of CTDs over one turn of the helix near the dyad center on the histone surface was analyzed by hydroxyl radical footprinting. Surprisingly, the position of CTDs over one turn of the helix does not affect the rotational setting of DNA on the nucleosome surface. Gel-shift analysis indicates that one CTD destabilizes histone-DNA interactions by 0.6 or 1.1 kJ/mol when facing away or toward the histone surface, respectively. Thus, 0.5 kJ/mol energy penalty for a buried CTD is not enough to change the rotational setting of sequences with strong rotational preference. The effect of rotational setting on CTD removal by nucleotide excision repair (NER) was examined using Xenopus oocyte nuclear extracts. The NER rates are only 2-3 times lower in nucleosomes and change by only 1.5-fold when CTDs face away or toward the histone surface. Therefore, in Xenopus nuclear extracts, the rotational orientation of CTDs on nucleosomes has surprisingly little effect on rates of repair. These results indicate that nucleosome dynamics and/or chromatin remodeling may facilitate NER in gaining access to DNA damage in nucleosomes.
Collapse
Affiliation(s)
- Zeljko M Svedruzić
- Department of Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
| | | | | | | |
Collapse
|
44
|
Smith CL, Peterson CL. A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol Cell Biol 2005; 25:5880-92. [PMID: 15988005 PMCID: PMC1168809 DOI: 10.1128/mcb.25.14.5880-5892.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast (Saccharomyces cerevisiae) SWI/SNF is a prototype for a large family of ATP-dependent chromatin-remodeling enzymes that facilitate numerous DNA-mediated processes. Swi2/Snf2 is the catalytic subunit of SWI/SNF, and it is the founding member of a novel subfamily of the SF2 superfamily of DNA helicase/ATPases. Here we present a functional analysis of the diagnostic set of helicase/ATPase sequence motifs found within all Swi2p/Snf2p family members. Whereas many of these motifs play key roles in ATP binding and/or hydrolysis, we identify residues within conserved motif V that are specifically required to couple ATP hydrolysis to chromatin-remodeling activity. Interestingly, motif V of the human Swi2p/Snf2p homolog, Brg1p, has been shown to be a possible hot spot for mutational alterations associated with cancers.
Collapse
Affiliation(s)
- Corey L Smith
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, Suite 210, Worcester, Massachusetts 01605, USA
| | | |
Collapse
|
45
|
Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol 2005; 12:747-55. [PMID: 16086025 DOI: 10.1038/nsmb973] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 07/01/2005] [Indexed: 11/08/2022]
Abstract
The RSC chromatin remodeler contains Sth1, an ATP-dependent DNA translocase. On DNA substrates, RSC/Sth1 tracks along one strand of the duplex with a 3' --> 5' polarity and a tracking requirement of one base, properties that may enable directional DNA translocation on nucleosomes. The binding of RSC or Sth1 elicits a DNase I-hypersensitive site approximately two DNA turns from the nucleosomal dyad, and the binding of Sth1 requires intact DNA at this location. Results with various nucleosome substrates suggest that RSC/Sth1 remains at a fixed position on the histone octamer and that Sth1 conducts directional DNA translocation from a location about two turns from the nucleosomal dyad, drawing in DNA from one side of the nucleosome and pumping it toward the other. These studies suggest that nucleosome mobilization involves directional DNA translocation initiating from a fixed internal site on the nucleosome.
Collapse
Affiliation(s)
- Anjanabha Saha
- Howard Hughes Medical Institute and the Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | | | | |
Collapse
|
46
|
Abstract
The yeast SWI/SNF ATP-dependent chromatin remodeling complex was first identified and characterized over 10 years ago (F. Winston and M. Carlson. 1992. Trends Genet. 8: 387-391.) Since then, the number of distinct ATP-dependent chromatin remodeling complexes and the variety of roles they play in nuclear processes have become dizzying (J.A. Martens and F. Winston. 2003. Curr. Opin. Genet. Dev. 13: 136-142; A. Vacquero et al. 2003. Sci. Aging Knowledge Environ. 2003: RE4)--and that does not even include the companion suite of histone modifying enzymes, which exhibit a comparable diversity in both number of complexes and variety of functions (M.J. Carrozza et al. 2003. Trends Genet. 19: 321-329; W. Fischle et al. 2003. Curr. Opin. Cell Biol. 15: 172-183; M. Iizuka and M.M. Smith. 2003. Curr. Opin. Genet. Dev. 13: 1529-1539). This vast complexity is hardly surprising, given that all nuclear processes that involve DNA--transcription, replication, repair, recombination, sister chromatid cohesion, etc.--must all occur in the context of chromatin. The SWI/SNF-related ATP-dependent remodelers are divided into a number of subfamilies, all related by the SWI2/SNF2 ATPase at their catalytic core. In nearly every species where researchers have looked for them, one or more members of each subfamily have been identified. Even the budding yeast, with its comparatively small genome, contains eight different chromatin remodelers in five different subfamilies. This review will focus on just one subfamily, the Imitation Switch (ISWI) family, which is proving to be one of the most diverse groups of chromatin remodelers in both form and function.
