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Bhawsinghka N, Burkholder A, Schaaper RM. Detection of DNA replication errors and 8-oxo-dGTP-mediated mutations in E. coli by Duplex DNA Sequencing. DNA Repair (Amst) 2023; 123:103462. [PMID: 36738688 PMCID: PMC9992157 DOI: 10.1016/j.dnarep.2023.103462] [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: 10/27/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Mutation is a phenomenon inescapable for all life-forms, including bacteria. While bacterial mutation rates are generally low due to the operation of error-avoidance systems, sometimes they are elevated by many orders of magnitude. Such a state, known as a hypermutable state, can result from exposure to stress or to harmful environments. Studies of bacterial mutation frequencies and analysis of the precise types of mutations can provide insights into the mechanisms by which mutations occur and the possible involvement of error-avoidance pathways. Several approaches have been used for this, like reporter assays involving non-essential genes or mutation accumulation over multiple generations. However, these approaches give an indirect estimation, and a more direct approach for determining mutations is desirable. With the recent development of a DNA sequencing technique known as Duplex Sequencing, it is possible to detect rare variants in a population at a frequency of 1 in 107 base pairs or less. Here, we have applied Duplex Sequencing to study spontaneous mutations in E. coli. We also investigated the production of replication errors by using a mismatch-repair defective (mutL) strain as well as oxidative-stress associated mutations using a mutT-defective strain. For DNA from a wild-type strain we obtained mutant frequencies in the range of 10-7 to 10-8 depending on the specific base-pair substitution, but we argue that these mutants merely represent a background of the system, rather than mutations that occurred in vivo. In contrast, bona-fide in vivo mutations were identified for DNA from both the mutL and mutT strains, as indicated by specific increases in base substitutions that are fully consistent with their established in vivo roles. Notably, the data reproduce the specific context effects of in vivo mutations as well as the leading vs. lagging strand bias among DNA replication errors.
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Affiliation(s)
- Niketa Bhawsinghka
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
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2
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Lee M, Joehanes R, McCartney DL, Kho M, Hüls A, Wyss AB, Liu C, Walker RM, R Kardia SL, Wingo TS, Burkholder A, Ma J, Campbell A, Wingo AP, Huan T, Sikdar S, Keshawarz A, Bennett DA, Smith JA, Evans KL, Levy D, London SJ. Opioid medication use and blood DNA methylation: epigenome-wide association meta-analysis. Epigenomics 2022; 14:1479-1492. [PMID: 36700736 PMCID: PMC9979153 DOI: 10.2217/epi-2022-0353] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
Aim: To identify differential methylation related to prescribed opioid use. Methods: This study examined whether blood DNA methylation, measured using Illumina arrays, differs by recent opioid medication use in four population-based cohorts. We meta-analyzed results (282 users; 10,560 nonusers) using inverse-variance weighting. Results: Differential methylation (false discovery rate <0.05) was observed at six CpGs annotated to the following genes: KIAA0226, CPLX2, TDRP, RNF38, TTC23 and GPR179. Integrative epigenomic analyses linked implicated loci to regulatory elements in blood and/or brain. Additionally, 74 CpGs were differentially methylated in males or females. Methylation at significant CpGs correlated with gene expression in blood and/or brain. Conclusion: This study identified DNA methylation related to opioid medication use in general populations. The results could inform the development of blood methylation biomarkers of opioid use.
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Affiliation(s)
- Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Roby Joehanes
- Department of Health and Human Services, Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA 01702, USA
| | - Daniel L McCartney
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anke Hüls
- Department of Epidemiology & Gangarosa, Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02215, USA
- Framingham Heart Study, Boston University, Framingham, MA 01702, USA
| | - Rosie M Walker
- Centre for Clinical Brain Science, Chancellor's Building, 49 Little France Crescent, Edinburgh Bioquarter, Edinburgh, UK
- School of Psychology, University of Exeter, Exeter, UK
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas S Wingo
- Department of Neurology & Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jiantao Ma
- Department of Health and Human Services, Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA 01702, USA
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Aliza P Wingo
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA 30322, USA
| | - Tianxiao Huan
- Department of Health and Human Services, Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA 01702, USA
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sinjini Sikdar
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Department of Mathematics & Statistics, Old Dominion University, Norfolk, VA 23529, USA
| | - Amena Keshawarz
- Framingham Heart Study, Framingham, MA 01702, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathryn L Evans
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Daniel Levy
