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Zhou M, Riva A, Gauthier MPL, Kladde MP, Ferl RJ, Paul AL. Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight. Biol Direct 2024; 19:33. [PMID: 38689301 PMCID: PMC11059628 DOI: 10.1186/s13062-024-00476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The Advanced Plant Experiment-04 - Epigenetic Expression (APEX-04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines of Arabidopsis thaliana, wild-type Col-0 and the mutant elp2-5, which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to explore specific space-altered methylation at single-molecule resolution to associate specific changes over large regions of spaceflight related genes. To date, tools of multiplexed targeted DNA methylation sequencing remain limited for plant genomes. RESULTS To provide methylation data at single-molecule resolution, Flap-enabled next-generation capture (FENGC), a novel targeted multiplexed DNA capture and enrichment technique allowing cleavage at any specified sites, was applied to survey spaceflight-altered DNA methylation in genic regions of interest. The FENGC capture panel contained 108 targets ranging from 509 to 704 nt within the promoter or gene body regions of gene targets derived from spaceflight whole-genome data sets. In addition to genes with significant changes in expression and average methylation levels between spaceflight and ground control, targets with space-altered distributions of the proportion of methylated cytosines per molecule were identified. Moreover, trends of co-methylation of different cytosine contexts were exhibited in the same DNA molecules. We further identified significant DNA methylation changes in three previously biological process-unknown genes, and loss-of-function mutants of two of these genes (named as EMO1 and EMO2 for ELP2-regulated Methylation in Orbit 1 and 2) showed enhanced root growth rate. CONCLUSIONS FENGC simplifies and reduces the cost of multiplexed, targeted, single-molecule profiling of methylation in plants, providing additional resolution along each DNA molecule that is not seen in population-based short-read data such as WGBS. This case study has revealed spaceflight-altered regional modification of cytosine methylation occurring within single DNA molecules of cell subpopulations, which were not identified by WGBS. The single-molecule survey by FENGC can lead to identification of novel functional genes. The newly identified EMO1 and EMO2 are root growth regulators which may be epigenetically involved in plant adaptation to spaceflight.
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Affiliation(s)
- Mingqi Zhou
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, 32611, Gainesville, FL, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, 32610, Gainesville, FL, USA
| | - Marie-Pierre L Gauthier
- Department of Biochemistry and Molecular Biology, University of Florida, 2033 Mowry Rd, 32610, Gainesville, FL, USA
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, University of Florida, 2033 Mowry Rd, 32610, Gainesville, FL, USA
| | - Robert J Ferl
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, 32611, Gainesville, FL, USA.
- UF Research, University of Florida, 1523 Union Rd, Grinter Hall, 32611, Gainesville, FL, USA.
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, 32611, Gainesville, FL, USA.
- Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, 32610, Gainesville, FL, USA.
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Murray KO, Brant JO, Spradlin RA, Thome T, Laitano O, Ryan TE, Riva A, Kladde MP, Clanton TL. Exertional heat stroke causes long-term skeletal muscle epigenetic reprogramming, altered gene expression, and impaired satellite cell function in mice. Am J Physiol Regul Integr Comp Physiol 2024; 326:R160-R175. [PMID: 38047316 DOI: 10.1152/ajpregu.00226.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/26/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
The effect of exertional heat stroke (EHS) exposure on skeletal muscles is incompletely understood. Muscle weakness is an early symptom of EHS but is not considered a major target of multiorgan injury. Previously, in a preclinical mouse model of EHS, we observed the vulnerability of limb muscles to a second EHS exposure, suggesting hidden processes contributing to declines in muscle resilience. Here, we evaluated the possible molecular origins of EHS-induced declines in muscle resilience. Female C57BL/6 mice [total n = 56; 28/condition, i.e., EHS and exercise control (EXC)] underwent forced wheel running at 37.5°C/40% relative humidity until symptom limitation (unconsciousness). EXC mice exercised identically at room temperature (22-23°C). After 1 mo of recovery, the following were assessed: 1) specific force and caffeine-induced contracture in soleus (SOL) and extensor digitorum longus (EDL) muscles; 2) transcriptome and DNA methylome responses in gastrocnemius (GAST); and 3) primary satellite cell function (proliferation and differentiation). There were no differences in specific force in either SOL or EDL from EXC. Only EHS solei exhibited lower caffeine sensitivity. EHS GAST exhibited higher RNA expression of genes encoding structural proteins of slow fibers, heat shock proteins, and myogenesis. A total of ∼2,500 differentially methylated regions of DNA that could potentially affect many cell functions were identified. Primary satellite cells exhibited suppressed proliferation rates but normal differentiation responses. Results demonstrate long-term changes in skeletal muscles 1 mo after EHS that could contribute to declines in muscle resilience. Skeletal muscle may join other, more recognized tissues considered vulnerable to long-term effects of EHS.NEW & NOTEWORTHY Exertional heat stroke (EHS) in mice induces long-term molecular and functional changes in limb muscle that could reflect a loss of "resilience" to further stress. The phenotype was characterized by altered caffeine sensitivity and suppressed satellite cell proliferative potential. This was accompanied by changes in gene expression and DNA methylation consistent with ongoing muscle remodeling and stress adaptation. We propose that EHS may induce a prolonged vulnerability of skeletal muscle to further stress or injury.
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Affiliation(s)
- Kevin O Murray
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, United States
| | - Jason O Brant
- Department of Biostatistics, University of Florida, Gainesville, Florida, United States
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, United States
| | - Ray A Spradlin
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, United States
| | - Trace Thome
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, United States
| | - Orlando Laitano
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, United States
| | - Terence E Ryan
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, United States
| | - Alberto Riva
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, United States
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, United States
| | - Thomas L Clanton
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, United States
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3
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Murray KO, Brant JO, Kladde MP, Clanton TL. Long-term epigenetic and metabolomic changes in the mouse ventricular myocardium after exertional heat stroke. Physiol Genomics 2022; 54:486-500. [PMID: 36215393 PMCID: PMC9705024 DOI: 10.1152/physiolgenomics.00147.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 12/15/2022] Open
Abstract
Evidence from human epidemiological studies suggests that exertional heat stroke (EHS) results in an elevated risk of long-term cardiovascular and systemic disease. Previous results using a preclinical mouse model of EHS demonstrated severe metabolic imbalances in ventricular myocardium developing at 9-14 days of recovery. Whether this resolves over time is unknown. We hypothesized that the long-term effects of EHS on the heart reflect retained maladaptive epigenetic responses. In this study, we evaluated genome-wide DNA methylation, RNA-Seq, and metabolomic profiles of the left ventricular myocardium in female C57BL/6 mice, 30 days after EHS (exercise in 37.5°C; n = 7-8), compared with exercise controls. EHS mice ran to loss of consciousness, reaching core temperatures of 42.4 ± 0.2°C. All mice recovered quickly. After 30 days, the left ventricles were rapidly frozen for DNA methyl sequencing, RNA-Seq, and untargeted metabolomics. Ventricular DNA from EHS mice revealed >13,000 differentially methylated cytosines (DMCs) and >900 differentially methylated regions (DMRs; ≥5 DMCs with ≤300 bp between each CpG). Pathway analysis using DMRs revealed alterations in genes regulating basic cell functions, DNA binding, transcription, and metabolism. Metabolomics and mRNA expression revealed modest changes that are consistent with a return to homeostasis. Methylation status did not predict RNA expression or metabolic state at 30 days. We conclude that EHS induces a sustained DNA methylation memory lasting over 30 days of recovery, but ventricular gene expression and metabolism return to a relative homeostasis at rest. Such long-lasting alterations to the DNA methylation landscape could alter responsiveness to environmental or clinical challenges later in life.
