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Wiggans M, Zhu SJ, Molinaro AM, Pearson BJ. The BAF chromatin remodeling complex licenses planarian stem cells access to ectodermal and mesodermal cell fates. BMC Biol 2023; 21:227. [PMID: 37864247 PMCID: PMC10589948 DOI: 10.1186/s12915-023-01730-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND The flatworm planarian, Schmidtea mediterranea, has a large population of adult stem cells (ASCs) that replace any cell type during tissue turnover or regeneration. How planarian ASCs (called neoblasts) manage self-renewal with the ability to produce daughter cells of different cell lineages (multipotency) is not well understood. Chromatin remodeling complexes ultimately control access to DNA regions of chromosomes and together with specific transcription factors determine whether a gene is transcribed in a given cell type. Previous work in planarians determined that RNAi of core components of the BAF chromatin remodeling complex, brg1 and smarcc2, caused increased ASCs and failed regeneration, but how these cellular defects arise at the level of gene regulation in neoblasts is unknown. RESULTS Here, we perform ATAC and RNA sequencing on purified neoblasts, deficient for the BAF complex subunits brg-1 and smarcc2. The data demonstrate that the BAF complex promotes chromatin accessibility and facilitates transcription at target loci, as in other systems. Interestingly, we find that the BAF complex enables access to genes known to be required for the generation of mesoderm- and ectoderm-derived lineages, including muscle, parenchymal cathepsin, neural, and epithelial lineages. BAF complex knockdowns result in disrupted differentiation into these cell lineages and functional consequences on planarian regeneration and tissue turnover. Notably, we did not detect a role for the BAF complex in neoblasts making endodermal lineages. CONCLUSIONS Our study provides functional insights into how the BAF complex contributes to cell fate decisions in planarian ASCs in vivo.
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Affiliation(s)
- Mallory Wiggans
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Shu Jun Zhu
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Alyssa M Molinaro
- Present address: Oregon Health & Science University, Portland, OR, 97239, USA
| | - Bret J Pearson
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.
- Present address: Oregon Health & Science University, Portland, OR, 97239, USA.
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2
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Martinet B, Zambra E, Przybyla K, Lecocq T, Anselmo A, Nonclercq D, Rasmont P, Michez D, Hennebert E. Mating under climate change: Impact of simulated heatwaves on the reproduction of model pollinators. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13738] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Baptiste Martinet
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
- Evolutionary Biology & Ecology Université Libre de Bruxelles Bruxelles Belgium
| | - Ella Zambra
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
| | - Kimberly Przybyla
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
| | - Thomas Lecocq
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
- INRAEURAFPAUniversity of Lorraine Nancy France
| | - Abigaël Anselmo
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
| | - Denis Nonclercq
- Laboratory of Histology Research Institute of BiosciencesUniversity of Mons Mons Belgium
| | - Pierre Rasmont
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
| | - Denis Michez
- Laboratory of Zoology Research Institute of Biosciences University of Mons Mons Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology Research Institute of BiosciencesUniversity of Mons Mons Belgium
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3
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Sokpor G, Abbas E, Rosenbusch J, Staiger JF, Tuoc T. Transcriptional and Epigenetic Control of Mammalian Olfactory Epithelium Development. Mol Neurobiol 2018. [PMID: 29532253 DOI: 10.1007/s12035-018-0987-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The postnatal mammalian olfactory epithelium (OE) represents a major aspect of the peripheral olfactory system. It is a pseudostratified tissue that originates from the olfactory placode and is composed of diverse cells, some of which are specialized receptor neurons capable of transducing odorant stimuli to afford the perception of smell (olfaction). The OE is known to offer a tractable miniature model for studying the systematic generation of neurons and glia that typify neural tissue development. During OE development, stem/progenitor cells that will become olfactory sensory neurons and/or non-neuronal cell types display fine spatiotemporal expression of neuronal and non-neuronal genes that ensures their proper proliferation, differentiation, survival, and regeneration. Many factors, including transcription and epigenetic factors, have been identified as key regulators of the expression of such requisite genes to permit normal OE morphogenesis. Typically, specific interactive regulatory networks established between transcription and epigenetic factors/cofactors orchestrate histogenesis in the embryonic and adult OE. Hence, investigation of these regulatory networks critical for OE development promises to disclose strategies that may be employed in manipulating the stepwise transition of olfactory precursor cells to become fully differentiated and functional neuronal and non-neuronal cell types. Such strategies potentially offer formidable means of replacing injured or degenerated neural cells as therapeutics for nervous system perturbations. This review recapitulates the developmental cellular diversity of the olfactory neuroepithelium and discusses findings on how the precise and cooperative molecular control by transcriptional and epigenetic machinery is indispensable for OE ontogeny.