- Department of Health and Human Services, Framingham Heart Study, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA 01702, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Akhtari FS, Lloyd D, Burkholder A, Tong X, House JS, Lee EY, Buse J, Schurman SH, Fargo DC, Schmitt CP, Hall J, Motsinger-Reif AA. Questionnaire-Based Polyexposure Assessment Outperforms Polygenic Scores for Classification of Type 2 Diabetes in a Multiancestry Cohort. Diabetes Care 2022; 46:929-937. [PMID: 36383734 PMCID: PMC10154656 DOI: 10.2337/dc22-0295] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Environmental exposures may have greater predictive power for type 2 diabetes than polygenic scores (PGS). Studies examining environmental risk factors, however, have included only individuals with European ancestry, limiting the applicability of results. We conducted an exposome-wide association study in the multiancestry Personalized Environment and Genes Study to assess the effects of environmental factors on type 2 diabetes. RESEARCH DESIGN AND METHODS Using logistic regression for single-exposure analysis, we identified exposures associated with type 2 diabetes, adjusting for age, BMI, household income, and self-reported sex and race. To compare cumulative genetic and environmental effects, we computed an overall clinical score (OCS) as a weighted sum of BMI and prediabetes, hypertension, and high cholesterol status and a polyexposure score (PXS) as a weighted sum of 13 environmental variables. Using UK Biobank data, we developed a multiancestry PGS and calculated it for participants. RESULTS We found 76 significant associations with type 2 diabetes, including novel associations of asbestos and coal dust exposure. OCS, PXS, and PGS were significantly associated with type 2 diabetes. PXS had moderate power to determine associations, with larger effect size and greater power and reclassification improvement than PGS. For all scores, the results differed by race. CONCLUSIONS Our findings in a multiancestry cohort elucidate how type 2 diabetes odds can be attributed to clinical, genetic, and environmental factors and emphasize the need for exposome data in disease-risk association studies. Race-based differences in predictive scores highlight the need for genetic and exposome-wide studies in diverse populations.
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Affiliation(s)
- Farida S Akhtari
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC.,Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Dillon Lloyd
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Adam Burkholder
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC
| | - Xiaoran Tong
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - John S House
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Eunice Y Lee
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - John Buse
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - David C Fargo
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC
| | - Charles P Schmitt
- Office of Data Science, National Institute of Environmental Health Science, Durham, NC
| | - Janet Hall
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Alison A Motsinger-Reif
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
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Bushel PR, Ward J, Burkholder A, Li J, Anchang B. Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology. Sci Rep 2022; 12:1393. [PMID: 35082309 PMCID: PMC8791930 DOI: 10.1038/s41598-022-05148-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Received: 06/15/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
The interplay between genes harboring single nucleotide polymorphisms (SNPs) is vital to better understand underlying contributions to the etiology of breast cancer. Much attention has been paid to epistasis between nuclear genes or mutations in the mitochondrial genome. However, there is limited understanding about the epistatic effects of genetic variants in the nuclear and mitochondrial genomes jointly on breast cancer. We tested the interaction of germline SNPs in the mitochondrial (mtSNPs) and nuclear (nuSNPs) genomes of female breast cancer patients in The Cancer Genome Atlas (TCGA) for association with morphological features extracted from hematoxylin and eosin (H&E)-stained pathology images. We identified 115 significant (q-value < 0.05) mito-nuclear interactions that increased nuclei size by as much as 12%. One interaction between nuSNP rs17320521 in an intron of the WSC Domain Containing 2 (WSCD2) gene and mtSNP rs869096886, a synonymous variant mapped to the mitochondrially-encoded NADH dehydrogenase 4 (MT-ND4) gene, was confirmed in an independent breast cancer data set from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). None of the 10 mito-nuclear interactions identified from non-diseased female breast tissues from the Genotype-Expression (GTEx) project resulted in an increase in nuclei size. Comparisons of gene expression data from the TCGA breast cancer patients with the genotype homozygous for the minor alleles of the SNPs in WSCD2 and MT-ND4 versus the other genotypes revealed core transcriptional regulator interactions and an association with insulin. Finally, a Cox proportional hazards ratio = 1.7 (C.I. 0.98–2.9, p-value = 0.042) and Kaplan–Meier plot suggest that the TCGA female breast cancer patients with low gene expression of WSCD2 coupled with large nuclei have an increased risk of mortality. The intergenomic dependency between the two variants may constitute an inherent susceptibility of a more severe form of breast cancer and points to genetic targets for further investigation of additional determinants of the disease.