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Affiliation(s)
- Kevin O Murray
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida
| | - Jason O Brant
- Department of Biostatistics, University of Florida, Gainesville, Florida
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida
- University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Thomas L Clanton
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida
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Affiliation(s)
- Kevin O. Murray
- Applied PhysiologyUniversity of FloridaGainesvilleFL
- Integrative PhysiologyUniversity of ColoradoBoulderCO
| | | | - Michael P. Kladde
- Biochemistry and Molecular BiologyUniversity of FloridaGainesvilleFL
| | - Thomas L. Clanton
- Applied Physiology and KinesiologyUniversity of FloridaGainesvilleFL
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Knight P, Gauthier MPL, Pardo CE, Darst RP, Kapadia K, Browder H, Morton E, Riva A, Kladde MP, Bacher R. Methylscaper: an R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. Bioinformatics 2021; 37:4857-4859. [PMID: 34125875 PMCID: PMC8665741 DOI: 10.1093/bioinformatics/btab438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/19/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we present methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin accessibility landscapes. Methylscaper implements a weighted principal component analysis that orders DNA molecules, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper's utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit-BGS) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets. AVAILABILITY AND IMPLEMENTATION Methylscaper, is implemented in R (version > 4.1) and available on Bioconductor: https://bioconductor.org/packages/methylscaper/, GitHub: https://github.com/rhondabacher/methylscaper/, and Web: https://methylscaper.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Parker Knight
- Department of Biostatistics, University of Florida, Gainesville, FL
| | | | - Carolina E Pardo
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL
| | - Russell P Darst
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL
| | - Kevin Kapadia
- Department of Statistics, University of Florida, Gainesville, FL
| | - Hadley Browder
- Department of Statistics, University of Florida, Gainesville, FL
| | - Eliza Morton
- Department of Statistics, University of Florida, Gainesville, FL
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL
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Murray KO, Brant JO, Iwaniec JD, Sheikh LH, de Carvalho L, Garcia CK, Robinson GP, Alzahrani JM, Riva A, Laitano O, Kladde MP, Clanton TL. Exertional heat stroke leads to concurrent long-term epigenetic memory, immunosuppression and altered heat shock response in female mice. J Physiol 2020; 599:119-141. [PMID: 33037634 DOI: 10.1113/jp280518] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022] Open
Abstract
KEY POINTS Exposure to exertional heat stroke (EHS) has been linked to increased long-term decrements of health. Epigenetic reprogramming is involved in the response to heat acclimation; however, whether the long-term effects of EHS are mediated by epigenetic reprogramming is unknown. In female mice, we observed DNA methylation reprogramming in bone marrow-derived (BMD) monocytes as early as 4 days of recovery from EHS and as late as 30 days compared with sham exercise controls. Whole blood, collected after 30 days of recovery from EHS, exhibited an immunosuppressive phenotype when challenged in vitro by lipopolysaccharide. After 30 days of recovery from EHS, BMD monocytes exhibited an altered in vitro heat shock response. The location of differentially methylated CpGs are predictive of both the immunosuppressive phenotype and altered heat shock responses. ABSTRACT Exposure to exertional heat stroke (EHS) has been linked to increased susceptibility to a second heat stroke, infection and cardiovascular disease. Whether these clinical outcomes are mediated by an epigenetic memory is unknown. Using a preclinical mouse model of EHS, we investigated whether EHS exposure produces a lasting epigenetic memory in monocytes and whether there are phenotypic alterations that may be consistent with these epigenetic changes. Female mice underwent forced wheel running at 37.5°C/40% relative humidity until symptom limitation, characterized by CNS dysfunction. Results were compared with matched exercise controls at 22.5°C. Monocytes were isolated from bone marrow after 4 or 30 days of recovery to extract DNA and analyse methylation. Broad-ranging alterations to the DNA methylome were observed at both time points. At 30 days, very specific alterations were observed to the promoter regions of genes involved with immune responsiveness. To test whether these changes might be related to phenotype, whole blood at 30 days was challenged with lipopolysaccharide (LPS) to measure cytokine secretion; monocytes were also challenged with heat shock to quantify mRNA expression. Whole blood collected from EHS mice showed markedly attenuated inflammatory responses to LPS challenge. Furthermore, monocyte mRNA from EHS mice showed significantly altered responses to heat shock challenge. These results demonstrate that EHS leads to a unique DNA methylation pattern in monocytes and altered immune and heat shock responsiveness after 30 days. These data support the hypothesis that EHS exposure can induce long-term physiological changes that may be linked to altered epigenetic profiles.
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Affiliation(s)
- Kevin O Murray
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Jason O Brant
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - John D Iwaniec
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Laila H Sheikh
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Lucas de Carvalho
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Christian K Garcia
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Gerard P Robinson
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Jamal M Alzahrani
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Orlando Laitano
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Thomas L Clanton
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA
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Murray KO, Iwaniec J, Brant J, de Carvalho L, Robinson GP, Garcia CK, Alzahrani J, Laitano O, Kladde MP, Clanton TL. Suppressed inflammatory phenotype following exertional heat stroke in mice: an epigenetic link? FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lorentsen KJ, Cho JJ, Luo X, Zuniga AN, Urban JF, Zhou L, Gharaibeh R, Jobin C, Kladde MP, Avram D. Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma. Nat Commun 2018; 9:1679. [PMID: 29700302 PMCID: PMC5920086 DOI: 10.1038/s41467-018-04111-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/03/2018] [Indexed: 12/24/2022] Open
Abstract
During helminth infection and allergic asthma, naive CD4+ T-cells differentiate into cytokine-producing Type-2 helper (Th2) cells that resolve the infection or induce asthma-associated pathology. Mechanisms regulating the Th2 differentiation in vivo remain poorly understood. Here we report that mice lacking Bcl11b in mature T-cells have a diminished capacity to mount Th2 responses during helminth infection and allergic asthma, showing reduced Th2 cytokines and Gata3, and elevated Runx3. We provide evidence that Bcl11b is required to maintain chromatin accessibility at Th2-cytokine promoters and locus-control regions, and binds the Il4 HS IV silencer, reducing its accessibility. Bcl11b also binds Gata3-intronic and downstream-noncoding sites, sustaining the Gata3 expression. In addition, Bcl11b binds and deactivates upstream enhancers at Runx3 locus, restricting the Runx3 expression and its availability to act at the Il4 HS IV silencer. Thus, our results establish novel roles for Bcl11b in the regulatory loop that licenses Th2 program in vivo.
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Affiliation(s)
- Kyle J Lorentsen
- Department of Medicine, Division of Pulmonary Medicine, College of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Jonathan J Cho
- Department of Medicine, Division of Pulmonary Medicine, College of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL, 32610, USA.,Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Xiaoping Luo
- Department of Medicine, Division of Pulmonary Medicine, College of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL, 32610, USA.,Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Ashley N Zuniga
- Department of Medicine, Division of Pulmonary Medicine, College of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL, 32610, USA.,Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Joseph F Urban
- Beltsville Human Nutrition Research Center, Agricultural Research Service, Diet, Genomic and Immunology Laboratory, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave, Gainesville, FL, 32608, USA.,UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Raad Gharaibeh
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.,Department of Medicine, Division of Gastroenterology, College of Medicine, University of Florida, 2033 Mowry Rd., CGRC 461, Gainesville, FL, 32610, USA
| | - Christian Jobin
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.,Department of Medicine, Division of Gastroenterology, College of Medicine, University of Florida, 2033 Mowry Rd., CGRC 461, Gainesville, FL, 32610, USA
| | - Michael P Kladde
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 2033 Mowry Rd., CGRC 359, Gainesville, FL, 32610, USA
| | - Dorina Avram
- Department of Medicine, Division of Pulmonary Medicine, College of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL, 32610, USA. .,Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA. .,UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
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Lu Z, Lieber MR, Tsai AG, Pardo CE, Müschen M, Kladde MP, Hsieh CL. Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin. Mol Cell Biol 2015; 35:1209-22. [PMID: 25624348 PMCID: PMC4355534 DOI: 10.1128/mcb.01085-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/26/2014] [Accepted: 01/16/2015] [Indexed: 12/19/2022] Open
Abstract
Chromosomal translocations are a hallmark of hematopoietic malignancies. CG motifs within translocation fragile zones (typically 20 to 600 bp in size) are prone to chromosomal translocation in lymphomas. Here we demonstrate that the CG motifs in human translocation fragile zones are hypomethylated relative to the adjacent DNA. Using a methyltransferase footprinting assay on isolated nuclei (in vitro), we find that the chromatin at these fragile zones is accessible. We also examined in vivo accessibility using cellular expression of a prokaryotic methylase. Based on this assay, which measures accessibility over a much longer time interval than is possible with in vitro methods, these fragile zones were found to be more accessible than the adjacent DNA. Because DNA within the fragile zones can be methylated by both cellular and exogenous methyltransferases, the fragile zones are predominantly in a duplex DNA conformation. These observations permit more-refined models for why these zones are 100- to 1,000-fold more prone to undergo chromosomal translocation than the adjacent regions.
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Affiliation(s)
- Zhengfei Lu
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Albert G Tsai
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Carolina E Pardo
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Markus Müschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michael P Kladde
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
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Ai L, Kim WJ, Alpay M, Tang M, Pardo CE, Hatakeyama S, May WS, Kladde MP, Heldermon CD, Siegel EM, Brown KD. TRIM29 suppresses TWIST1 and invasive breast cancer behavior. Cancer Res 2014; 74:4875-87. [PMID: 24950909 DOI: 10.1158/0008-5472.can-13-3579] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
TRIM29 (ATDC) exhibits a contextual function in cancer, but seems to exert a tumor-suppressor role in breast cancer. Here, we show that TRIM29 is often silenced in primary breast tumors and cultured tumor cells as a result of aberrant gene hypermethylation. RNAi-mediated silencing of TRIM29 in breast tumor cells increased their motility, invasiveness, and proliferation in a manner associated with increased expression of mesenchymal markers (N-cadherin and vimentin), decreased expression of epithelial markers (E-cadherin and EpCAM), and increased expression and activity of the oncogenic transcription factor TWIST1, an important driver of the epithelial-mesenchymal transition (EMT). Functional investigations revealed an inverse relationship in the expression of TRIM29 and TWIST1, suggesting the existence of a negative regulatory feedback loop. In support of this relationship, we found that TWIST1 inhibited TRIM29 promoter activity through direct binding to a region containing a cluster of consensus E-box elements, arguing that TWIST1 transcriptionally represses TRIM29 expression. Analysis of a public breast cancer gene-expression database indicated that reduced TRIM29 expression was associated with reduced relapse-free survival, increased tumor size, grade, and metastatic characteristics. Taken together, our results suggest that TRIM29 acts as a tumor suppressor in breast cancer through its ability to inhibit TWIST1 and suppress EMT.