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Affiliation(s)
- Godwin Sokpor
- Institute of Neuroanatomy, University Medical Center, Georg-August-University Goettingen, 37075, Goettingen, Germany
| | - Eman Abbas
- Institute of Neuroanatomy, University Medical Center, Georg-August-University Goettingen, 37075, Goettingen, Germany.,Zoology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Joachim Rosenbusch
- Institute of Neuroanatomy, University Medical Center, Georg-August-University Goettingen, 37075, Goettingen, Germany
| | - Jochen F Staiger
- Institute of Neuroanatomy, University Medical Center, Georg-August-University Goettingen, 37075, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075, Goettingen, Germany
| | - Tran Tuoc
- Institute of Neuroanatomy, University Medical Center, Georg-August-University Goettingen, 37075, Goettingen, Germany. .,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37075, Goettingen, Germany.
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4
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Li Y, Wang J, Yu M, Wang Y, Zhang H, Yin J, Li Z, Li T, Yan H, Li F, Wang X. SNF5 deficiency induces apoptosis resistance by repressing SATB1 expression in Sézary syndrome. Leuk Lymphoma 2018; 59:2405-2413. [PMID: 29334836 DOI: 10.1080/10428194.2017.1422861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SNF5, is a core member of the SWI/SNF chromatin remodeling complex. It's deficiency leads to multiple types of aggressive cancer. Sézary syndrome, a leukemic variant of cutaneous T-cell lymphoma, is characterized by its resistance to apoptosis. Although the cause of apoptosis resistance is still poorly understood, recent evidence has revealed the importance of SATB1 in the apoptosis resistance of Sézary syndrome. In this study, we show that SNF5 is an upstream regulator of SATB1 in several conditions and that both are deficient in Sézary cells. Additionally, SNF5 not only controls the expression of SATB1, but also utilizes SATB1 to recruit itself to specific sites. Overexpression of SNF5 induces SATB1 expression and partially reverse apoptosis resistance phenotype in Sézary cells. These results suggest that both SNF5 and SATB1 may regulate apoptosis-related genes in Sézary syndrome. Thus, targeting SWI/SNF complex may represent a promising approach for Sézary syndrome therapy.
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Affiliation(s)
- Yang Li
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Jin Wang
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Minghang Yu
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Yang Wang
- b Department of Dermatology and Venerology , Peking University First Hospital , Beijing , China
| | - Huilai Zhang
- c Departments of Lymphoma , Sino-US Center for Lymphoma and Leukemia, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy , Tianjin , China
| | - Jie Yin
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Zexing Li
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Ting Li
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Han Yan
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Fajin Li
- d School of Biomedical Engineering and Technology , Tianjin Medical University , Tianjin , China
| | - Xi Wang
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China.,e Department of Immunology, School of Basic Medical Sciences , Capital Medical University , Beijing , P. R. China
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5
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Sokpor G, Xie Y, Rosenbusch J, Tuoc T. Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders. Front Mol Neurosci 2017; 10:243. [PMID: 28824374 PMCID: PMC5540894 DOI: 10.3389/fnmol.2017.00243] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.