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Affiliation(s)
- Pierre R Bushel
- Massive Genome Informatics Group, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC, 27709, USA. .,Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
| | - James Ward
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.,Kelly Government Solutions, Research Triangle Park, NC, 27709, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Jianying Li
- Massive Genome Informatics Group, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC, 27709, USA.,Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.,Kelly Government Solutions, Research Triangle Park, NC, 27709, USA
| | - Benedict Anchang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
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5
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Kiktev DA, Dominska M, Zhang T, Dahl J, Stepchenkova EI, Mieczkowski P, Burgers PM, Lujan S, Burkholder A, Kunkel TA, Petes TD. The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ. Nucleic Acids Res 2021; 49:5623-5636. [PMID: 34019669 PMCID: PMC8191807 DOI: 10.1093/nar/gkab371] [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: 03/09/2021] [Revised: 04/22/2021] [Accepted: 05/16/2021] [Indexed: 11/12/2022] Open
Abstract
Iron-sulfur clusters (4Fe–4S) exist in many enzymes concerned with DNA replication and repair. The contribution of these clusters to enzymatic activity is not fully understood. We identified the MET18 (MMS19) gene of Saccharomyces cerevisiae as a strong mutator on GC-rich genes. Met18p is required for the efficient insertion of iron-sulfur clusters into various proteins. met18 mutants have an elevated rate of deletions between short flanking repeats, consistent with increased DNA polymerase slippage. This phenotype is very similar to that observed in mutants of POL3 (encoding the catalytic subunit of Pol δ) that weaken binding of the iron-sulfur cluster. Comparable mutants of POL2 (Pol ϵ) do not elevate deletions. Further support for the conclusion that met18 strains result in impaired DNA synthesis by Pol δ are the observations that Pol δ isolated from met18 strains has less bound iron and is less processive in vitro than the wild-type holoenzyme.
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Affiliation(s)
- Denis A Kiktev
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tony Zhang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joseph Dahl
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Elena I Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, St. Petersburg, Russia.,Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russia
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
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6
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Lujan SA, Longley MJ, Humble MH, Lavender CA, Burkholder A, Blakely EL, Alston CL, Gorman GS, Turnbull DM, McFarland R, Taylor RW, Kunkel TA, Copeland WC. Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging. Genome Biol 2020; 21:248. [PMID: 32943091 PMCID: PMC7500033 DOI: 10.1186/s13059-020-02138-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Acquired human mitochondrial genome (mtDNA) deletions are symptoms and drivers of focal mitochondrial respiratory deficiency, a pathological hallmark of aging and late-onset mitochondrial disease. RESULTS To decipher connections between these processes, we create LostArc, an ultrasensitive method for quantifying deletions in circular mtDNA molecules. LostArc reveals 35 million deletions (~ 470,000 unique spans) in skeletal muscle from 22 individuals with and 19 individuals without pathogenic variants in POLG. This nuclear gene encodes the catalytic subunit of replicative mitochondrial DNA polymerase γ. Ablation, the deleted mtDNA fraction, suffices to explain skeletal muscle phenotypes of aging and POLG-derived disease. Unsupervised bioinformatic analyses reveal distinct age- and disease-correlated deletion patterns. CONCLUSIONS These patterns implicate replication by DNA polymerase γ as the deletion driver and suggest little purifying selection against mtDNA deletions by mitophagy in postmitotic muscle fibers. Observed deletion patterns are best modeled as mtDNA deletions initiated by replication fork stalling during strand displacement mtDNA synthesis.
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Affiliation(s)
- Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Margaret H Humble
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Grainne S Gorman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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7
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Burkholder A, Akrobetu D, Pandiri AR, Ton K, Kim S, Labow BI, Nuzzi LC, Firriolo JM, Schneider SS, Fenton SE, Shaw ND. Investigation of the adolescent female breast transcriptome and the impact of obesity. Breast Cancer Res 2020; 22:44. [PMID: 32393308 PMCID: PMC7216667 DOI: 10.1186/s13058-020-01279-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/15/2020] [Indexed: 01/07/2023] Open
Abstract
Background Early life environmental exposures affect breast development and breast cancer risk in adulthood. The breast is particularly vulnerable during puberty when mammary epithelial cells proliferate exponentially. In overweight/obese (OB) women, inflammation increases breast aromatase expression and estrogen synthesis and promotes estrogen-receptor (ER)-positive breast cancer. In contrast, recent epidemiological studies suggest that obesity during childhood decreases future breast cancer risk. Studies on environmental exposures and breast cancer risk have thus far been limited to animal models. Here, we present the first interrogation of the human adolescent breast at the molecular level and investigate how obesity affects the immature breast. Methods We performed RNA-seq in 62 breast tissue samples from adolescent girls/young women (ADOL; mean age 17.8 years) who underwent reduction mammoplasty. Thirty-one subjects were non-overweight/obese (NOB; mean BMI 23.4 kg/m2) and 31 were overweight/obese (OB; BMI 32.1 kg/m2). We also compared our data to published mammary transcriptome datasets from women (mean age 39 years) and young adult mice, rats, and macaques. Results The ADOL breast transcriptome showed limited (30%) overlap with other species, but 88% overlap with adult women for the 500 most highly expressed genes in each dataset; only 43 genes were shared by all groups. In ADOL, there were 120 differentially expressed genes (DEG) in OB compared with NOB samples (padj < 0.05). Based on these DEG, Ingenuity Pathway Analysis (IPA) identified the cytokines CSF1 and IL-10 and the chemokine receptor CCR2 as among the most highly activated upstream regulators, suggesting increased inflammation in the OB breast. Classical ER targets (e.g., PR, AREG) were not differentially expressed, yet IPA identified the ER and PR and growth factors/receptors (VEGF, HGF, HER3) and kinases (AKT1) involved in hormone-independent ER activation as activated upstream regulators in OB breast tissue. Conclusions These studies represent the first investigation of the human breast transcriptome during late puberty/young adulthood and demonstrate that obesity is associated with a transcriptional signature of inflammation which may augment estrogen action in the immature breast microenvironment. We anticipate that these studies will prompt more comprehensive cellular and molecular investigations of obesity and its effect on the breast during this critical developmental window.
