1
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Morgan D, DeMeo DL, Glass K. Using methylation data to improve transcription factor binding prediction. Epigenetics 2024; 19:2309826. [PMID: 38300850 PMCID: PMC10841018 DOI: 10.1080/15592294.2024.2309826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Modelling the regulatory mechanisms that determine cell fate, response to external perturbation, and disease state depends on measuring many factors, a task made more difficult by the plasticity of the epigenome. Scanning the genome for the sequence patterns defined by Position Weight Matrices (PWM) can be used to estimate transcription factor (TF) binding locations. However, this approach does not incorporate information regarding the epigenetic context necessary for TF binding. CpG methylation is an epigenetic mark influenced by environmental factors that is commonly assayed in human cohort studies. We developed a framework to score inferred TF binding locations using methylation data. We intersected motif locations identified using PWMs with methylation information captured in both whole-genome bisulfite sequencing and Illumina EPIC array data for six cell lines, scored motif locations based on these data, and compared with experimental data characterizing TF binding (ChIP-seq). We found that for most TFs, binding prediction improves using methylation-based scoring compared to standard PWM-scores. We also illustrate that our approach can be generalized to infer TF binding when methylation information is only proximally available, i.e. measured for nearby CpGs that do not directly overlap with a motif location. Overall, our approach provides a framework for inferring context-specific TF binding using methylation data. Importantly, the availability of DNA methylation data in existing patient populations provides an opportunity to use our approach to understand the impact of methylation on gene regulatory processes in the context of human disease.
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Affiliation(s)
- Daniel Morgan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
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2
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Viner C, Ishak CA, Johnson J, Walker NJ, Shi H, Sjöberg-Herrera MK, Shen SY, Lardo SM, Adams DJ, Ferguson-Smith AC, De Carvalho DD, Hainer SJ, Bailey TL, Hoffman MM. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome Biol 2024; 25:11. [PMID: 38191487 PMCID: PMC10773111 DOI: 10.1186/s13059-023-03070-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/21/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult. RESULTS Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We adapt the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet. Using these methods, we identify modification-sensitive transcription factor binding motifs. We confirm established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs. CONCLUSIONS Using known binding preferences to tune model parameters, we discover novel modified motifs for a wide array of transcription factors. Finally, we validate our binding preference predictions for OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.
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Affiliation(s)
- Coby Viner
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James Johnson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicolas J Walker
- Department of Genetics, University of Cambridge, Cambridge, England
| | - Hui Shi
- Department of Genetics, University of Cambridge, Cambridge, England
| | - Marcela K Sjöberg-Herrera
- Wellcome Sanger Institute, Cambridge, England
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy L Bailey
- Department of Pharmacology, University of Nevada, Reno, Reno, NV, USA
| | - Michael M Hoffman
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
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3
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Brown AP, Parameswaran S, Cai L, Elston S, Pham C, Barski A, Weirauch MT, Ji H. TET1 regulates responses to house dust mite by altering chromatin accessibility, DNA methylation, and gene expression in airway epithelial cells. RESEARCH SQUARE 2023:rs.3.rs-3726852. [PMID: 38168374 PMCID: PMC10760239 DOI: 10.21203/rs.3.rs-3726852/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Previous studies have identified TET1 as a potential key regulator of genes linked to asthma. TET1 has been shown to transcriptionally respond to house dust mite extract, an allergen known to directly cause allergic asthma development, and regulate the expression of genes involved in asthma. How TET1 regulates expression of these genes, however, is unknown. TET1 is a DNA demethylase; therefore, most prior research on TET1-based gene regulation has focused on how TET1 affects methylation. However, TET1 can also interact directly with transcription factors and histone modifiers to regulate gene expression. Understanding how TET1 regulates expression to contribute to allergic responses and asthma development thus requires a comprehensive approach. To this end, we measured mRNA expression, DNA methylation, chromatin accessibility and histone modifications in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. Results Throughout our analyses, we detected strong similarities between the effects of TET1 knockdown alone and the effects of HDM treatment alone. One especially striking pattern was that both TET1 knockdown and HDM treatment generally led to decreased chromatin accessibility at largely the same genomic loci. Transcription factor enrichment analyses indicated that altered chromatin accessibility following the loss of TET1 may affect, or be affected by, CTCF and CEBP binding. TET1 loss also led to changes in DNA methylation, but these changes were generally in regions where accessibility was not changing. Conclusions TET1 regulates gene expression through different mechanisms (DNA methylation and chromatin accessibility) in different parts of the genome in the airway epithelial cells, which mediates inflammatory responses to allergen. Collectively, our data suggest novel molecular mechanisms through which TET1 regulates critical pathways following allergen challenges and contributes to the development of asthma.