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Affiliation(s)
- Godwin Sokpor
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Yuanbin Xie
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Joachim Rosenbusch
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Tran Tuoc
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the BrainGoettingen, Germany
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6
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Wang Y, van Merwyk L, Tönsing K, Walhorn V, Anselmetti D, Fernàndez-Busquets X. Biophysical characterization of the association of histones with single-stranded DNA. Biochim Biophys Acta Gen Subj 2017; 1861:2739-2749. [PMID: 28756274 DOI: 10.1016/j.bbagen.2017.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. METHODS Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. RESULTS Histones have a high affinity for ssDNA in 0.15M NaCl ionic strength, with an apparent binding constant similar to that calculated for their association with double-stranded DNA (dsDNA). The length of DNA (number of nucleotides in ssDNA or base pairs in dsDNA) associated with a fixed core histone mass is the same for both ssDNA and dsDNA. Although histone-ssDNA complexes show a high tendency to aggregate, nucleosome-like structures are formed at physiological salt concentrations. Core histones are able to protect ssDNA from digestion by micrococcal nuclease, and a shortening of ssDNA occurs upon its interaction with histones. The purified (+) strand of a cloned DNA fragment of nucleosomal origin has a higher affinity for histones than the purified complementary (-) strand. CONCLUSIONS At physiological ionic strength histones have high affinity for ssDNA, possibly associating with it into nucleosome-like structures. GENERAL SIGNIFICANCE In the cell nucleus histones may spontaneously interact with ssDNA to facilitate their participation in the replication and transcription of chromatin.
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Affiliation(s)
- Ying Wang
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Luis van Merwyk
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Katja Tönsing
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Volker Walhorn
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Dario Anselmetti
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Barcelona Institute for Global Health (ISGlobal), Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, Barcelona 08036, Spain; Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, Barcelona 08028, Spain.
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7
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Gordon JAR, Montecino MA, Aqeilan RI, Stein JL, Stein GS, Lian JB. Epigenetic pathways regulating bone homeostasis: potential targeting for intervention of skeletal disorders. Curr Osteoporos Rep 2014; 12:496-506. [PMID: 25260661 PMCID: PMC4216616 DOI: 10.1007/s11914-014-0240-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation utilizes different mechanisms to convey heritable traits to progeny cells that are independent of DNA sequence, including DNA silencing, post-translational modifications of histone proteins, and the post-transcriptional modulation of RNA transcript levels by non-coding RNAs. Although long non-coding RNAs have recently emerged as important regulators of gene imprinting, their functions during osteogenesis are as yet unexplored. In contrast, microRNAs (miRNAs) are well characterized for their control of osteogenic and osteoclastic pathways; thus, further defining how gene regulatory networks essential for skeleton functions are coordinated and finely tuned through the activities of miRNAs. Roles of miRNAs are constantly expanding as new studies uncover associations with skeletal disorders. The distinct functions of epigenetic regulators and evidence for integrating their activities to control normal bone gene expression and bone disease will be presented. In addition, potential for using "signature miRNAs" to identify, manage, and therapeutically treat osteosarcoma will be discussed in this review.
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Affiliation(s)
- Jonathan A. R. Gordon
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Martin A. Montecino
- Centro de Investigaciones Biomedicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, PO Box 12272, Ein Karem Campus, Jerusalem 91120, Israel
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
- Corresponding Author: Jane B. Lian – P: 802-656-4872, F: 802-656-8216,
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8
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Masliah-Planchon J, Bièche I, Guinebretière JM, Bourdeaut F, Delattre O. SWI/SNF chromatin remodeling and human malignancies. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2014; 10:145-71. [PMID: 25387058 DOI: 10.1146/annurev-pathol-012414-040445] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The SWI/SNF complexes, initially identified in yeast 20 years ago, are a family of multi-subunit complexes that use the energy of adenosine triphosphate (ATP) hydrolysis to remodel nucleosomes. Chromatin remodeling processes mediated by the SWI/SNF complexes are critical to the modulation of gene expression across a variety of cellular processes, including stemness, differentiation, and proliferation. The first evidence of the involvement of these complexes in carcinogenesis was provided by the identification of biallelic, truncating mutations of the SMARCB1 gene in malignant rhabdoid tumors, a highly aggressive childhood cancer. Subsequently, genome-wide sequencing technologies have identified mutations in genes encoding different subunits of the SWI/SNF complexes in a large number of tumors. SWI/SNF mutations, and the subsequent abnormal function of SWI/SNF complexes, are among the most frequent gene alterations in cancer. The mechanisms by which perturbation of the SWI/SNF complexes promote oncogenesis are not fully elucidated; however, alterations of SWI/SNF genes obviously play a major part in cancer development, progression, and/or resistance to therapy.