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Affiliation(s)
- Lingbao Ai
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida.
| | - Wan-Ju Kim
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Merve Alpay
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Ming Tang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Carolina E Pardo
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - W Stratford May
- UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida. Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Coy D Heldermon
- UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida. Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Erin M Siegel
- Division of Population Sciences, Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin D Brown
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida.
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11
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Nabilsi NH, Ryder DJ, Peraza-Penton AC, Poudyal R, Loose DS, Kladde MP. Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter. J Biol Chem 2013; 288:35940-51. [PMID: 24163369 DOI: 10.1074/jbc.m113.523837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genome-scale mapping suggests that the function of DNA methylation varies with genomic context beyond transcriptional repression. However, the use of DNA-demethylating agents (e.g. 5-aza-2'-deoxycytidine (5aza-dC)) to study epigenetic regulation often focuses on gene activation and ignores repression elicited by 5aza-dC. Here, we show that repression of NEK2, which encodes the never in mitosis A (NIMA)-related kinase, by 5aza-dC is context-specific as NEK2 transcript levels were reduced in HCT116 colon cancer cells but not in isogenic p53(-/-) cells. Bisulfite sequencing showed that DNA methylation was restricted to the distal region of the NEK2 promoter. Demethylation by 5aza-dC was associated with increased accessibility to micrococcal nuclease, i.e. nucleosome depletion. Conversely, methyltransferase accessibility protocol for individual templates (MAPit) methylation footprinting showed that nucleosome occupancy and DNA methylation at the distal promoter were significantly increased in p53(-/-) cells, suggesting dynamic regulation of chromatin structure at this region by p53 in HCT116 cells. Stabilization of endogenous p53 by doxorubicin or ectopic expression of p53, but not a p53 DNA-binding mutant, decreased NEK2 expression. Chromatin immunoprecipitation demonstrated direct and specific association of p53 with the distal NEK2 promoter, which was enhanced by doxorubicin. Luciferase reporters confirmed that this region is required for p53-mediated repression of NEK2 promoter activity. Lastly, modulation of p53 abundance altered nucleosome occupancy and DNA methylation at its binding region. These results identify NEK2 as a novel p53-repressed gene, illustrate that its repression by 5aza-dC is specific and associated with nucleosome reorganization, and provide evidence that identification of partially methylated regions can reveal novel p53 target genes.
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Affiliation(s)
- Nancy H Nabilsi
- From the Department of Biochemistry and Molecular Biology, University of Florida Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610
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12
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Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, Reynolds BA, Kladde MP. Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma. Genome Res 2013; 24:329-39. [PMID: 24105770 PMCID: PMC3912423 DOI: 10.1101/gr.161737.113] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed amplification of targeted sequences from submicrogram quantities of genomic DNA followed by next generation bisulfite sequencing. This provides highly scalable and simultaneous mapping of chromatin accessibility and DNA methylation on single molecules at high resolution. Long sequencing reads from targeted regions maintain the structural integrity of epigenetic information and provide substantial depth of coverage, detecting for the first time minority subpopulations of epigenetic configurations formerly obscured by existing genome-wide and population-ensemble methodologies. Analyzing a cohort of 71 promoters of genes with exons commonly mutated in cancer, MAPit-patch uncovered several differentially accessible and methylated promoters that are associated with altered gene expression between neural stem cell (NSC) and glioblastoma (GBM) cell populations. In addition, considering each promoter individually, substantial epigenetic heterogeneity was observed across the sequenced molecules, indicating the presence of epigenetically distinct cellular subpopulations. At the divergent MLH1/EPM2AIP1 promoter, a locus with three well-defined, nucleosome-depleted regions (NDRs), a fraction of promoter copies with inaccessible chromatin was detected and enriched upon selection of temozolomide-tolerant GBM cells. These results illustrate the biological relevance of epigenetically distinct subpopulations that in part underlie the phenotypic heterogeneity of tumor cell populations. Furthermore, these findings show that alterations in chromatin accessibility without accompanying changes in DNA methylation may constitute a novel class of epigenetic biomarker.
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Affiliation(s)
- Nancy H Nabilsi
- Department of Biochemistry and Molecular Biology, University of Florida Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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13
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Yang T, Owen JL, Lightfoot YL, Kladde MP, Mohamadzadeh M. Microbiota impact on the epigenetic regulation of colorectal cancer. Trends Mol Med 2013; 19:714-25. [PMID: 24051204 DOI: 10.1016/j.molmed.2013.08.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/02/2013] [Accepted: 08/22/2013] [Indexed: 12/12/2022]
Abstract
Mechanisms of colorectal cancer (CRC) development can be generally divided into three categories: genetic, epigenetic, and aberrant immunologic signaling pathways, all of which may be triggered by an imbalanced intestinal microbiota. Aberrant gut microbial composition, termed 'dysbiosis', has been reported in inflammatory bowel disease patients who are at increased risk for CRC development. Recent studies indicate that it is feasible to rescue experimental models of colonic cancer by oral treatment with genetically engineered beneficial bacteria and/or their immune-regulating gene products. Here, we review the mechanisms of epigenetic modulation implicated in the development and progression of CRC, which may be the result of dysbiosis, and therefore may be amenable to therapeutic intervention.
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Affiliation(s)
- Tao Yang
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL 32608 USA; Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Florida, Gainesville, FL 32610 USA
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14
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Siebzehnrubl FA, Silver DJ, Tugertimur B, Deleyrolle LP, Siebzehnrubl D, Sarkisian MR, Devers KG, Yachnis AT, Kupper MD, Neal D, Nabilsi NH, Kladde MP, Suslov O, Brabletz S, Brabletz T, Reynolds BA, Steindler DA. The ZEB1 pathway links glioblastoma initiation, invasion and chemoresistance. EMBO Mol Med 2013; 5:1196-212. [PMID: 23818228 PMCID: PMC3944461 DOI: 10.1002/emmm.201302827] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma remains one of the most lethal types of cancer, and is the most common brain tumour in adults. In particular, tumour recurrence after surgical resection and radiation invariably occurs regardless of aggressive chemotherapy. Here, we provide evidence that the transcription factor ZEB1 (zinc finger E-box binding homeobox 1) exerts simultaneous influence over invasion, chemoresistance and tumourigenesis in glioblastoma. ZEB1 is preferentially expressed in invasive glioblastoma cells, where the ZEB1-miR-200 feedback loop interconnects these processes through the downstream effectors ROBO1, c-MYB and MGMT. Moreover, ZEB1 expression in glioblastoma patients is predictive of shorter survival and poor Temozolomide response. Our findings indicate that this regulator of epithelial-mesenchymal transition orchestrates key features of cancer stem cells in malignant glioma and identify ROBO1, OLIG2, CD133 and MGMT as novel targets of the ZEB1 pathway. Thus, ZEB1 is an important candidate molecule for glioblastoma recurrence, a marker of invasive tumour cells and a potential therapeutic target, along with its downstream effectors.
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15
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Siebzehnrubl FA, Silver DJ, Tugertimur B, Deleyrolle LP, Siebzehnrubl D, Sarkisian MR, Devers KG, Yachnis AT, Kupper MD, Neal D, Nabilsi NH, Kladde MP, Suslov O, Brabletz S, Brabletz T, Reynolds BA, Steindler DA. Abstract 4906: ZEB1 maintains self-renewal, invasion and chemoresistance of glioblastoma stem cells. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite intense efforts in basic research and clinical medicine, glioblastoma remains one of the most lethal types of cancer. In particular, tumor recurrence after surgical resection, targeted radiation, and aggressive chemotherapy remains an insurmountable obstacle. Recurrence has been attributed to residual cancer cells that re-initiate tumor growth after primary clinical intervention. Hierarchical attribution of this capacity for tumor (re-)initiation to a specific cellular subpopulation is one of the hallmarks of the cancer stem cell hypothesis. In cancers outside the CNS, a considerable overlap between cancer stem cell phenotypes and Epithelial-Mesenchymal-Transition (EMT) has been found. EMT is frequently associated with distant spreading and the generation of secondary tumors. Tumor cells undergoing EMT have a higher propensity for invasion and therapy resistance, as well as greater stemness potential. Transcription factors regulating EMT, including ZEB1 (zinc finger E-box binding homeobox 1), have been found to regulate typical stem cell-associated genes. We therefore tested whether the EMT-associated transcription factor ZEB1 may coordinate mechanisms of invasion, therapy resistance and recurrence in glioblastoma.
ZEB1 is preferentially expressed at the tumor invasion front, and its knockdown results in a dramatic reduction of tumorigenicity, invasion and increased sensitivity to the chemotherapeutic agent Temozolomide (Temodar®, TMZ). We found that ZEB1 indirectly controls expression of the chemoresistance-mediating enzyme MGMT (O-6-Methylguanine DNA Methyltransferase), as well as cell-cell adhesion and stemness pathways, thus linking chemoresistance and invasion in brain cancer stem cells.
Moreover, ZEB1 expression in glioblastoma patients is predictive of shorter survival and poor TMZ response. These results indicate that invasive glioblastoma cells are particularly sheltered from current therapeutic approaches, rendering them likely candidates for tumor recurrence. This offers a potential novel model for GBM recurrence, and a potential therapeutic target.