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Affiliation(s)
| | | | | | | | | | | | | | - Hong Ji
- University of California Davis
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4
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Khan AB, Lee S, Harmanci AS, Patel R, Latha K, Yang Y, Marisetty A, Lee HK, Heimberger AB, Fuller GN, Deneen B, Rao G. CXCR4 expression is associated with proneural-to-mesenchymal transition in glioblastoma. Int J Cancer 2023; 152:713-724. [PMID: 36250346 PMCID: PMC10071545 DOI: 10.1002/ijc.34329] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 02/01/2023]
Abstract
Glioblastoma (GBM) is the most common primary intracranial malignant tumor and consists of three molecular subtypes: proneural (PN), mesenchymal (MES) and classical (CL). Transition between PN to MES subtypes (PMT) is the glioma analog of the epithelial-mesenchymal transition (EMT) in carcinomas and is associated with resistance to therapy. CXCR4 signaling increases the expression of MES genes in glioma cell lines and promotes EMT in other cancers. RNA sequencing (RNAseq) data of PN GBMs in The Cancer Genome Atlas (TCGA) and secondary high-grade gliomas (HGGs) from an internal cohort were examined for correlation between CXCR4 expression and survival as well as expression of MES markers. Publicly available single-cell RNA sequencing (scRNAseq) data was analyzed for cell type specific CXCR4 expression. These results were validated in a genetic mouse model of PN GBM. Higher CXCR4 expression was associated with significantly reduced survival and increased expression of MES markers in TCGA and internal cohorts. CXCR4 was expressed in immune and tumor cells based on scRNAseq analysis. Higher CXCR4 expression within tumor cells on scRNAseq was associated with increased MES phenotype, suggesting a cell-autonomous effect. In a genetically engineered mouse model, tumors induced with CXCR4 exhibited a mesenchymal phenotype and shortened survival. These results suggest that CXCR4 signaling promotes PMT and shortens survival in GBM and highlights its inhibition as a potential therapeutic strategy.
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Affiliation(s)
- A. Basit Khan
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Sungho Lee
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | | | - Rajan Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Khatri Latha
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Yuhui Yang
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | | | - Hyun-Kyoung Lee
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | | | | | - Benjamin Deneen
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Ganesh Rao
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
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5
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Lountos GT, Cherry S, Tropea JE, Wlodawer A, Miller M. Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter. J Struct Biol 2022; 214:107918. [PMID: 36343842 PMCID: PMC9909937 DOI: 10.1016/j.jsb.2022.107918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
C/EBPβ is a key regulator of numerous cellular processes, but it can also contribute to tumorigenesis and viral diseases. It binds to specific DNA sequences (C/EBP sites) and interacts with other transcription factors to control expression of multiple eukaryotic genes in a tissue and cell-type dependent manner. A body of evidence has established that cell-type-specific regulatory information is contained in the local DNA sequence of the binding motif. In human epithelial cells, C/EBPβ is an essential cofactor for TGFβ signaling in the case of Smad2/3/4 and FoxO-dependent induction of the cell cycle inhibitor, p15INK4b. In the TGFβ-responsive region 2 of the p15INK4b promoter, the Smad binding site is flanked by a C/EBP site, CTTAA•GAAAG, which differs from the canonical, palindromic ATTGC•GCAAT motif. The X-ray crystal structure of C/EBPβ bound to the p15INK4b promoter fragment shows how GCGC-to-AAGA substitution generates changes in the intermolecular interactions in the protein-DNA interface that enhances C/EBPβ binding specificity, limits possible epigenetic regulation of the promoter, and generates a DNA element with a unique pattern of methyl groups in the major groove. Significantly, CT/GA dinucleotides located at the 5'ends of the double stranded element maintain local narrowing of the DNA minor groove width that is necessary for DNA recognition. Our results suggest that C/EBPβ would accept all forms of modified cytosine in the context of the CpT site. This contrasts with the effect on the consensus motif, where C/EBPβ binding is modestly increased by cytosine methylation, but substantially decreased by hydroxymethylation.