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9
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Bravo S, Núñez F, Cruzat F, Cafferata EG, De Ferrari GV, Montecino M, Podhajcer OL. Enhanced CRAd activity using enhancer motifs driven by a nucleosome positioning sequence. Mol Ther 2013; 21:1403-12. [PMID: 23712038 PMCID: PMC3702098 DOI: 10.1038/mt.2013.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/10/2013] [Indexed: 01/13/2023] Open
Abstract
Cancer development involves changes driven by the epigenetic machinery, including nucleosome positioning. Recently, the concept that adenoviral replication may be driven by tumor specific promoters (TSPs) gained support, and several conditionally replicative adenoviruses (CRAd) exhibited therapeutic efficacy in clinical trials. Here, we show for the first time that placing a nucleosome positioning sequence (NPS) upstream of a TSP combined with Wnt-responsive motifs (pART enhancer) enhanced the TSP transcriptional activity and increased the lytic activity of a CRAd. pART enhanced the transcriptional activity of the gastrointestinal cancer (GIC)-specific REG1A promoter (REG1A-pr); moreover, pART also increased the in vitro lytic activity of a CRAd whose replication was driven by REG1A-Pr. The pART enhancer effect in vitro and in vivo was strictly dependent on the presence of the NPS. Indeed, deletion of the NPS was strongly deleterious for the in vivo antitumor efficacy of the CRAd on orthotopically established pancreatic xenografts. pART also enhanced the specific activity of other heterologous promoters; moreover, the NPS was also able to enhance the responsiveness of hypoxia- and NFκB-response elements. We conclude that NPS could be useful for gene therapy approaches in cancer as well as other diseases.
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Affiliation(s)
- Soraya Bravo
- Centro de Investigaciones Biomédicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Felipe Núñez
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Fernando Cruzat
- Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Giancarlo V De Ferrari
- Centro de Investigaciones Biomédicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Martín Montecino
- Centro de Investigaciones Biomédicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
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10
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Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res 2011; 21:1650-8. [PMID: 21795385 DOI: 10.1101/gr.121145.111] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound distal sites genome-wide and find a global reorganization of the nucleosomes at these potential enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these distal sites during differentiation and generates a longer nucleosome linker region surrounding the GATA1 sites by shifting the flanking nucleosomes away. Intriguingly, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1 and is linked to subsequent transcriptional regulation of target genes.
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Affiliation(s)
- Gangqing Hu
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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11
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Abstract
Steroid hormone receptors regulate gene transcription in a highly tissue-specific manner. The local chromatin structure underlying promoters and hormone response elements is a major component involved in controlling these highly restricted expression patterns. Chromatin remodeling complexes, as well as histone and DNA modifying enzymes, are directed to gene-specific regions and create permissive or repressive chromatin environments. These structures further enable proper communication between transcription factors, co-regulators and basic transcription machinery. The regulatory elements active at target genes can be either constitutively accessible to receptors or subject to rapid receptor-dependent modification. The chromatin states responsible for these processes are in turn determined during development and differentiation. Thus access of regulatory factors to elements in chromatin provides a major level of cell selective regulation.
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Affiliation(s)
- Malgorzata Wiench
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD 20892-5055, USA
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12
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Bakshi R, Hassan MQ, Pratap J, Lian JB, Montecino MA, van Wijnen AJ, Stein JL, Imbalzano AN, Stein GS. The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes. J Cell Physiol 2010; 225:569-76. [PMID: 20506188 DOI: 10.1002/jcp.22240] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The acute myeloid leukemia 1 (AML1, RUNX1) transcription factor is a key regulator of hematopoietic differentiation that forms multi-protein complexes with co-regulatory proteins. These complexes are assembled at target gene promoters in nuclear microenvironments to mediate phenotypic gene expression and chromatin-related epigenetic modifications. Here, immunofluorescence microscopy and biochemical assays are used to show that RUNX1 associates with the human ATP-dependent SWI/SNF chromatin remodeling complex. The SWI/SNF subunits BRG1 and INI1 bind in vivo to RUNX1 target gene promoters (e.g., GMCSF, IL3, MCSF-R, MIP, and p21). These interactions correlate with histone modifications characteristic of active chromatin, including acetylated H4 and dimethylated H3 lysine 4. Downregulation of RUNX1 by RNA interference diminishes the binding of BRG1 and INI1 at selected target genes. Taken together, our findings indicate that RUNX1 interacts with the human SWI/SNF complex to control hematopoietic-specific gene expression.