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Affiliation(s)
- Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA
| | - Dennis Akrobetu
- Clinical Research Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, MD A2-03, Research Triangle Park, NC, 27709, USA
| | - Arun R Pandiri
- Cellular and Molecular Pathology Branch, Division of National Toxicology Program (DNTP), NIEHS, Research Triangle Park, NC, USA
| | - Kiki Ton
- Cellular and Molecular Pathology Branch, Division of National Toxicology Program (DNTP), NIEHS, Research Triangle Park, NC, USA
| | - Sue Kim
- Clinical Research Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, MD A2-03, Research Triangle Park, NC, 27709, USA
| | - Brian I Labow
- Adolescent Breast Clinic, the Department of Plastic and Oral Surgery, Division of Adolescent/Young Adult Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura C Nuzzi
- Adolescent Breast Clinic, the Department of Plastic and Oral Surgery, Division of Adolescent/Young Adult Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph M Firriolo
- Adolescent Breast Clinic, the Department of Plastic and Oral Surgery, Division of Adolescent/Young Adult Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sallie S Schneider
- Biospecimen Resource and Molecular Analysis Facility, Baystate Medical Center, Springfield, MA, USA
| | - Suzanne E Fenton
- National Toxicology Program Laboratory, DNTP, NIEHS, Research Triangle Park, NC, USA
| | - Natalie D Shaw
- Clinical Research Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, MD A2-03, Research Triangle Park, NC, 27709, USA.
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8
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Delaney A, Plummer L, Burkholder A, Mericq M, Merino P, Quinton R, Lewis K, Meader B, Meader B, Shaw N, Welt C, Martin K, Seminara S, Biesecker L, Bailey-Wilson J, Hall J. OR11-6 Rare Sequence Variants in GnRH-Associated Genes May Contribute to Variable Susceptibility to Environmental Stressors in Functional Hypothalamic Amenorrhea. J Endocr Soc 2019. [PMCID: PMC6554862 DOI: 10.1210/js.2019-or11-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Some, but not all, women develop hypothalamic amenorrhea (HA) in association with exercise and/or food restriction. We hypothesized that variants in genes associated with the more severe hypogonadotropic disorder, idiopathic hypogonadotropic hypogonadism (IHH), may contribute to a given woman’s susceptibility to HA when she is faced with a physiologic stressor. Indeed, rare sequence variants (RSVs) in IHH-associated genes were previously identified in women with HA that were absent in controls1. This study, however, used a variant-level, as opposed to the now preferred gene-level, approach and only examined 7 genes. To build upon these earlier findings and provide more definitive support for our hypothesis, we screened 106 women with HA and 477 controls for RSVs in a much larger IHH-gene panel (n=54 genes) using exome sequencing. Healthy controls were a convenience sample drawn from the ClinSeq Project2 who had originally been selected for a range of atherosclerosis risk phenotypes, but were unselected for reproductive phenotypes. We compared the frequency of RSVs (moderate- to high-impact, minor allele frequency [MAF] < 1%) across all 54 genes in HA compared with controls using a rare variant burden test (Fisher’s exact test. We identified 54 heterozygous RSVs (51 missense, 1 nonsense, 2 frameshift; 27.4% of alleles) in 46 HA women (1-3 RSVs/woman, 58 total RSVs, 12 subjects with >1 RSV) and 149 heterozygous RSVs (141 missense, 1 nonsense, 4 frameshift, 3 inframe indels; 18.8%) in 146 control women (1-4 RSVs/woman, 179 total RSVs, 28 subjects with >1 RSV) which represents a significantly increased burden of RSVs in HA (P = 0.006). A slightly greater proportion of RSVs in the HA group were considered damaging/deleterious by both Polyphen2 and SIFT vs controls (41.1% vs 36.0%), but this was not statistically significant. Thus, women with HA are significantly enriched for RSVs in genes that cause IHH as compared with controls. These results indicate that the risk of developing HA with exposure to physiologic stressors may indeed be increased in the presence of heterozygous protein-altering variants in genes related to the regulation of GnRH neuronal development and function. 1 Caronia LM, et al. N Engl J Med. 2011;364:215-25. 2 Biesecker LG, et al. Genome Res. 2009;19:1665-74. Unless otherwise noted, all abstracts presented at ENDO are embargoed until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. Abstracts presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.