Citation Format: Florian A. Siebzehnrubl, Daniel J. Silver, Bugra Tugertimur, Loic P. Deleyrolle, Dorit Siebzehnrubl, Matthew R. Sarkisian, Kelly G. Devers, Antony T. Yachnis, Marius D. Kupper, Daniel Neal, Nancy H. Nabilsi, Michael P. Kladde, Oleg Suslov, Simone Brabletz, Thomas Brabletz, Brent A. Reynolds, Dennis A. Steindler. ZEB1 maintains self-renewal, invasion and chemoresistance of glioblastoma stem cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4906. doi:10.1158/1538-7445.AM2013-4906
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Daniel Neal
- 1Univ Florida McnKnight Brain Inst, Gainesville, FL
| | | | | | - Oleg Suslov
- 1Univ Florida McnKnight Brain Inst, Gainesville, FL
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16
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Abstract
Spontaneous lytic reactivation of Kaposi’s sarcoma–associated herpesvirus (KSHV) occurs at a low rate in latently infected cells in disease and culture. This suggests imperfect epigenetic maintenance of viral transcription programs, perhaps due to variability in chromatin structure at specific loci across the population of KSHV episomal genomes. To characterize this locus-specific chromatin structural diversity, we used MAPit single-molecule footprinting, which simultaneously maps endogenous CG methylation and accessibility to M.CviPI at GC sites. Diverse chromatin structures were detected at the LANA, RTA and vIL6 promoters. At each locus, chromatin ranged from fully closed to fully open across the population. This diversity has not previously been reported in a virus. Phorbol ester and RTA transgene induction were used to identify chromatin conformations associated with reactivation of lytic transcription, which only a fraction of episomes had. Moreover, certain chromatin conformations correlated with CG methylation patterns at the RTA and vIL6 promoters. This indicated that some of the diverse chromatin conformations at these loci were epigenetically distinct. Finally, by comparing chromatin structures from a cell line infected with constitutively latent virus, we identified products of lytic replication. Our findings show that epigenetic drift can restrict viral propagation by chromatin compaction at latent and lytic promoters.
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Affiliation(s)
- Russell P Darst
- Department of Biochemistry and Molecular Biology, 2033 Mowry Road, Box 103633, University of Florida College of Medicine, Gainesville, FL, 32610, USA
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17
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Santostefano KE, Hamazaki T, Pardo CE, Kladde MP, Terada N. Fibroblast growth factor receptor 2 homodimerization rapidly reduces transcription of the pluripotency gene Nanog without dissociation of activating transcription factors. J Biol Chem 2012; 287:30507-17. [PMID: 22787153 DOI: 10.1074/jbc.m112.388181] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nanog or Gata6-positive cells co-exist and are convertible within the inner cell mass of murine blastocysts and embryonic stem (ES) cells. Previous studies demonstrate fibroblast growth factor receptor 2 (FGFR2) triggers Nanog gene down-regulation and differentiation to primitive endoderm (PE); however, the underlying mechanisms responsible for reversible and fluctuating cell fate are poorly understood. Using an inducible FGFR2 dimerization system in ES cells, we demonstrate that FGFR2 activation rapidly down-regulated Nanog gene transcription through activation of the Mek pathway and subsequently differentiated ES cells into PE cells. FGFR2 rather selectively repressed the Nanog gene with minimal effect on other pluripotency genes, including Oct4 and Sox2. We determined the Nanog promoter region containing minimum Oct4/Sox2 binding sites was sufficient for this transcriptional down-regulation by FGFR2, when the reporter transgenes were integrated with insulators. Of interest, FGFR2-mediated Nanog transcriptional reduction occurred without dissociation of RNA polymerase II, p300, Oct4, Sox2, and Tet1 from the Nanog proximal promoter region and with no increase in repressive histone methylation marks or DNA methylation, implying the gene repression is in the early and transient phase. Furthermore, addition of a specific FGFR inhibitor readily reversed this Nanog repression status. These findings illustrate well how FGFR2 induces rapid but reversible Nanog repression within ES cells.
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18
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Darst RP, Pardo CE, Pondugula S, Gangaraju VK, Nabilsi NH, Bartholomew B, Kladde MP. Simultaneous single-molecule detection of endogenous C-5 DNA methylation and chromatin accessibility using MAPit. Methods Mol Biol 2012; 833:125-41. [PMID: 22183592 DOI: 10.1007/978-1-61779-477-3_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Bisulfite genomic sequencing provides a single-molecule view of cytosine methylation states. After deamination, each cloned molecule contains a record of methylation within its sequence. The full power of this technique is harnessed by treating nuclei with an exogenous DNMT prior to DNA extraction. This exogenous methylation marks regions of accessibility and footprints nucleosomes, as well as other DNA-binding proteins. Thus, each cloned molecule records not only the endogenous methylation present (at CG sites, in mammals), but also the exogenous (GC, when using the Chlorella virus protein M.CviPI). We term this technique MAPit, methylation accessibility protocol for individual templates.
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Affiliation(s)
- Russell P Darst
- Department of Biochemistry and Molecular Biology, University of Florida and Shands Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
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19
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Abstract
A single-molecule probe of chromatin structure can uncover dynamic chromatin states and rare epigenetic variants of biological importance that bulk measures of chromatin structure miss. In bisulfite genomic sequencing, each sequenced clone records the methylation status of multiple sites on an individual molecule of DNA. An exogenous DNA methyltransferase can thus be used to image nucleosomes and other protein-DNA complexes. In this chapter, we describe the adaptation of this technique, termed Methylation Accessibility Protocol for individual templates, to modern high-throughput sequencing, which both simplifies the workflow and extends its utility.
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Affiliation(s)
- Russell P Darst
- Department of Biochemistry and Molecular Biology, University of Florida Shands Cancer Center Program in Cancer Genetics, Epigenetics, and Tumor Virology, Gainesville, Florida, USA
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20
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Delmas AL, Riggs BM, Pardo CE, Dyer LM, Darst RP, Izumchenko EG, Monroe M, Hakam A, Kladde MP, Siegel EM, Brown KD. WIF1 is a frequent target for epigenetic silencing in squamous cell carcinoma of the cervix. Carcinogenesis 2011; 32:1625-33. [PMID: 21873353 PMCID: PMC3204350 DOI: 10.1093/carcin/bgr193] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/22/2011] [Accepted: 08/08/2011] [Indexed: 02/07/2023] Open
Abstract
Aberrant activation of the Wnt/β-catenin signaling axis is a prominent oncogenic mechanism in numerous cancers including cervical cancer. Wnt inhibitory factor-1 (WIF1) is a secreted protein that binds Wnt and antagonizes Wnt activity. While the WIF1 gene is characterized as a target for epigenetic silencing in some tumor types, WIF1 expression has not been examined in human cervical tissue and cervical cancer. Here, we show that WIF1 is unmethylated and its gene product is expressed in normal cervical epithelium and some cultured cervical tumor lines. In contrast, several cervical cancer lines contained dense CpG methylation within the WIF1 gene, and expression of both WIF1 transcript and protein was restored by culturing cells in the presence of the global DNA demethylating agent 5-aza-2'-deoxycytidine. Using single-molecule MAPit methylation footprinting, we observed differences in chromatin structure within the WIF1 promoter region between cell lines that express and those that do not express WIF1, consistent with transcriptional activity and repression, respectively. The WIF1 promoter was aberrantly methylated in ∼60% (10 of 17) high-grade highly undifferentiated squamous cell cervical tumors examined, whereas paired normal tissue showed significantly lower levels of CpG methylation. WIF1 protein was not detectable by immunohistochemistry in tumors with quantitatively high levels of WIF1 methylation. Of note, WIF1 protein was not detectable in two of the seven unmethylated cervical tumors examined, suggesting other mechanisms may contribute WIF1 repression. Our findings establish the WIF1 gene as a frequent target for epigenetic silencing in squamous cell carcinoma of the cervix.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Blotting, Western
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line
- Cervix Uteri/metabolism
- CpG Islands/genetics
- DNA Methylation
- Decitabine
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Humans
- Immunoenzyme Techniques
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/metabolism
- Uterine Cervical Neoplasms/pathology
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Affiliation(s)
| | - Bridget M. Riggs
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | | | | | | | | | - Mänette Monroe
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ardeshir Hakam
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Michael P. Kladde
- To whom correspondence should be addressed. Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA. Tel: +352 273 5458,
| | - Erin M. Siegel
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Kevin D. Brown
- To whom correspondence should be addressed. Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA. Tel: +352 273 5458,
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21
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Pardo CE, Darst RP, Nabilsi NH, Delmas AL, Kladde MP. Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit. ACTA ACUST UNITED AC 2011; Chapter 21:Unit 21.22. [PMID: 21732317 DOI: 10.1002/0471142727.mb2122s95] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sites of protein binding to DNA are inferred from footprints or spans of protection against a probing reagent. In most protocols, sites of accessibility to a probe are detected by mapping breaks in DNA strands. As discussed in this unit, such methods obscure molecular heterogeneity by averaging cuts at a given site over all DNA strands in a sample population. The DNA methyltransferase accessibility protocol for individual templates (MAPit), an alternative method described in this unit, localizes protein-DNA interactions by probing with cytosine-modifying DNA methyltransferases followed by bisulfite sequencing. Sequencing individual DNA products after amplification of bisulfite-converted sequences permits assignment of the methylation status of every enzyme target site along a single DNA strand. Use of the GC-methylating enzyme M.CviPI allows simultaneous mapping of chromatin accessibility and endogenous CpG methylation. MAPit is therefore the only footprinting method that can detect subpopulations of molecules with distinct patterns of protein binding or chromatin architecture and correlate them directly with the occurrence of endogenous methylation. Additional advantages of MAPit methylation footprinting as well as considerations for experimental design and potential sources of error are discussed.