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Affiliation(s)
- George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Scott Cherry
- Protein Purification Core, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joseph E Tropea
- Protein Purification Core, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201 USA
| | - Maria Miller
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201 USA
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6
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Li J, Hong T, Wei Y, Guo L, Lee M, Yang H, Class C, Yang Y, Wang X, He H, Siwko S, You MJ, Zhou Y, Garcia-Manero G, Huang Y. Aberrant DNA hydroxymethylation reshapes transcription factor binding in myeloid neoplasms. Clin Epigenetics 2022; 14:81. [PMID: 35765052 PMCID: PMC9241241 DOI: 10.1186/s13148-022-01297-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/05/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetic abnormalities in DNA hydroxymethylation (5hmC) have been detected in patients with myeloid neoplasms, suggesting that 5hmC might act as a valuable epigenetic mark to reflect the disease status of myeloid neoplasms. Here, we report systematic genome-wide mapping of the DNA hydroxymethylomes in over 70 patients with myeloid neoplasms. Our integrative analysis leads to the identification of distinct 5hmC signatures that can sensitively discriminate patients from healthy individuals. At the molecular level, we unveiled dynamic 5hmC changes within key transcription factor (e.g., the CEBP family) binding motifs that are essential for hematopoiesis and myeloid lineage specification. 5hmC redistribution was found to alter the genome-wide binding of CEBP-α, thereby reprogramming transcriptional outputs to affect leukemia cell survival and stemness. Taken together, we provide a comprehensive 5hmC atlas representative of myeloid neoplasms, which sets the stage for future exploration on the epigenetic etiology of hematological malignancies. Mechanistically, our study further furnishes important insights into how abnormal 5hmC distribution in patients directly interrupts the binding of transcription factors to reshape transcriptional landscapes and aggravate leukemogenesis.
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Affiliation(s)
- Jia Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA.
| | - Tingting Hong
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA
| | - Yue Wei
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lei Guo
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA
| | - Minjung Lee
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA
| | - Hui Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Caleb Class
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Yaling Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoqiong Wang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hua He
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Stefan Siwko
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - M James You
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Room 404, 2121. W. Holcombe Blvd, Houston, TX, 77030, USA.
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7
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Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C. Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182. ACS OMEGA 2022; 7:129-139. [PMID: 35036684 PMCID: PMC8756438 DOI: 10.1021/acsomega.1c04148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Zta, the Epstein-Barr virus bZIP transcription factor (TF), binds both unmethylated and methylated double-stranded DNA (dsDNA) in a sequence-specific manner. We studied the contribution of a conserved asparagine (N182) to sequence-specific dsDNA binding to four types of dsDNA: (i) dsDNA with cytosine in both strands ((DNA(C|C)), (ii, iii) dsDNA with 5-methylcytosine (5mC, M) or 5-hydroxymethylcytosine (5hmC, H) in one strand and cytosine in the second strand ((DNA(5mC|C) and DNA(5hmC|C)), and (iv) dsDNA with methylated cytosine in both strands in all CG dinucleotides ((DNA(5mCG)). We replaced asparagine with five similarly sized amino acids (glutamine (Q), serine (S), threonine (T), isoleucine (I), or valine (V)) and used protein binding microarrays to evaluate sequence-specific dsDNA binding. Zta preferentially binds the pseudo-palindrome TRE (AP1) motif (T-4G-3A-2G/C 0T2C3A4 ). Zta (N182Q) changes binding to A3 in only one half-site. Zta(N182S) changes binding to G3 in one or both halves of the motif. Zta(N182S) and Zta(N182Q) have 34- and 17-fold weaker median dsDNA binding, respectively. Zta(N182V) and Zta(N182I) have increased binding to dsDNA(5mC|C). Molecular dynamics simulations rationalize some of these results, identifying hydrogen bonds between glutamine and A3 , but do not reveal why serine preferentially binds G3 , suggesting that entropic interactions may mediate this new binding specificity.