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Affiliation(s)
- Angela Delaney
- National Institutes of Health, Bethesda, MD, United States
| | - Lacey Plummer
- Massachusetts General Hospital, Boston, MA, United States
| | - Adam Burkholder
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Maria Mericq
- Institutite of Maternal and Child Research University of Chili, Santiago, , Chile
| | - Paulina Merino
- Institute of Maternal and Child Research, University of Chile, Santiago, , Chile
| | - Richard Quinton
- Endocrinology, Newcastle-upon-Tyne Hospitals, Newcastle Upon Tyne, , United Kingdom
| | - Katie Lewis
- National Institutes of Health, Bethesda, MD, United States
| | - Brooke Meader
- National Institutes of Health, Bethesda, MD, United States
| | - Brooke Meader
- National Institutes of Health, Bethesda, MD, United States
| | | | - Corrine Welt
- Endocrinology, Metabolism and Diabetes, The University of Utah, Salt Lake City, UT, United States
| | - Kathryn Martin
- Massachusetts General Hospital, Boston, MA, United States
| | | | | | | | - Janet Hall
- NIH-NIEHS, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
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Aden K, Bartsch K, Dahl J, Reijns MA, Esser D, Sheibani-Tezerji R, Sinha A, Wottawa F, Ito G, Mishra N, Knittler K, Burkholder A, Welz L, van Es J, Tran F, Lipinski S, Kakavand N, Boeger C, Lucius R, von Schoenfels W, Schafmayer C, Lenk L, Chalaris A, Clevers H, Röcken C, Kaleta C, Rose-John S, Schreiber S, Kunkel T, Rabe B, Rosenstiel P. Epithelial RNase H2 Maintains Genome Integrity and Prevents Intestinal Tumorigenesis in Mice. Gastroenterology 2019; 156:145-159.e19. [PMID: 30273559 PMCID: PMC6311085 DOI: 10.1053/j.gastro.2018.09.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/06/2018] [Accepted: 09/24/2018] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS RNase H2 is a holoenzyme, composed of 3 subunits (ribonuclease H2 subunits A, B, and C), that cleaves RNA:DNA hybrids and removes mis-incorporated ribonucleotides from genomic DNA through ribonucleotide excision repair. Ribonucleotide incorporation by eukaryotic DNA polymerases occurs during every round of genome duplication and produces the most frequent type of naturally occurring DNA lesion. We investigated whether intestinal epithelial proliferation requires RNase H2 function and whether RNase H2 activity is disrupted during intestinal carcinogenesis. METHODS We generated mice with epithelial-specific deletion of ribonuclease H2 subunit B (H2bΔIEC) and mice that also had deletion of tumor-suppressor protein p53 (H2b/p53ΔIEC); we compared phenotypes with those of littermate H2bfl/fl or H2b/p53fl/fl (control) mice at young and old ages. Intestinal tissues were collected and analyzed by histology. We isolated epithelial cells, generated intestinal organoids, and performed RNA sequence analyses. Mutation signatures of spontaneous tumors from H2b/p53ΔIEC mice were characterized by exome sequencing. We collected colorectal tumor specimens from 467 patients, measured levels of ribonuclease H2 subunit B, and associated these with patient survival times and transcriptome data. RESULTS The H2bΔIEC mice had DNA damage to intestinal epithelial cells and proliferative exhaustion of the intestinal stem cell compartment compared with controls and H2b/p53ΔIEC mice. However, H2b/p53ΔIEC mice spontaneously developed small intestine and colon carcinomas. DNA from these tumors contained T>G base substitutions at GTG trinucleotides. Analyses of transcriptomes of human colorectal tumors associated lower levels of RNase H2 with shorter survival times. CONCLUSIONS In analyses of mice with disruption of the ribonuclease H2 subunit B gene and colorectal tumors from patients, we provide evidence that RNase H2 functions as a colorectal tumor suppressor. H2b/p53ΔIEC mice can be used to study the roles of RNase H2 in tissue-specific carcinogenesis.
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Affiliation(s)
- Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany; First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany.
| | - Kareen Bartsch
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Joseph Dahl
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
| | - Martin A.M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniela Esser
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Raheleh Sheibani-Tezerji
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Felix Wottawa
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Go Ito
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Katharina Knittler
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Adam Burkholder
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
| | - Lina Welz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Johan van Es
- Hubrecht Institute/Royal Netherlands Academy of Arts and Sciences, Princess Maxima Centre and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany,First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Simone Lipinski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nassim Kakavand
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christine Boeger
- Department of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ralph Lucius
- Anatomical Institute, Christian-Albrechts-University, Kiel, Germany
| | | | - Clemens Schafmayer
- Department of Surgery, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lennart Lenk
- Department of Pediatrics, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Athena Chalaris
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Hans Clevers
- Hubrecht Institute/Royal Netherlands Academy of Arts and Sciences, Princess Maxima Centre and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany,First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Thomas Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
| | - Björn Rabe
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
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10
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Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. eLife 2017; 6:32537. [PMID: 29280736 PMCID: PMC5762160 DOI: 10.7554/elife.32537] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning (‘intron definition’) or exon-spanning (‘exon definition’) pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila, using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60–70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. We observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.