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Affiliation(s)
- Rachit Bakshi
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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13
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Tomazou EM, Meissner A. Epigenetic regulation of pluripotency. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:26-40. [PMID: 21222197 DOI: 10.1007/978-1-4419-7037-4_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epigenetic regulation refers to the mechanisms that alter gene expression patterns in the absence of changes in the nucleotide sequence of the DNA molecule. The best understood epigenetic marks include posttranslational modifications of the histone tails and DNA methylation. Both play central roles in normal development and in diseases. Pluripotent stem cells have great promise for regenerative medicine and recent efforts have focused on identifying molecular networks that govern pluripotency. This chapter provides an overview of epigenetic regulation in embryonic stem cells. We present a brief introduction into epigenetic mechanisms and focus on their role in pluripotent cells.
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Affiliation(s)
- Eleni M Tomazou
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusettes, 02138, USA
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14
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Pham CD, He X, Schnitzler GR. Divergent human remodeling complexes remove nucleosomes from strong positioning sequences. Nucleic Acids Res 2009; 38:400-13. [PMID: 19906705 PMCID: PMC2811002 DOI: 10.1093/nar/gkp1030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nucleosome positioning plays a major role in controlling the accessibility of DNA to transcription factors and other nuclear processes. Nucleosome positions after assembly are at least partially determined by the relative affinity of DNA sequences for the histone octamer. Nucleosomes can be moved, however, by a class of ATP dependent chromatin remodeling complexes. We recently showed that the human SWI/SNF remodeling complex moves nucleosomes in a sequence specific manner, away from nucleosome positioning sequences (NPSes). Here, we compare the repositioning specificity of five remodelers of diverse biological functions (hSWI/SNF, the SNF2h ATPase and the hACF, CHRAC and WICH complexes than each contain SNF2h) on 5S rDNA, MMTV and 601 NPS polynucleosomal templates. We find that all five remodelers act similarly to reduce nucleosome occupancy over the strongest NPSes, an effect that could directly contribute to the function of WICH in activating 5S rDNA transcription. While some differences were observed between complexes, all five remodelers were found to result in surprisingly similar nucleosome distributions. This suggests that remodeling complexes may share a conserved repositioning specificity, and that their divergent biological functions may largely arise from other properties conferred by complex-specific subunits.
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Affiliation(s)
- Chuong D Pham
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
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15
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Stein GS, Stein JL, Van Wijnen AJ, Lian JB, Montecino M, Croce CM, Choi JY, Ali SA, Pande S, Hassan MQ, Zaidi SK, Young DW. Transcription factor-mediated epigenetic regulation of cell growth and phenotype for biological control and cancer. ACTA ACUST UNITED AC 2009; 50:160-7. [PMID: 19896493 DOI: 10.1016/j.advenzreg.2009.10.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Gary S Stein
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School and Cancer Center, Worcester, MA 01655, USA.
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16
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Teif VB, Rippe K. Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res 2009; 37:5641-55. [PMID: 19625488 PMCID: PMC2761276 DOI: 10.1093/nar/gkp610] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 07/03/2009] [Accepted: 07/06/2009] [Indexed: 01/09/2023] Open
Abstract
Nucleosome positions on the DNA are determined by the intrinsic affinities of histone proteins to a given DNA sequence and by the ATP-dependent activities of chromatin remodeling complexes that can translocate nucleosomes with respect to the DNA. Here, we report a theoretical approach that takes into account both contributions. In the theoretical analysis two types of experiments have been considered: in vitro experiments with a single reconstituted nucleosome and in vivo genome-scale mapping of nucleosome positions. The effect of chromatin remodelers was described by iteratively redistributing the nucleosomes according to certain rules until a new steady state was reached. Three major classes of remodeler activities were identified: (i) the establishment of a regular nucleosome spacing in the vicinity of a strong positioning signal acting as a boundary, (ii) the enrichment/depletion of nucleosomes through amplification of intrinsic DNA-sequence-encoded signals and (iii) the removal of nucleosomes from high-affinity binding sites. From an analysis of data for nucleosome positions in resting and activated human CD4(+) T cells [Schones et al., Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality.