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Affiliation(s)
- Sreejana Ray
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Desiree Tillo
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
- Cancer
Genetics Branch, National Cancer Institute,
National Institutes of Health, Building 37, Bethesda, Maryland 20892, United States
| | - Nima Assad
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Aniekanabasi Ufot
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Aleksey Porollo
- Center
for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, United States
- Department
of Pediatrics, University of Cincinnati
College of Medicine, Cincinnati, Ohio 45267, United States
| | - Stewart R. Durell
- Laboratory
of Cell Biology, National Cancer Institute,
National Institutes of Health, Building 37, Bethesda, Maryland 20892, United States
| | - Charles Vinson
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
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8
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Umer HM, Smolinska K, Komorowski J, Wadelius C. Functional annotation of noncoding mutations in cancer. Life Sci Alliance 2021; 4:4/9/e201900523. [PMID: 34282050 PMCID: PMC8321657 DOI: 10.26508/lsa.201900523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Recurrent regulatory mutations affecting transcription factor binding sites in 2,500 cancer samples. In a cancer genome, the noncoding sequence contains the vast majority of somatic mutations. While very few are expected to be cancer drivers, those affecting regulatory elements have the potential to have downstream effects on gene regulation that may contribute to cancer progression. To prioritize regulatory mutations, we screened somatic mutations in the Pan-Cancer Analysis of Whole Genomes cohort of 2,515 cancer genomes on individual bases to assess their potential regulatory roles in their respective cancer types. We found a highly significant enrichment of regulatory mutations associated with the deamination signature overlapping a CpG site in the CCAAT/Enhancer Binding Protein β recognition sites in many cancer types. Overall, 5,749 mutated regulatory elements were identified in 1,844 tumor samples from 39 cohorts containing 11,962 candidate regulatory mutations. Our analysis indicated 20 or more regulatory mutations in 5.5% of the samples, and an overall average of six per tumor. Several recurrent elements were identified, and major cancer-related pathways were significantly enriched for genes nearby the mutated regulatory elements. Our results provide a detailed view of the role of regulatory elements in cancer genomes.
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Affiliation(s)
- Husen M Umer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Karolina Smolinska
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Swedish Collegium for Advanced Study, Uppsala, Sweden.,Washington National Primate Research Center, Seattle, WA, USA
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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9
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Ershova AS, Eliseeva IA, Nikonov OS, Fedorova AD, Vorontsov IE, Papatsenko D, Kulakovskiy IV. Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells. Cell Rep 2021; 35:109221. [PMID: 34107262 DOI: 10.1016/j.celrep.2021.109221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 03/21/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022] Open
Abstract
Somatic mutations in regulatory sites of human stem cells affect cell identity or cause malignant transformation. By mining the human genome for co-occurrence of mutations and transcription factor binding sites, we show that C/EBP binding sites are strongly enriched with [C > T]G mutations in cancer and adult stem cells, which is of special interest because C/EBPs regulate cell fate and differentiation. In vitro protein-DNA binding assay and structural modeling of the CEBPB-DNA complex show that the G·T mismatch in the core CG dinucleotide strongly enhances affinity of the binding site. We conclude that enhanced binding of C/EBPs shields CpG·TpG mismatches from DNA repair, leading to selective accumulation of [C > T]G mutations and consequent deterioration of the binding sites. This mechanism of targeted mutagenesis highlights the effect of a mutational process on certain regulatory sites and reveals the molecular basis of putative regulatory alterations in stem cells.
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Affiliation(s)
- Anna S Ershova
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Irina A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Oleg S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Ilya E Vorontsov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Dmitry Papatsenko
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
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10
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Fachim HA, Siddals K, Malipatil N, Donn RP, Moreno GYC, Dalton CF, Adam S, Soran H, Gibson JM, Heald AH. Lifestyle intervention in individuals with impaired glucose regulation affects Caveolin-1 expression and DNA methylation. Adipocyte 2020; 9:96-107. [PMID: 32125224 PMCID: PMC7153542 DOI: 10.1080/21623945.2020.1732513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aims: We investigated whether a lifestyle intervention could influence expression and DNA methylation of diabetes-related genes in patients with impaired glucose regulation (IGR), the results were compared to bariatric surgery, considering it an intensive change. Methods: Twenty participants with IGR had adipose tissue biopsy and blood collected pre- and post-lifestyle (6 months) intervention; 12 obese patients had subcutaneous fat taken before and after bariatric surgery. RNA/DNA was extracted from all samples and underwent qPCR. DNA was bisulphite converted and 12 CpG sites of Caveolin-1 (CAV1) promoter were pyrosequenced. Results: lifestyle intervention resulted in opposite direction changes in fat tissue and blood for CAV1 expression and DNA methylation and these changes were correlated between tissues, while no significative differences were found in CAV1 expression after bariatric surgery. Conclusions: Our findings suggest a role for CAV1 in modulating adipocyte function as a consequence of lifestyle changes, as exercises and diet. These results may provide insights into new therapeutic targets for diabetes prevention.