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Affiliation(s)
- Carolina E Pardo
- Department of Biochemistry and Molecular Biology and UF Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, University of Florida College of Medicine, Gainesville, Florida, USA
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22
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Pardo CE, Carr IM, Hoffman CJ, Darst RP, Markham AF, Bonthron DT, Kladde MP. MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects. Nucleic Acids Res 2010; 39:e5. [PMID: 20959287 PMCID: PMC3017589 DOI: 10.1093/nar/gkq716] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at nucleotide resolution along single DNA strands. Probing with cytosine DNA methyltransferases followed by bisulfite sequencing (MAPit) is an effective technique for mapping protein-DNA interactions. Here, MAPit methylation footprinting with M.CviPI, a GC methyltransferase we previously cloned and characterized, was used to probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells. Because M.CviPI-probed samples contain both CG and GC methylation, we developed a versatile, visually-intuitive program, called MethylViewer, for evaluating the bisulfite sequencing results. Uniquely, MethylViewer can simultaneously query cytosine methylation status in bisulfite-converted sequences at as many as four different user-defined motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data can also be exported for statistical analysis and as publication-quality images. Analysis of hMLH1 MAPit data with MethylViewer showed that endogenous CG methylation and accessible GC sites were both mapped on single molecules at high resolution. Disruption of positioned nucleosomes on single molecules of the PHO5 promoter was detected in budding yeast using M.CviPII, increasing the number of enzymes available for probing protein-DNA interactions. MethylViewer provides an integrated solution for primer design and rapid, accurate and detailed analysis of bisulfite sequencing or MAPit datasets from virtually any biological or biochemical system.
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Affiliation(s)
- Carolina E Pardo
- Department of Biochemistry and Molecular Biology, University of Florida Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, Gainesville, FL 32610-3633, USA
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23
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Abstract
Exact positions of 5-methylcytosine (m(5)C) on a single strand of DNA can be determined by bisulfite genomic sequencing (BGS). Treatment with bisulfite ion preferentially deaminates unmethylated cytosines, which are then converted to uracil upon desulfonation. Amplifying regions of interest from deaminated DNA and sequencing products cloned from amplicons permits determination of methylation at single-nucleotide resolution along single DNA molecules, which is not possible with other methylation analysis techniques. This unit describes a BGS technique suitable for most DNA sources, including formaldehyde-fixed tissue. Considerations for experimental design and common sources of error are discussed.
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Affiliation(s)
- Russell P Darst
- University of Florida College of Medicine, Gainesville, Florida, USA
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24
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Dechassa ML, Sabri A, Pondugula S, Kassabov SR, Chatterjee N, Kladde MP, Bartholomew B. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol Cell 2010; 38:590-602. [PMID: 20513433 DOI: 10.1016/j.molcel.2010.02.040] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/26/2009] [Accepted: 02/22/2010] [Indexed: 01/12/2023]
Abstract
The ATP-dependent chromatin remodeling complex SWI/SNF regulates transcription and has been implicated in promoter nucleosome eviction. Efficient nucleosome disassembly by SWI/SNF alone in biochemical assays, however, has not been directly observed. Employing a model system of dinucleosomes rather than mononucleosomes, we demonstrate that remodeling leads to ordered and efficient disassembly of one of the two nucleosomes. An H2A/H2B dimer is first rapidly displaced, and then, in a slower reaction, an entire histone octamer is lost. Nucleosome disassembly by SWI/SNF did not require additional factors such as chaperones or acceptors of histones. Observations in single molecules as well as bulk measurement suggest that a key intermediate in this process is one in which a nucleosome is moved toward the adjacent nucleosome. SWI/SNF recruited by the transcriptional activator Gal4-VP16 preferentially mobilizes the proximal nucleosome and destabilizes the adjacent nucleosome.
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Affiliation(s)
- Mekonnen Lemma Dechassa
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901-4413, USA
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25
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Bartholomew B, Dechassa ML, Hota SK, Prasad P, Sen P, Gosh S, Hemeryck CS, Pugh F, Pondugula S, Kladde MP. The structure and function of ATP‐dependent chromatin remodeling complexes. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.310.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Blaine Bartholomew
- Biochemistry and Molecular BiologySouthern Illinois UniversityCarbondaleIL
| | - Mekonnen Lemma Dechassa
- Biochemistry and Molecular BiologySouthern Illinois UniversityCarbondaleIL
- Department of Biochemistry and Molecular BiologyColorado State UniversityFort CollinsCO
| | - Swetansu K Hota
- Biochemistry and Molecular BiologySouthern Illinois UniversityCarbondaleIL
| | - Punit Prasad
- Biochemistry and Molecular BiologySouthern Illinois UniversityCarbondaleIL
| | - Payel Sen
- Biochemistry and Molecular BiologySouthern Illinois UniversityCarbondaleIL
| | - Sujana Gosh
- Biochemistry and Molecular BiologyPennsylvania State UniversityUniversity ParkPA
| | | | - Frank Pugh
- Biochemistry and Molecular BiologyPennsylvania State UniversityUniversity ParkPA
| | - Santhi Pondugula
- Biochemistry and Molecular BiologyUniversity of FloridaGainesvilleFL
| | - Michael P. Kladde
- Biochemistry and Molecular BiologyUniversity of FloridaGainesvilleFL
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26
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Abstract
Wrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non-histone protein-DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA-bound proteins, such as histones or site-specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage-based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single-hit kinetics. Moreover, cleavage-based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase-based, single-molecule MAP-IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP-IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation.
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Affiliation(s)
- Santhi Pondugula
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-3633, USA
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27
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Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods 2007; 41:320-32. [PMID: 17309843 PMCID: PMC2923433 DOI: 10.1016/j.ymeth.2006.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 08/15/2006] [Indexed: 11/20/2022] Open
Abstract
Probing chromatin structure with DNA methyltransferases offers advantages over more commonly used nuclease-based and chromatin immunoprecipitation methods for detection of nucleosomes and non-histone protein-DNA interactions. Here, we describe two related methods in which the readout of MTase accessibility is obtained by assaying 5-methylcytosine in DNA through the PCR-based technique of bisulfite genomic sequencing. The methyltransferase accessibility protocol (MAP) determines the relative frequency at which the enzyme accesses each of its target sites over an entire population of PCR amplified product. While MAP yields much quantitative information about relative accessibility of a region of chromatin, a complementary single-molecule view of methyltransferase accessibility, termed MAP for individual templates (MAP-IT), is provided by analysis of cloned PCR products. Absolute rather than relative methylation frequencies in a region are obtained by summing the methylation status at each site over a cohort of clones. Moreover, as the integrity of individual molecules is maintained in MAP-IT, unique information about the distribution of multiple footprints along continuous regions is gleaned. In principle, the population MAP and single-molecule MAP-IT strategies can be used to analyze chromatin structure in a variety of model systems. Here, we describe the application of MAP in living Saccharomyces cerevisiae cells and MAP-IT in the analysis of a mammalian tumor suppressor gene in nuclei. This application of MAP-IT provides the first means to simultaneously determine CpG methylation of mammalian genes and their overlying chromatin structure in the same single DNA molecule.
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Affiliation(s)
- Jessica A. Kilgore
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Scott A. Hoose
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Tanya L. Gustafson
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, TX 77843-4458, USA
| | - Weston Porter
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, TX 77843-4458, USA
| | - Michael P. Kladde
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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28
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Abstract
Effective methods of probing chromatin structure without disrupting DNA-protein interactions and associations are necessary for creating an accurate picture of chromatin and its processes in vivo. Expression of cytidine-5 DNA methyltransferases (C5 DMTases) in Saccharomyces cerevisiae provides a powerful noninvasive method of assaying relative DNA accessibility in chromatin. DNA MTases are occluded from protein-associated DNA based on the strength and span of the DNA-protein interaction. Ectopic regulation of C5 DMTase expression systems allows for minimal disruption of yeast physiology. Methylated sites are detected by bisulfite genomic sequencing, which leads to a positive signal corresponding to modified cytidine residues. High-resolution C5 DMTases with dinucleotide recognition specificity are shown to provide sufficient coverage to map interactions spanning a relatively short distance.
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Affiliation(s)
- Scott A Hoose
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, TX, USA
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29
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Jessen WJ, Hoose SA, Kilgore JA, Kladde MP. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat Struct Mol Biol 2006; 13:256-63. [PMID: 16491089 DOI: 10.1038/nsmb1062] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 12/29/2005] [Indexed: 01/08/2023]
Abstract
Transcriptional activation is often associated with chromatin remodeling. However, little is known about the dynamics of remodeling of nucleosome arrays in vivo. Upon induction of Saccharomyces cerevisiae PHO5, a novel kinetic assay of DNA methyltransferase accessibility showed that nucleosomes adjacent to the histone-free upstream activating sequence (UASp1) are disrupted earlier and at higher frequency in the cell population than are those more distal. Individually cloned molecules, each representing the chromatin state of a full promoter from a single cell, revealed multiple promoter classes with either no remodeling or variable numbers of disrupted nucleosomes. Individual promoters in the remodeled fraction were highly enriched for contiguous blocks of disrupted nucleosomes, the majority of which overlapped the UAS region. These results support a probabilistic model in which chromatin remodeling at PHO5 spreads from sites of transactivator association with DNA and attenuates with distance.