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Affiliation(s)
- Athma A Pai
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Kayla McCue
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle, United States
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
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11
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Adelman K, Scruggs BS, Henriques T, Burkholder A, Fargo DC. Abstract IA10: Regulating transcription elongation at stimulus responsive genes. Cancer Res 2016. [DOI: 10.1158/1538-7445.chromepi15-ia10] [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
The majority of mammalian protein-coding genes display transcription in both sense and anti-sense directions. At such bidirectional promoters, Pol II has been shown to initiate transcription and undergo promoter-proximal pausing near both the sense-strand mRNA transcription start site (TSS) and from within the upstream region in the anti-sense direction. This enigmatic, dual promoter structure raises fundamental questions about the specificity, purpose and regulation of upstream anti-sense transcription. Interestingly, transcription in the anti-sense direction is generally non-processive and creates short, unstable non-coding RNAs (ncRNAs). Intriguingly, many distal enhancer regions display bidirectional transcription and generate short unstable ncRNAs, raising parallels between enhancers and anti-sense promoters near protein-coding genes.
Importantly, enhancers and upstream anti-sense promoters show exquisite cell type specificity in their location and activity, suggesting key roles in establishing cell state and behavior. Further, perturbation of either transcription or chromatin structure at such non-coding loci has been implicated in the development of cancer and disease, with a profound impact on maintenance of cell state and responsiveness to stimuli. These recent findings raise a number of intriguing questions about the communication between promoters and non-coding loci.
Our work has recently defined a mechanism through which upstream anti-sense transcription impacts stimulus-responsive gene expression. Specifically, we found that the distance between sense and anti-sense TSSs at bidirectional promoters strongly influences activation of pro-inflammatory genes in macrophages. We discovered that anti-sense TSSs organize chromatin structure, creating a region of open chromatin between bidirectional TSSs that is optimal for recruitment of the transcription machinery and signal-dependent transcription factors like NF-kB. Further, we discovered that key inflammatory genes possess enhancer-like histone modifications around the anti-sense TSS, and that this characteristic selectively marks genes that are highly activated upon immune stimulation.
Citation Format: Karen Adelman, Benjamin S. Scruggs, Telmo Henriques, Adam Burkholder, David C. Fargo. Regulating transcription elongation at stimulus responsive genes. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA10.
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Affiliation(s)
- Karen Adelman
- 1Laboratory of Epigenetics & Stem Cell Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC,
| | - Benjamin S. Scruggs
- 1Laboratory of Epigenetics & Stem Cell Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC,
| | - Telmo Henriques
- 1Laboratory of Epigenetics & Stem Cell Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC,
| | - Adam Burkholder
- 2Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - David C. Fargo
- 2Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC
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12
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Shimbo T, Lavender C, Grimm SA, Doi MI, Henriques T, Cannady KR, Murphy KJ, Gilchrist DA, Burkholder A, Hayes JJ, Adelman K, Archer TK, Zaret KS, Wade PA. Abstract 2862: MBD3 regulates chromatin accessibility at active promoters. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2862] [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
Chromatin structure is tightly regulated in cells and its dysregulation is associated with diseases such as cancer. The Mi-2/NuRD (Nucleosome Remodeling Deacetylase) complex is postulated to organize chromatin structure using its nucleosome remodeling and histone deacetylase activities. MBD3 is an integral component of NuRD, which potentially targets the complex to the specific sites of the genome. Recently, we have demonstrated that MBD3/NuRD targets regulatory elements of active genes, a finding diametrically opposed to historical models depicting NuRD as a co-repressor localized to transcriptionally non-permissive chromatin. Moreover, MBD3 co-localized with RNA polymerase II (pol II) at loci where promoter-enhancer loops are formed. Although our previous findings shed light on the role of NuRD in the regulation of active genes, the detailed mechanism of how NuRD is involved in transcriptional regulation is yet not fully understood. To investigate this question, we have developed a next generation, tagmentation based chromatin immunoprecipitation method followed by massively parallel sequencing (ChIP-nexo), which substantially increased the resolution of the MBD3/NuRD mapping. ChIP-nexo defined MBD3/NuRD localization at high resolution, showing accumulation of MBD3 at active promoters with a dip at transcription start site, suggesting an active role of NuRD in modulation of the cell-type specific transcriptional network. To interrogate the detailed functions of NuRD at active promoters, we conducted MNase-seq using conditions which measures both nucleosome positioning and sensitivity, in MBD3 depleted cells. Depletion of MBD3 changed the accessibility of nucleosomes at promoters, while maintaining overall nucleosome positioning. These data indicate an active regulatory function of NuRD in fine tuning the transcriptional network by modulating transcription rates of pol II. We propose that NuRD may be involved in establishing cell type specific gene expression patterns in diverse cell types by organizing promoter nucleoprotein architecture.