Collapse
Affiliation(s)
- Sara S Dirscherl
- Dept. of Biological Sciences, University of Alaska Anchorage, 99508, USA
| | | |
Collapse
|
47
|
Mohrmann L, Langenberg K, Krijgsveld J, Kal AJ, Heck AJR, Verrijzer CP. Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol 2004; 24:3077-88. [PMID: 15060132 PMCID: PMC381637 DOI: 10.1128/mcb.24.8.3077-3088.2004] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The SWI/SNF family of ATP-dependent chromatin-remodeling factors plays a central role in eukaryotic transcriptional regulation. In yeast and human cells, two subclasses have been recognized: one comprises yeast SWI/SNF and human BAF, and the other includes yeast RSC and human PBAF. Therefore, it was puzzling that Drosophila appeared to contain only a single SWI/SNF-type remodeler, the Brahma (BRM) complex. Here, we report the identification of two novel BRM complex-associated proteins: Drosophila Polybromo and BAP170, a conserved protein not described previously. Biochemical analysis established that Drosophila contains two distinct BRM complexes: (i) the BAP complex, defined by the presence of OSA and the absence of Polybromo and BAP170, and (ii) the PBAP complex, containing Polybromo and BAP170 but lacking OSA. Determination of the genome-wide distributions of OSA and Polybromo on larval salivary gland polytene chromosomes revealed that BAP and PBAP display overlapping but distinct distribution patterns. Both complexes associate predominantly with regions of open, hyperacetylated chromatin but are largely excluded from Polycomb-bound repressive chromatin. We conclude that, like yeast and human cells, Drosophila cells express two distinct subclasses of the SWI/SNF family. Our results support a close reciprocity of chromatin regulation by ATP-dependent remodelers and histone-modifying enzymes.
Collapse
Affiliation(s)
- Lisette Mohrmann
- Gene Regulation Laboratory, Centre for Biomedical Genetics, Department of Molecular and Cell Biology, Leiden University Medical Centre, 2300 RA Leiden, The Netherlands
| | | | | | | | | | | |
Collapse
|
48
|
Affiliation(s)
- Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester 01605, USA.
| | | |
Collapse
|
49
|
Kinyamu HK, Archer TK. Modifying chromatin to permit steroid hormone receptor-dependent transcription. ACTA ACUST UNITED AC 2004; 1677:30-45. [PMID: 15020043 DOI: 10.1016/j.bbaexp.2003.09.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Revised: 09/24/2003] [Accepted: 09/24/2003] [Indexed: 02/07/2023]
Abstract
Lipophilic hormones, including steroids, exert their physiological effects through binding to high-affinity superfamily of steroid hormone receptor (SR) proteins that function as ligand-dependent DNA binding transcription factors. To date, SR proteins are among a few transcription factors shown to directly interact with higher order chromatin structures to regulate gene expression. To perturb chromatin, SRs employ enzymatic multicomplexes that can either remodel or modify chromatin. Here we examine the current state of knowledge concerning multicomplex chromatin remodeling/modification machines and SR-dependent transcription. We will focus on the role of these protein-protein and chromatin-protein interactions in vivo with the MMTV promoter as a primary model. In addition, we discuss emerging evidence implicating chaperone proteins and proteasome degradation machinery in SR-mediated gene regulation within chromatin.
Collapse
Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, 111 Alexander Drive, PO Box 12233 (MD E4-06), Research Triangle Park, NC 27709, USA
| | | |
Collapse
|
50
|
Boyer LA, Latek RR, Peterson CL. The SANT domain: a unique histone-tail-binding module? Nat Rev Mol Cell Biol 2004; 5:158-63. [PMID: 15040448 DOI: 10.1038/nrm1314] [Citation(s) in RCA: 284] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Laurie A Boyer
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | | | | |
Collapse
|