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Affiliation(s)
- Walter J Jessen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
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30
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Jessen WJ, Dhasarathy A, Hoose SA, Carvin CD, Risinger AL, Kladde MP. Mapping chromatin structure in vivo using DNA methyltransferases. Methods 2005; 33:68-80. [PMID: 15039089 DOI: 10.1016/j.ymeth.2003.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2003] [Indexed: 11/24/2022] Open
Abstract
Cytosine-5 DNA methyltransferases (C5 DMTases) are effective reagents for analyzing chromatin and footprinting DNA-bound factors in vivo. Cytosine methylation in accessible regions is assayed positively by the PCR-based technique of bisulfite sequencing. In this article, we outline two complementary uses for the DNA methyltransferase CviPI (M.CviPI, GC specificity) in probing chromatin organization. First, we describe the use of the naturally occurring, free enzyme as a diffusible probe to map changes in nucleosome structure and to footprint factor interactions at cis-regulatory sequences. In a second application, termed targeted gene methylation (TAGM), the DMTase is targeted via in-frame fusion to a DNA-binding factor. The rapid accumulation of DNA methylation enables highly sensitive detection of factor binding. Both strategies can be applied with any C5 DMTase, such as M.SssI, which also possesses a short-recognition specificity (CG). A description of methods for constructing C5 DMTase-expressing strains of Saccharomyces cerevisiae and analyzing chromatin regions is provided. We also include comprehensive protocols for the isolation and bisulfite treatment of genomic DNA as well as the subsequent bisulfite sequencing steps. Data demonstrating the efficacy of both DMTase probing techniques, theoretical considerations, and experimental analyses are presented at GAL1 and PHO5.
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Affiliation(s)
- Walter J Jessen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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31
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Abstract
Chromatin creates transcriptional barriers that are overcome by coactivator activities such as histone acetylation by Gcn5 and ATP-dependent chromatin remodeling by SWI/SNF. Factors defining the differential coactivator requirements in the transactivation of various promoters remain elusive. Induction of the Saccharomyces cerevisiae PHO5 promoter does not require Gcn5 or SWI/SNF under fully inducing conditions of no phosphate. We show that PHO5 activation is highly dependent on both coactivators at intermediate phosphate concentrations, conditions that reduce the nuclear concentration of the Pho4 transactivator and severely diminish its association with PHO5 in the absence of Gcn5 or SWI/SNF. Conversely, physiological increases in Pho4 nuclear concentration and binding at PHO5 suppress the need for both Gcn5 and SWI/SNF, suggesting that coactivator redundancy is established at high Pho4 binding site occupancy. Consistent with this, we demonstrate, using chromatin immunoprecipitation, that Gcn5 and SWI/SNF are directly recruited to PHO5 and other strongly transcribed promoters, including GAL1-10, RPL19B, RPS22B, PYK1, and EFT2, which do not require either coactivator for expression. These results show that activator concentration and binding site occupancy play crucial roles in defining the extent to which transcription requires individual chromatin remodeling enzymes. In addition, Gcn5 and SWI/SNF associate with many more genomic targets than previously appreciated.
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Affiliation(s)
- Archana Dhasarathy
- Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, TX 77843-2128, USA
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32
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Norwood LE, Grade SK, Cryderman DE, Hines KA, Furiasse N, Toro R, Li Y, Dhasarathy A, Kladde MP, Hendrix MJC, Kirschmann DA, Wallrath LL. Conserved properties of HP1Hsα. Gene 2004; 336:37-46. [PMID: 15225874 DOI: 10.1016/j.gene.2004.04.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2003] [Revised: 03/03/2004] [Accepted: 04/05/2004] [Indexed: 10/26/2022]
Abstract
Heterochromatin protein 1 Hsalpha (HP1(Hsalpha)) is one of three human proteins that share sequence similarity with Drosophila HP1. HP1 proteins are enriched at centric heterochromatin and play a role in chromatin packaging and gene regulation. In humans, HP1(Hsalpha) is down-regulated in highly invasive/metastatic breast cancer cells, compared to poorly invasive/non-metastatic breast cancer cells. To gain insight into this differential regulation, we have cloned the HP1(Hsalpha) gene and characterized its genomic region. HP1(Hsalpha) is located on human chromosome 12q13.13, 589 bp upstream of the divergently transcribed hnRNPA1 gene. Analysis of the promoter region revealed that differential regulation of HP1(Hsalpha) between the two types of breast cancer cells is lost upon mutation of an USF/c-myc transcription factor binding site located 172 bp upstream of the predicted HP1(Hsalpha) transcription start site. These findings provide insights into the down-regulation of HP1(Hsalpha) in highly invasive/metastatic breast cancer cells. To examine the functional properties of HP1(Hsalpha), experiments were performed using Drosophila melanogaster as a genetic system. When human HP1(Hsalpha) was expressed in transgenic Drosophila, silencing of reporter genes inserted at centric and telomeric locations was enhanced. Furthermore, expression of HP1(Hsalpha) rescued the lethality of homozygous Su(var)2-5 mutants lacking HP1. Taken together, these results demonstrate the participation of HP1(Hsalpha) in silent chromatin formation and that HP1(Hsalpha) is a functional homologue of Drosophila HP1.
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Affiliation(s)
- Laura E Norwood
- The Department of Biochemistry, The University of Iowa, 3136 MERF, Iowa City, IA 52242, USA
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33
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Abstract
Post-translational modifications of histone amino-terminal tails are a key determinant in gene expression. Histone methylation plays a dual role in gene regulation. Methylation of lysine 9 of histone H3 in higher eukaryotes is associated with transcriptionally inactive heterochromatin, whereas H3 lysine 4 methylation correlates with active chromatin. Methylation of lysine 4 of H3 via Set1, a component of the Saccharomyces cerevisiae COMPASS complex, is regulated by the transcriptional elongation Paf1-Rtf1 and histone ubiquitination Rad6-Bre1 complexes, which are required for the expression of a subset of genes. This suggests that lysine 4 methylation of histone H3 may play an activating role in transcription; however, the mechanism of Set1 function remains unclear. We show here that H3 lysine 4 methylation also negatively regulated gene expression, as strains without Set1 showed enhanced expression of PHO5, wherein chromatin structure plays an important transcriptional regulatory role. Di- and trimethylation of H3 lysine 4 was detected at the PHO5 promoter, and a strain expressing a mutant version of histone H3 with lysine 4 changed to arginine, (which cannot be methylated) exhibited PHO5 derepression. Moreover, PHO5 was derepressed in strains that lacked components of either the Paf1-Rtf1 elongation or Rad6-Bre1 histone ubiquitination complexes. Lastly, PHO84 and GAL1-10 transcription was also increased in set1Delta cells. These results suggest that H3 methylation at lysine 4, in conjunction with transcriptional elongation, may function in a negative feedback pathway for basal transcription of some genes, although being a positive effector at others.
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Affiliation(s)
| | - Michael P. Kladde
- To whom correspondence should be addressed: Dept. of Biochemistry & Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128. Tel.: 979-862-6677; Fax: 979-845-4946;
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34
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Abstract
Cytosine-5 DNA methylation is a critical signal defining heritable epigenetic states of transcription. As aberrant methylation patterns often accompany disease states, the ability to target cytosine methylation to preselected regions could prove valuable in re-establishing proper gene regulation. We employ the strategy of targeted gene methylation in yeast, which has a naturally unmethylated genome, selectively directing de novo DNA methylation via the fusion of C5 DNA methyltransferases to heterologous DNA-binding proteins. The zinc-finger proteins Zif268 and Zip53 can target DNA methylation by M.CviPI or M.SssI 5-52 nt from single zinc-factor binding sites. Modification at specific GC (M.CviPI) or CG (M.SssI) sites is enhanced as much as 20-fold compared with strains expressing either the free enzyme or a fusion protein with the zinc-finger protein moiety unable to bind to DNA. Interestingly, methylation is also selectively targeted as far as 353 nt from the zinc-finger protein binding sites, possibly indicative of looping, nucleosomes or higher-order chromatin structure. These data demonstrate that methylation can be targeted in vivo to a potentially broad range of sequences using specifically engineered zinc-finger proteins. Further more, the selective targeting of methylation by zinc-finger proteins demonstrates that binding of distinct classes of factors can be monitored in living cells.