Citation Format: Takashi Shimbo, Christopher Lavender, Sara A. Grimm, Makiko I. Doi, Telmo Henriques, Kimberly R. Cannady, Kevin J. Murphy, Daniel A. Gilchrist, Adam Burkholder, Jeffrey J. Hayes, Karen Adelman, Trevor K. Archer, Kenneth S. Zaret, Paul A. Wade. MBD3 regulates chromatin accessibility at active promoters. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2862. doi:10.1158/1538-7445.AM2015-2862
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Affiliation(s)
| | | | | | - Makiko I. Doi
- 2Perelman School of Medicine University of Pennsylvania, PA
| | | | | | - Kevin J. Murphy
- 3Department of Biochemistry and Biophysics, University of Rochester, NY
| | | | | | - Jeffrey J. Hayes
- 3Department of Biochemistry and Biophysics, University of Rochester, NY
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Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K. Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. Mol Cell 2015; 58:1101-12. [PMID: 26028540 DOI: 10.1016/j.molcel.2015.04.006] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/29/2015] [Accepted: 04/01/2015] [Indexed: 11/26/2022]
Abstract
Anti-sense transcription originating upstream of mammalian protein-coding genes is a well-documented phenomenon, but remarkably little is known about the regulation or function of anti-sense promoters and the non-coding RNAs they generate. Here we define at nucleotide resolution the divergent transcription start sites (TSSs) near mouse mRNA genes. We find that coupled sense and anti-sense TSSs precisely define the boundaries of a nucleosome-depleted region (NDR) that is highly enriched in transcription factor (TF) motifs. Notably, as the distance between sense and anti-sense TSSs increases, so does the size of the NDR, the level of signal-dependent TF binding, and gene activation. We further discover a group of anti-sense TSSs in macrophages with an enhancer-like chromatin signature. Interestingly, this signature identifies divergent promoters that are activated during immune challenge. We propose that anti-sense promoters serve as platforms for TF binding and establishment of active chromatin to further regulate or enhance sense-strand mRNA expression.
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Affiliation(s)
- Benjamin S Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Daniel A Gilchrist
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sergei Nechaev
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ginger W Muse
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - David C Fargo
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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14
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Bunch H, Zheng X, Burkholder A, Dillon ST, Motola S, Birrane G, Ebmeier CC, Levine S, Fargo D, Hu G, Taatjes DJ, Calderwood SK. TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release. Nat Struct Mol Biol 2014; 21:876-83. [PMID: 25173174 PMCID: PMC4189995 DOI: 10.1038/nsmb.2878] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [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] [Received: 09/19/2013] [Accepted: 07/30/2014] [Indexed: 01/19/2023]
Abstract
Promoter-proximal pausing of RNA polymerase II (Pol II) is a major checkpoint in transcription. An unbiased search for new human proteins that could regulate paused Pol II at the HSPA1B gene identified TRIM28. In vitro analyses indicated HSF1-dependent attenuation of Pol II pausing upon TRIM28 depletion, whereas in vivo data revealed de novo expression of HSPA1B and other known genes regulated by paused Pol II upon TRIM28 knockdown. These results were supported by genome-wide ChIP-sequencing analyses of Pol II occupancy that revealed a global role for TRIM28 in regulating Pol II pausing and pause release. Furthermore, in vivo and in vitro mechanistic studies suggest that transcription-coupled phosphorylation regulates Pol II pause release by TRIM28. Collectively, our findings identify TRIM28 as a new factor that modulates Pol II pausing and transcriptional elongation at a large number of mammalian genes.
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Affiliation(s)
- Heeyoun Bunch
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaofeng Zheng
- 1] Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA. [2]
| | - Adam Burkholder
- 1] Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA. [2]
| | - Simon T Dillon
- 1] Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA. [2] Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shmulik Motola
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gabriel Birrane
- 1] Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher C Ebmeier
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Stuart Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Guang Hu
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
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15
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Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, Hu G. The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell 2014; 13:676-90. [PMID: 24315442 DOI: 10.1016/j.stem.2013.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/14/2013] [Accepted: 10/16/2013] [Indexed: 12/20/2022]
Abstract
Embryonic stem cell (ESC) self-renewal and differentiation are governed by a broad-ranging regulatory network. Although the transcriptional regulatory mechanisms involved have been investigated extensively, posttranscriptional regulation is still poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5 and is required for self-renewal at least in part by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, leading to decreased expression of pluripotency proteins that facilitates exit from self-renewal. THO is also important for the establishment of pluripotency, because its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicate that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and therefore uncover a role for this aspect of posttranscriptional regulation in stem cell fate specification.