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Affiliation(s)
- Vladimir B. Teif
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Kuprevich 5/2, 220141, Minsk, Belarus
| | - Karsten Rippe
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Kuprevich 5/2, 220141, Minsk, Belarus
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17
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Stein GS, Zaidi SK, Stein JL, Lian JB, van Wijnen AJ, Montecino M, Young DW, Javed A, Pratap J, Choi JY, Ali SA, Pande S, Hassan MQ. Transcription-factor-mediated epigenetic control of cell fate and lineage commitment. Biochem Cell Biol 2009; 87:1-6. [PMID: 19234518 DOI: 10.1139/o08-094] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Epigenetic control is required to maintain competency for the activation and suppression of genes during cell division. The association between regulatory proteins and target gene loci during mitosis is a parameter of the epigenetic control that sustains the transcriptional regulatory machinery that perpetuates gene-expression signatures in progeny cells. The mitotic retention of phenotypic regulatory factors with cell cycle, cell fate, and tissue-specific genes supports the coordinated control that governs the proliferation and differentiation of cell fate and lineage commitment.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655-0002, USA.
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18
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Stein GS, Zaidi SK, Stein JL, Lian JB, van Wijnen AJ, Montecino M, Young DW, Javed A, Pratap J, Choi JY, Ali SA, Pande S, Hassan MQ. Organization, integration, and assembly of genetic and epigenetic regulatory machinery in nuclear microenvironments: implications for biological control in cancer. Ann N Y Acad Sci 2009; 1155:4-14. [PMID: 19250187 DOI: 10.1111/j.1749-6632.2009.03697.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is growing awareness that the fidelity of gene expression necessitates coordination of transcription factor metabolism and organization of genes and regulatory proteins within the three-dimensional context of nuclear architecture. The regulatory machinery that governs genetic and epigenetic control of gene expression is compartmentalized in nuclear microenvironments. Temporal and spatial parameters of regulatory complex organization and assembly are functionally linked to biological control and are compromised with the onset and progression of tumorigenesis. High throughput imaging of cells, tissues, and tumors, including live cell analysis, is expanding research's capabilities toward translating components of nuclear organization into novel strategies for cancer diagnosis and therapy.
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Affiliation(s)
- Gary S Stein
- University of Massachusetts Medical School, Department of Cell Biology and Cancer Center, Worcester, Massachusetts 01655, USA.
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19
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Lelièvre SA. Contributions of extracellular matrix signaling and tissue architecture to nuclear mechanisms and spatial organization of gene expression control. Biochim Biophys Acta Gen Subj 2009; 1790:925-35. [PMID: 19328836 DOI: 10.1016/j.bbagen.2009.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/13/2009] [Accepted: 03/15/2009] [Indexed: 12/22/2022]
Abstract
Post-translational modification of histones, ATP-dependent chromatin remodeling, and DNA methylation are interconnected nuclear mechanisms that ultimately lead to the changes in chromatin structure necessary to carry out epigenetic gene expression control. Tissue differentiation is characterized by a specific gene expression profile in association with the acquisition of a defined tissue architecture and function. Elements critical for tissue differentiation, like extracellular stimuli, adhesion and cell shape properties, and transcription factors all contribute to the modulation of gene expression and thus, are likely to impinge on the nuclear mechanisms of epigenetic gene expression control. In this review, we analyze how these elements modify chromatin structure in a hierarchical manner by acting on the nuclear machinery. We discuss how mechanotransduction via the structural continuum of the cell and biochemical signaling to the cell nucleus integrate to provide a comprehensive control of gene expression. The role of nuclear organization in this control is highlighted, with a presentation of differentiation-induced nuclear structure and the concept of nuclear organization as a modulator of the response to incoming signals.