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Affiliation(s)
- Helene A. Fachim
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal NHS Foundation Trust, Salford, UK
| | - Kirk Siddals
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal NHS Foundation Trust, Salford, UK
| | - Nagaraj Malipatil
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal NHS Foundation Trust, Salford, UK
| | - Rachelle P Donn
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Gabriela YC Moreno
- Dirección General de Calidad y Educación en Salud, Secretaría de Salud, Mexico City, Mexico
| | - Caroline F Dalton
- Biomolecular Science Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Safwaan Adam
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Endocrinology, The Christie NHS Foundation Trust, Manchester, UK
- Department of Endocrinology, Diabetes and Metabolism, Manchester Royal Infirmary, Manchester, UK
| | - Handrean Soran
- Department of Endocrinology, Diabetes and Metabolism, Manchester Royal Infirmary, Manchester, UK
- Lipoprotein Research Group, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Core Technology Facility, Manchester, UK
| | - J Martin Gibson
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal NHS Foundation Trust, Salford, UK
| | - Adrian H Heald
- Faculty of Biology, Medicine and Health and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal NHS Foundation Trust, Salford, UK
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11
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Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
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Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
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12
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Ray S, Tillo D, Ufot A, Assad N, Durell S, Vinson C. bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine. Biochemistry 2020; 59:3529-3540. [PMID: 32902247 DOI: 10.1021/acs.biochem.0c00475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mammalian cells, 5-methylcytosine (5mC) occurs in genomic double-stranded DNA (dsDNA) and is enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), then to 5-formylcytosine (5fC), and finally to 5-carboxylcytosine (5caC). These cytosine modifications are enriched in regulatory regions of the genome. The effect of these oxidative products on five bZIP dimers (CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun) binding to five types of dsDNA was measured using protein binding microarrays. The five dsDNAs contain either cytosine in both DNA strands or cytosine in one strand and either 5mC, 5hmC, 5fC, or 5caC in the second strand. Some sequences containing the CEBP half-site GCAA are bound more strongly by all five bZIP domains when dsDNA contains 5mC, 5hmC, or 5fC. dsDNA containing 5caC in some TRE (AP-1)-like sequences, e.g., TGACTAA, is better bound by Zta, ATF3|cJun, and cFos|cJun.
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13
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Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. J Mol Biol 2019:S0022-2836(19)30617-5. [PMID: 31689433 DOI: 10.1016/j.jmb.2019.10.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 01/09/2023]
Abstract
Epigenetic DNA modification impacts gene expression, but the underlying molecular mechanisms are only partly understood. Adding a methyl group to a cytosine base locally modifies the structural features of DNA in multiple ways, which may change the interaction with DNA-binding transcription factors (TFs) and trigger a cascade of downstream molecular events. Cells can be probed using various functional genomics assays, but it is difficult to disentangle the confounded effects of DNA modification on TF binding, chromatin accessibility, intranuclear variation in local TF concentration, and rate of transcription. Here we discuss how high-throughput in vitro profiling of protein-DNA interactions has enabled comprehensive characterization and quantification of the methylation sensitivity of TFs. Despite the limited structural data for DNA containing methylated cytosine, automated analysis of structural information in the Protein Data Bank (PDB) shows how 5-methylcytosine (5mC) can be recognized in various ways by amino acid side chains. We discuss how a context-dependent effect of methylation on DNA groove geometry can affect DNA binding by homeodomain proteins and how principled modeling of ChIP-seq data can overcome the confounding that makes the interpretation of in vivo data challenging. The emerging picture is that epigenetic modifications affect TF binding in a highly context-specific manner, with a direction and effect size that depend critically on their position within the TF binding site and the amino acid sequence of the TF. With this improved mechanistic knowledge, we have come closer to understanding how cells use DNA modification to acquire, retain, and change their identity.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Remo Rohs
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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14