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Affiliation(s)
- Li Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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16
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Li R, Grimm SA, Chrysovergis K, Kosak J, Wang X, Du Y, Burkholder A, Janardhan K, Mav D, Shah R, Eling TE, Wade PA. Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling cancer progression. Cell Metab 2014; 19:702-11. [PMID: 24703701 PMCID: PMC4050048 DOI: 10.1016/j.cmet.2014.03.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [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] [Received: 06/30/2013] [Revised: 12/16/2013] [Accepted: 01/27/2014] [Indexed: 02/03/2023]
Abstract
While obesity represents one of several risk factors for colorectal cancer in humans, the mechanistic underpinnings of this association remain unresolved. Environmental stimuli, including diet, can alter the epigenetic landscape of DNA cis-regulatory elements affecting gene expression and phenotype. Here, we explored the impact of diet and obesity on gene expression and the enhancer landscape in murine colonic epithelium. Obesity led to the accumulation of histone modifications associated with active enhancers at genomic loci downstream of signaling pathways integral to the initiation and progression of colon cancer. Meanwhile, colon-specific enhancers lost the same histone mark, poising cells for loss of differentiation. These alterations reflect a transcriptional program with many features shared with the program driving colon cancer progression. The interrogation of enhancer alterations by diet in colonic epithelium provides insights into the biology underlying high-fat diet and obesity as risk factors for colon cancer.
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Affiliation(s)
- Ruifang Li
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sara A Grimm
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Kaliopi Chrysovergis
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Justin Kosak
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xingya Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ying Du
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | | | - Deepak Mav
- SRA International, Inc., Durham, NC 27709, USA
| | - Ruchir Shah
- SRA International, Inc., Durham, NC 27709, USA
| | - Thomas E Eling
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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17
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Verhein KC, High M, Marzec J, McCaw Z, Wiltshire T, Chen Y, Burkholder A, Klimczak L, Fargo D, Kleeberger SR. Identification of candidate susceptibility genes in a murine model of respiratory syncytial virus (RSV)‐induced bronchiolitis. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1212.4] [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)
- Kirsten C Verhein
- Laboratory of Respiratory BiologyNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | - Monica High
- Laboratory of Respiratory BiologyNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | - Jacqui Marzec
- Laboratory of Respiratory BiologyNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | | | | | - Yu Chen
- Integrative BioinformaticsNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | - Adam Burkholder
- Integrative BioinformaticsNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | - Les Klimczak
- Integrative BioinformaticsNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | - David Fargo
- Integrative BioinformaticsNational Institute of Environmental Health SciencesResearch Triangle ParkNC
| | - Steven R Kleeberger
- Laboratory of Respiratory BiologyNational Institute of Environmental Health SciencesResearch Triangle ParkNC
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18
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Gilchrist DA, Fromm G, dos Santos G, Pham LN, McDaniel IE, Burkholder A, Fargo DC, Adelman K. Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks. Genes Dev 2012; 26:933-44. [PMID: 22549956 DOI: 10.1101/gad.187781.112] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The expression of many metazoan genes is regulated through controlled release of RNA polymerase II (Pol II) that has paused during early transcription elongation. Pausing is highly enriched at genes in stimulus-responsive pathways, where it has been proposed to poise downstream targets for rapid gene activation. However, whether this represents the major function of pausing in these pathways remains to be determined. To address this question, we analyzed pausing within several stimulus-responsive networks in Drosophila and discovered that paused Pol II is much more prevalent at genes encoding components and regulators of signal transduction cascades than at inducible downstream targets. Within immune-responsive pathways, we found that pausing maintains basal expression of critical network hubs, including the key NF-κB transcription factor that triggers gene activation. Accordingly, loss of pausing through knockdown of the pause-inducing factor NELF leads to broadly attenuated immune gene activation. Investigation of murine embryonic stem cells revealed that pausing is similarly widespread at genes encoding signaling components that regulate self-renewal, particularly within the MAPK/ERK pathway. We conclude that the role of pausing goes well beyond poising-inducible genes for activation and propose that the primary function of paused Pol II is to establish basal activity of signal-responsive networks.
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Affiliation(s)
- Daniel A Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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19
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Kemper J, Burkholder A, Jain A, Mustufa T, Wyrobek K, Burdette C, Song D, Okamura A, Fichtinger G. TU-EE-A1-06: Transrectal Fiducial Carrier for Radiographic Image Registration in Prostate Brachytherapy. Med Phys 2005. [DOI: 10.1118/1.1998447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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20
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Affiliation(s)
- L A Slone
- Sibley Memorial Hospital, Washington, DC
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