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Affiliation(s)
- Christopher D Carvin
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
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35
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Carvin CD, Dhasarathy A, Friesenhahn LB, Jessen WJ, Kladde MP. Targeted cytosine methylation for in vivo detection of protein-DNA interactions. Proc Natl Acad Sci U S A 2003; 100:7743-8. [PMID: 12808133 PMCID: PMC164658 DOI: 10.1073/pnas.1332672100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We report a technique, named targeted gene methylation (TAGM), for identifying in vivo protein-binding sites in chromatin. M.CviPI, a cytosine-5 DNA methyltransferase recognizing GC sites, is fused to a DNA-binding factor enabling simultaneous detection of targeted methylation, factor footprints, and chromatin structural changes by bisulfite genomic sequencing. Using TAGM with the yeast transactivator Pho4, methylation enrichments of up to 34- fold occur proximal to native Pho4-binding sites. Additionally, significant selective targeting of methylation is observed several hundred nucleotides away, suggesting the detection of long-range interactions due to higher-order chromatin structure. In contrast, at an extragenic locus lacking Pho4-binding sites, methylation levels are at the detection limit at early times after Pho4 transactivation. Notably, substantial amounts of methylation are targeted by Pho4-M.CviPI under repressive conditions when most of the transactivator is excluded from the nucleus. Thus, TAGM enables rapid detection of DNA-protein interactions even at low occupancies and has potential for identifying factor targets at the genome-wide level. Extension of TAGM from yeast to vertebrates, which use methylation to initiate and propagate repressed chromatin, could also provide a valuable strategy for heritable inactivation of gene expression.
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Affiliation(s)
- Christopher D Carvin
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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36
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Abstract
Approximately 800 transcripts in Saccharomyces cerevisiae are cell cycle regulated. The oscillation of approximately 40% of these genes, including a prominent subclass involved in nutrient acquisition, is not understood. To address this problem, we focus on the mitosis-specific activation of the phosphate-responsive promoter, PHO5. We show that the unexpected mitotic induction of the PHO5 acid phosphatase in rich medium requires the transcriptional activators Pho4 and Pho2, the cyclin-dependent kinase inhibitor Pho81, and the chromatin-associated enzymes Gcn5 and Snf2/Swi2. PHO5 mitotic activation is repressed by addition of orthophosphate, which significantly increases cellular polyphosphate. Polyphosphate levels also fluctuate inversely with PHO5 mRNA during the cell cycle, further substantiating an antagonistic link between this phosphate polymer and PHO5 mitotic regulation. Moreover, deletion of PHM3, required for polyphosphate accumulation, leads to premature onset of PHO5 expression, as well as an increased rate, magnitude, and duration of PHO5 activation. Orthophosphate addition, however, represses mitotic PHO5 expression in a phm3delta strain. Thus, polyphosphate per se is not necessary to repress PHO transcription but, when present, replenishes cellular phosphate during nutrient depletion. These results demonstrate a dynamic mechanism of mitotic transcriptional regulation that operates mostly independently of factors that drive progression through the cell cycle.
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Affiliation(s)
- Daniel W Neef
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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37
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Abstract
In yeast, a number of regulatory proteins expressed only in specific cell types interact with general transcription factors in a combinatorial manner to control expression of cell-type-specific genes. We report a detailed analysis of activation and repression events that occur at the promoter of the a-cell-specific STE6 gene fused to a beta-galactosidase gene in a yeast minichromosome, as well as factors that control the chromatin structure of this promoter both in the minichromosome and in the genomic STE6 locus. Mcm1p results in chromatin remodeling and is responsible for all transcriptional activity from the STE6 promoter in both wild-type a and alpha cells. Matalpha2p cooperates with Tup1p to block both chromatin remodeling and Mcm1p-associated activation. While Matalpha2p represses only Mcm1p, the Tup1p-mediated repression involves both Mcm1p-dependent and -independent mechanisms. Swi/Snf and Gcn5p, required for full induction of the STE6 gene, do not contribute to chromatin remodeling. We suggest that Tup1p can contribute to repression by blocking transcriptional activators, in addition to interacting with transcription machinery and stabilizing chromatin.
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Affiliation(s)
- I M Gavin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 308 Althouse Laboratory, University Park, PA 16802, USA
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38
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Kladde MP, Xu M, Simpson RT. DNA methyltransferases as probes for chromatin structure in yeast. Methods Mol Biol 2000; 119:395-416. [PMID: 10804528 DOI: 10.1385/1-59259-681-9:395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- M P Kladde
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, USA
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39
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Vyhlidal C, Samudio I, Kladde MP, Safe S. Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site. J Mol Endocrinol 2000; 24:329-38. [PMID: 10828826 DOI: 10.1677/jme.0.0240329] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
17beta-Estradiol (E2) induces transforming growth factor alpha (TGFalpha) gene expression in MCF-7 cells and previous studies have identified a 53 bp (-252 to -200) sequence containing two imperfect estrogen responsive elements (EREs) that contribute to E2 responsiveness. Deletion analysis of the TGFalpha gene promoter in this study identified a second upstream region of the promoter (-623 to -549) that is also E2 responsive. This sequence contains three GC-rich sites and an imperfect ERE half-site, and the specific cis-elements and trans-acting factors were determined by promoter analysis in transient transfection experiments, gel mobility shift assays and in vitro DNA footprinting. The results are consistent with an estrogen receptor alpha (ERalpha)/Sp1 complex interacting with an Sp1(N)(30) ERE half-site ((1/2)) motif in which both ERalpha and Sp1 bind promoter DNA. The ER/Sp1-DNA complex is formed using nuclear extracts from MCF-7 cells but not with recombinant human ERalpha or Sp1 proteins, suggesting that other nuclear factor(s) are required for complex stabilization. The E2-responsive Sp1(N)(x)ERE(1/2) motif identified in the TGFalpha gene promoter has also been characterized in the cathepsin D and heat shock protein 27 gene promoters; however, in the latter two promoters the numbers of intervening nucleotides are 23 and 10 respectively.
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Affiliation(s)
- C Vyhlidal
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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40
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Dong L, Wang W, Wang F, Stoner M, Reed JC, Harigai M, Samudio I, Kladde MP, Vyhlidal C, Safe S. Mechanisms of transcriptional activation of bcl-2 gene expression by 17beta-estradiol in breast cancer cells. J Biol Chem 1999; 274:32099-107. [PMID: 10542244 DOI: 10.1074/jbc.274.45.32099] [Citation(s) in RCA: 199] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
bcl-2 gene expression is induced by 17beta-estradiol (E2) in T47D and MCF-7 human breast cancer cells, and the mechanism of E2 responsiveness was further investigated by analysis of the bcl-2 gene promoter. The -1602 to -1534 distal region (bcl-2j) of the promoter was E2-responsive; however, in gel mobility shift assays, the estrogen receptor alpha (ER(alpha)) did not bind [(32)P]bcl-2j, whereas Sp1 protein formed a retarded band complex. Further analysis demonstrated that the upstream region (-1603 to -1579) of the bcl-2 gene promoter contained two GC/GA-rich sites at -1601 (5'-GGGCTGG-3') and -1588 (3'-GGAGGG-5') that bound Sp1 protein. Subsequent studies confirmed that transactivation by E2 was dependent on ER(alpha)/Sp1 interactions with both GC-rich sites, and this was confirmed by in vitro footprinting. In contrast, a 21-base pair E2-responsive downstream region (-1578 to -1534) did not bind Sp1 or ER(alpha) protein; however, analysis of a complex binding pattern with nuclear extracts showed that ATF-1 and CREB-1 bound to this motif. These data coupled with results of transient transfection studies demonstrated that transcriptional activation by E2 of the -1578 to -1534 region of the bcl-2 gene promoter was dependent on induction of cAMP and subsequent activation through a cAMP response element. Thus, hormone regulation of bcl-2 gene expression in breast cancer cells involves multiple enhancer elements and E2-mediated transactivation does not require direct binding of the estrogen receptor with promoter DNA.
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Affiliation(s)
- L Dong
- Department of Veterinary Physiology, Texas A&M University, College Station, Texas 77843, USA
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41
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Affiliation(s)
- M P Kladde
- Department of Biochemistry and Molecular Biology, Pennsylvania State University 16802-4500, USA
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42
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Du J, Nasir I, Benton BK, Kladde MP, Laurent BC. Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins. Genetics 1998; 150:987-1005. [PMID: 9799253 PMCID: PMC1460405 DOI: 10.1093/genetics/150.3.987] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The essential Sth1p is the protein most closely related to the conserved Snf2p/Swi2p in Saccharomyces cerevisiae. Sth1p purified from yeast has a DNA-stimulated ATPase activity required for its function in vivo. The finding that Sth1p is a component of a multiprotein complex capable of ATP-dependent remodeling of the structure of chromatin (RSC) in vitro, suggests that it provides RSC with ATP hydrolysis activity. Three sth1 temperature-sensitive mutations map to the highly conserved ATPase/helicase domain and have cell cycle and non-cell cycle phenotypes, suggesting multiple essential roles for Sth1p. The Sth1p bromodomain is required for wild-type function; deletion mutants lacking portions of this region are thermosensitive and arrest with highly elongated buds and 2C DNA content, indicating perturbation of a unique function. The pleiotropic growth defects of sth1-ts mutants imply a requirement for Sth1p in a general cellular process that affects several metabolic pathways. Significantly, an sth1-ts allele is synthetically sick or lethal with previously identified mutations in histones and chromatin assembly genes that suppress snf/swi, suggesting that RSC interacts differently with chromatin than Snf/Swi. These results provide a framework for understanding the ATP-dependent RSC function in modeling chromatin and its connection to the cell cycle.