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Affiliation(s)
- Sophie A Lelièvre
- Department of Basic Medical Sciences and Cancer Center, Purdue University, Lynn, West Lafayette, IN 47907-2026, USA.
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20
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Zhong Y, Armbrecht HJ, Christakos S. Calcitonin, a regulator of the 25-hydroxyvitamin D3 1alpha-hydroxylase gene. J Biol Chem 2009; 284:11059-69. [PMID: 19261615 DOI: 10.1074/jbc.m806561200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although parathyroid hormone (PTH) induces 25-hydroxyvitamin D(3) (25(OH)D(3)) 1alpha-hydroxylase (1alpha(OH)ase) under hypocalcemic conditions, previous studies showed that calcitonin, not PTH, has an important role in the maintenance of serum 1,25-dihydroxyvitamin D(3) (1,25(OH)(2)D(3)) under normocalcemic conditions. In this study we report that 1alpha(OH)ase transcription is strongly induced by calcitonin in kidney cells and indicate mechanisms that underlie this regulation. The transcription factor C/EBPbeta is up-regulated by calcitonin in kidney cells and results in a significant enhancement of calcitonin induction of 1alpha(OH)ase transcription and protein expression. Mutation constructs of the 1alpha(OH)ase promoter demonstrate the importance of the C/EBPbeta binding site at -79/-73 for activation of the 1alpha(OH)ase promoter by calcitonin. The SWI/SNF chromatin remodeling complex was found to cooperate with calcitonin in the regulation of 1alpha(OH)ase. Chromatin immunoprecipitation analysis showed that calcitonin recruits C/EBPbeta to the 1alpha(OH)ase promoter, and Re-chromatin immunoprecipitation analysis (sequential chromatin immunoprecipitations using different antibodies) showed that C/EBPbeta and BRG1, an ATPase that is a component of the SWI/SNF complex, bind simultaneously to the 1alpha(OH)ase promoter. These findings are the first to address the dynamics between calcitonin, C/EBPbeta, and SWI/SNF in the regulation of 1alpha(OH)ase and provide a mechanism, for the first time, for calcitonin induction of 1alpha(OH)ase. Because plasma calcitonin as well as 1,25(OH)(2)D(3) have been reported to be increased during pregnancy and lactation and in early development, these findings suggest a mechanism that may account, at least in part, for the increase in plasma 1,25(OH)(2)D(3) during these times of increased calcium requirement.
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Affiliation(s)
- Yan Zhong
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, Newark, New Jersey 07103, USA
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21
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Stein GS, Zaidi SK, Stein JL, Lian JB, van Wijnen AJ, Montecino M, Young DW, Javed A, Pratap J, Choi JY, Ali SA, Pande S, Hassan MQ. Genetic and epigenetic regulation in nuclear microenvironments for biological control in cancer. J Cell Biochem 2008; 104:2016-26. [PMID: 18615590 DOI: 10.1002/jcb.21813] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The regulatory machinery that governs genetic and epigenetic control of gene expression is compartmentalized in nuclear microenvironments. Temporal and spatial parameters of regulatory complex organization and assembly are functionally linked to biological control and are compromised with the onset and progression of tumorigenesis providing a novel platform for cancer diagnosis and treatment.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
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22
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Sims HI, Baughman CB, Schnitzler GR. Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes. Nucleic Acids Res 2008; 36:6118-31. [PMID: 18820294 PMCID: PMC2577362 DOI: 10.1093/nar/gkn623] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Studies in humans and other species have revealed that a surprisingly large fraction of nucleosomes adopt specific positions on promoters, and that these positions appear to be determined by nucleosome positioning DNA sequences (NPSs). Recent studies by our lab, using minicircles containing only one nucleosome, indicated that the human SWI/SNF complex (hSWI/SNF) prefers to relocate nucleosomes away from NPSs. We now make use of novel mapping techniques to examine the hSWI/SNF sequence preference for nucleosome movement in the context of polynucleosomal chromatin, where adjacent nucleosomes can limit movement and where hSWI/SNF forms altered dinucleosomal structures. Using two NPS templates (5S rDNA and 601) and two hSWI/SNF target promoter templates (c-myc and UGT1A1), we observed hSWI/SNF-driven depletion of normal mononucleosomes from almost all positions that were strongly favored by assembly. In some cases, these mononucleosomes were moved to hSWI/SNF-preferred sequences. In the majority of other cases, one repositioned mononucleosome appeared to combine with an unmoved mononucleosome forming a specifically localized altered or normal dinucleosome. These effects result in dramatic, template-specific changes in nucleosomal distribution. Taken together, these studies indicate hSWI/SNF is likely to activate or repress transcription of its target genes by generating promoter sequence-specific changes in chromatin configuration.