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Affiliation(s)
- J Du
- Department of Microbiology and Immunology and Morse Institute for Molecular Genetics, State University of New York, Brooklyn, New York 11203, USA
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43
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Xu M, Kladde MP, Van Etten JL, Simpson RT. Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC. Nucleic Acids Res 1998; 26:3961-6. [PMID: 9705505 PMCID: PMC147793 DOI: 10.1093/nar/26.17.3961] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A novel gene encoding a cytosine-5-DNA methyltransferase recognizing the dinucleotide GpC was cloned from Chlorella virus NYs-1 and expressed in both Escherichia coli and Saccharomyces cerevisiae . The gene was sequenced and a predicted polypeptide of 362 amino acids with a molecular weight of 41.903 kDa was identified. The protein contains several amino acid motifs with high similarity to those of other known 5-methylcytosine-forming methyltransferases. In addition, this enzyme, named M. Cvi PI, shares 66% identity and 76% similarity with M. Cvi JI, the only other cytosine-5-DNA methyltransferase cloned from a Chlorella virus. The short, frequently occurring recognition sequence of the new methyltransferase will be very useful for in vivo chromatin structure studies in both yeast and higher organisms.
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Affiliation(s)
- M Xu
- Department of Biochemistry and Molecular Biology and the Center for Gene Regulation, 308 Althouse Laboratory,The Pennsylvania State University, University Park, PA 16802-4500, USA
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44
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Xu M, Simpson RT, Kladde MP. Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication. Mol Cell Biol 1998; 18:1201-12. [PMID: 9488435 PMCID: PMC108833 DOI: 10.1128/mcb.18.3.1201] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biochemical studies have demonstrated decreased binding of various proteins to DNA in nucleosome cores as their cognate sites are moved from the edge of the nucleosome to the pseudodyad (center). However, to date no study has addressed whether this structural characteristic of nucleosomes modulates the function of a transcription factor in living cells, where processes of DNA replication and chromatin modification or remodeling could significantly affect factor binding. Using a sensitive, high-resolution methyltransferase assay, we have monitored the ability of Gal4p in vivo to interact with a nucleosome at positions that are known to be inaccessible in nucleosome cores in vitro. Gal4p efficiently bound a single cognate site (UASG) centered at 41 bp from the edge of a positioned nucleosome, perturbing chromatin structure and inducing transcription. DNA binding and chromatin perturbation accompanying this interaction also occurred in the presence of hydroxyurea, indicating that DNA replication is not necessary for Gal4p-mediated nucleosome disruption. These data extend previous studies, which demonstrated DNA replication-independent chromatin remodeling, by showing that a single dimer of Gal4p, without the benefit of cooperative interactions that occur at complex wild-type promoters, is competent for invasion of a preestablished nucleosome. When the UASG was localized at the nucleosomal pseudodyad, relative occupancy by Gal4p, nucleosome disruption, and transcriptional activation were substantially compromised. Therefore, despite the increased nucleosome binding capability of Gal4p in cells, the precise translational position of a factor binding site in one nucleosome in an array can affect the ability of a transcriptional regulator to overcome the repressive influence of chromatin.
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Affiliation(s)
- M Xu
- Department of Biochemistry and Molecular Biology and Center for Gene Regulation, The Pennsylvania State University, University Park 16802-4500, USA
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45
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Abstract
We have previously employed the cytosine-5-DNA methyltransferase (MTase), M. Sss I, as a probe for chromatin architecture in intact cells. Although M. Sss I offers the highest resolution of any currently available MTase, the difficulty in establishing stable, methylation-positive strains poses a barrier to its general utility as a chromatin probe. We describe a simple screen for M. Sss I-expressing strains that eliminates the purification of PCR products amplified from bisulfite-treated DNA, use of radioisotopes, polyacrylamide sequencing gel electrophoresis, and autoradiography. The high throughput of the method now makes it feasible to introduce M. Sss I into a variety of wild-type and mutant genetic backgrounds.
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Affiliation(s)
- M P Kladde
- Department of Biochemistry and Molecular Biology and Center for Gene Regulation, The Pennsylvania State University, 308 Althouse Laboratory, University Park, PA 16802-4500, USA.
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46
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Abstract
Previous studies have identified single amino acid changes within either histone H3 or H4 (Sin- versions) that allow transcription in the absence of the yeast SWI-SNF complex. The histone H4 mutants are competent for nucleosome assembly in vivo, and the residues that are altered appear to define a discrete domain on the surface of the histone octamer. We have analyzed the effects of the Sin- versions of histone H4 on transcription and chromatin structure in vivo. These histone H4 mutants cause an increased accessibility of nucleosomal DNA to Dam methyltransferase and to micrococcal nuclease. Sin- derivatives of histone H4 also grossly impair the ability of nucleosomes to constrain supercoils in vivo. Nucleosome-mediated repression of the PHO5 gene is severely impaired by these histone H4 mutants; PHO5 expression is derepressed to 31% of the wild-type induced level. In contrast to the induction caused by nucleosome depletion, full PHO5 derepression by Sin- versions of histone H4 requires upstream regulatory elements. In addition, Sin- derivatives of histone H4 do not activate expression from CYC1 or GAL1 promoters that lack UAS elements. We propose that these Sin- mutations alter histone-DNA contact residues that play key roles in restricting the accessibility of nucleosomal DNA to transcription factors.
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Affiliation(s)
- M A Wechser
- Program in Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical Center, Worcester 01605, USA
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47
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Kladde MP, Xu M, Simpson RT. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J 1996; 15:6290-300. [PMID: 8947052 PMCID: PMC452452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Current methods for analysis of chromatin architecture are invasive, utilizing chemicals or nucleases that damage DNA, making detection of labile constituents and conclusions about true in vivo structure problematic. We describe a sensitive assay of chromatin structure which is performed in intact, living yeast. The approach utilizes expression of SssI DNA methyltransferase (MTase) in Saccharomyces cerevisiae to provide an order-of-magnitude increase in resolution over previously introduced MTases. Combining this resolution increase with the novel application of a PCR-based, positive chemical display of modified cytosines provides a significant advance in the direct study of DNA-protein interactions in growing cells that enables quantitative footprinting. The validity and efficacy of the strategy are demonstrated in mini-chromosomes, where positioned nucleosomes and a labile, operator-bound repressor are detected. Also, using a heterologous system to study gene activation, we show that in vivo hormone occupancy of the estrogen receptor is required for maximal site-specific DNA binding, whereas, at very high receptor-expression levels, hormone-independent partial occupancy of an estrogen-responsive element was observed. Receptor binding to a palindromic estrogen-responsive element leads to a footprint with strand-specific asymmetry, which is explicable by known structural information.
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Affiliation(s)
- M P Kladde
- Department of Biochemistry and Molecular Biology and The Center for Gene Regulation, The Pennsylvania State University, University Park 16802, USA
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48
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Affiliation(s)
- M P Kladde
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA
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49
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Abstract
Chemical probing of two predominantly alternating purine-pyrimidine d(CA/TG)n repeats led us to propose previously that in supercoiled plasmids these elements adopt a non-B-DNA structure distinct from that of Z-DNA formed by d(CG)n sequences. Here, we present further evidence supporting this contention. Reactivity with the conformation-sensitive reagent chloroacetaldehyde, which reacts with unpaired adenines and cytosines, was confined strictly to adenines in the d(CA/TG)n repeat. In contrast, only bases outside the d(CG)n repeat exhibited chloroacetaldehyde reactivity. Two-dimensional gel analysis of topoisomers containing d(CA/TG)n tracts with bases out of strict purine-pyrimidine alteration revealed multiple superhelical-dependent transitions to an alternative left-handed structure. Within individual plasmid molecules, these multiple transitions resulted from the stepwise conversion of contiguous segments of alternating purine-pyrimidine sequence, which are delimited by bases out of alternation, to the full-length alternative conformation. When the left-handed helices increased in length to include more bases out of alternation, the average helical pitch changed substantially to produce a less tightly wound left-handed helix. Overall, these data indicate that d(CA/TG)n tracts adopt a left-handed conformation significantly different from that of the canonical Z-DNA structure of d(CG)n sequences.
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Affiliation(s)
- M P Kladde
- Department of Biochemistry, University of Wisconsin, Madison 53706
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50
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Abstract
Escherichia coli Dam DNA methyltransferase can methylate genomic GATC sites when expressed in Saccharomyces cerevisiae. Others have observed changes in the level of methylation at specific sites and suggested that these changes are related to transcriptional state or chromosomal context. To test directly the influence of nucleosome location on the ability of Dam methyltransferase to modify GATC sites in chromatin, we analyzed minichromosomes containing precisely positioned nucleosomes in dam-expressing yeast strains. Levels of methylation at individual GATC sites were rigorously quantified by an oligonucleotide-probing procedure. Within the linker and adjacent 21 bp of nucleosome-associated DNA, GATC sites were highly methylated, whereas methylation was severely inhibited by histone-DNA contacts nearer to the nucleosomal pseudodyad. Other DNA-protein complexes also interfere with Dam methylation. These data are consistent with a model in which nucleosomes exert a repressive influence on the biological functions of DNA by restricting access of trans-acting factors to DNA.
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Affiliation(s)
- M P Kladde
- Laboratory of Cellular and Developmental Biology, National Institutes of Health, Bethesda, MD 20892
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