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Affiliation(s)
- Hillel I Sims
- Department of Biochemistry, Tufts University School of Medicine, Boston, MA 02111, USA
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23
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Schnitzler GR. Control of Nucleosome Positions by DNA Sequence and Remodeling Machines. Cell Biochem Biophys 2008; 51:67-80. [DOI: 10.1007/s12013-008-9015-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2008] [Indexed: 12/24/2022]
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24
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Prediction and analysis of nucleosome exclusion regions in the human genome. BMC Genomics 2008; 9:186. [PMID: 18430246 PMCID: PMC2386137 DOI: 10.1186/1471-2164-9-186] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 04/22/2008] [Indexed: 11/28/2022] Open
Abstract
Background Nucleosomes are the basic structural units of eukaryotic chromatin, and they play a significant role in regulating gene expression. Specific DNA sequence patterns are known, from empirical and theoretical studies, to influence DNA bending and flexibility, and have been shown to exclude nucleosomes. A whole genome localization of these patterns, and their analysis, can add important insights on the gene regulation mechanisms that depend upon the structure of chromatin in and around a gene. Results A whole genome annotation for nucleosome exclusion regions (NXRegions) was carried out on the human genome. Nucleosome exclusion scores (NXScores) were calculated individually for each nucleotide, giving a measure of how likely a specific nucleotide and its immediate neighborhood would impair DNA bending and, consequently, exclude nucleosomes. The resulting annotations were correlated with 19055 gene expression profiles. We developed a new method based on Grubbs' outliers test for ranking genes based on their tissue specificity, and correlated this ranking with NXScores. The results show a strong correlation between tissue specificity of a gene and the propensity of its promoter to exclude nucleosomes (the promoter region was taken as -1500 to +500 bp from the RefSeq-annotated transcription start site). In addition, NXScores correlated well with gene density, gene expression levels, and DNaseI hypersensitive sites. Conclusion We present, for the first time, a whole genome prediction of nucleosome exclusion regions for the human genome (the data are available for download from Additional Materials). Nucleosome exclusion patterns are correlated with various factors that regulate gene expression, which emphasizes the need to include chromatin structural parameters in experimental analysis of gene expression.
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25
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Montecino M, Stein JL, Stein GS, Lian JB, van Wijnen AJ, Cruzat F, Gutiérrez S, Olate J, Marcellini S, Gutiérrez JL. Nucleosome organization and targeting of SWI/SNF chromatin-remodeling complexes: contributions of the DNA sequence. Biochem Cell Biol 2008; 85:419-25. [PMID: 17713577 DOI: 10.1139/o07-070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin organization within the nuclear compartment is a fundamental mechanism to regulate the expression of eukaryotic genes. During the last decade, a number of nuclear protein complexes with the ability to remodel chromatin and regulate gene transcription have been reported. Among these complexes is the SWI/SNF family, which alters chromatin structure in an ATP-dependent manner. A considerable effort has been made to understand the molecular mechanisms by which SWI/SNF catalyzes nucleosome remodeling. However, limited attention has been dedicated to studying the role of the DNA sequence in this remodeling process. Therefore, in this minireview, we discuss the contribution of nucleosome positioning and nucleosome excluding sequences to the targeting and activity of SWI/SNF complexes. This discussion includes results from our group using the rat osteocalcin gene promoter as a model. Based on these results, we postulate a model for chromatin remodeling and transcriptional activation of this gene in osteoblastic cells.
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Affiliation(s)
- Martin Montecino
- Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile.
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