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Genetic variation, intrauterine growth, and adverse pregnancy conditions predict leptin gene DNA methylation in blood at birth and 12 months of age. Int J Obes (Lond) 2019; 44:45-56. [PMID: 31636377 DOI: 10.1038/s41366-019-0472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/19/2019] [Accepted: 09/30/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Leptin regulates satiety and energy homoeostasis, and plays a key role in placentation in pregnancy. Previous studies have demonstrated regulation of leptin gene (LEP) expression and/or methylation in placenta and cord blood in association with early life exposures, but most have been small and have not considered the influence of genetic variation. Here, we investigated the relationship between maternal factors in pregnancy, infant anthropometry and LEP genetic variation with LEP promoter methylation at birth and 12 months of age. METHODS LEP methylation was measured in cord (n = 877) and 12-month (n = 734) blood in the Barwon Infant Study, a population-based pre-birth cohort. Infant adiposity at birth and 12-months was measured as triceps and subscapular skinfold thickness. Cross-sectional regression tested associations of methylation with pregnancy and anthropometry measures, while longitudinal regression tested if birth anthropometry predicted 12-month LEP methylation levels. RESULTS Male infants had lower LEP methylation in cord blood (-2.07% average methylation, 95% CI (-2.92, -1.22), p < 0.001). Genetic variation strongly influenced DNA methylation at a single CpG site, which was also negatively associated with birth weight (r = -0.10, p = 0.003). Pre-eclampsia was associated with lower cord blood methylation at another CpG site (-6.06%, 95% CI (-10.70, -1.42), p = 0.01). Gestational diabetes was more modestly associated with methylation at two other CpG units. Adiposity at birth was associated with 12-month LEP methylation, modified by rs41457646 genotype. There was no association of LEP methylation with 12-month anthropometric measures. CONCLUSIONS Infant sex, weight, genetic variation, and exposure to pre-eclampsia and gestational diabetes, are associated with LEP methylation in cord blood. Infant adiposity at birth predicts 12-month blood LEP methylation in a genotype-dependent manner. These findings are consistent with genetics and anthropometry driving altered LEP epigenetic profile and expression in infancy. Further work is required to confirm this and to determine the long-term impact of altered LEP methylation on health.
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15
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Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Nucleic Acids Res 2019; 47:1774-1785. [PMID: 30566668 PMCID: PMC6393304 DOI: 10.1093/nar/gky1264] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/28/2018] [Accepted: 12/08/2018] [Indexed: 12/30/2022] Open
Abstract
CCAAT/enhancer binding proteins (C/EBPs) regulate gene expression in a variety of cells/tissues/organs, during a range of developmental stages, under both physiological and pathological conditions. C/EBP-related transcription factors have a consensus binding specificity of 5'-TTG-CG-CAA-3', with a central CpG/CpG and two outer CpA/TpG dinucleotides. Methylation of the CpG and CpA sites generates a DNA element with every pyrimidine having a methyl group in the 5-carbon position (thymine or 5-methylcytosine (5mC)). To understand the effects of both CpG and CpA modification on a centrally-important transcription factor, we show that C/EBPβ binds the methylated 8-bp element with modestly-increased (2.4-fold) binding affinity relative to the unmodified cognate sequence, while cytosine hydroxymethylation (particularly at the CpA sites) substantially decreased binding affinity (36-fold). The structure of C/EBPβ DNA binding domain in complex with methylated DNA revealed that the methyl groups of the 5mCpA/TpG make van der Waals contacts with Val285 in C/EBPβ. Arg289 recognizes the central 5mCpG by forming a methyl-Arg-G triad, and its conformation is constrained by Val285 and the 5mCpG methyl group. We substituted Val285 with Ala (V285A) in an Ala-Val dipeptide, to mimic the conserved Ala-Ala in many members of the basic leucine-zipper family of transcription factors, important in gene regulation, cell proliferation and oncogenesis. The V285A variant demonstrated a 90-fold binding preference for methylated DNA (particularly 5mCpA methylation) over the unmodified sequence. The smaller side chain of Ala285 permits Arg289 to adopt two alternative conformations, to interact in a similar fashion with either the central 5mCpG or the TpG of the opposite strand. Significantly, the best-studied cis-regulatory elements in RNA polymerase II promoters and enhancers have variable sequences corresponding to the central CpG or reduced to a single G:C base pair, but retain a conserved outer CpA sequence. Our analyses suggest an important modification-dependent CpA recognition by basic leucine-zipper transcription factors.
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Affiliation(s)
- Jie Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Burleson JD, Siniard D, Yadagiri VK, Chen X, Weirauch MT, Ruff BP, Brandt EB, Hershey GKK, Ji H. TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells. Sci Rep 2019; 9:7361. [PMID: 31089182 PMCID: PMC6517446 DOI: 10.1038/s41598-019-43767-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 05/01/2019] [Indexed: 01/10/2023] Open
Abstract
Previous studies have suggested a role for Tet1 in the pathogenesis of childhood asthma. However, how Tet1 contributes to asthma remains unknown. Here we used mice deficient for Tet1 in a well-established model of allergic airway inflammation and demonstrated that loss of Tet1 increased disease severity including airway hyperresponsiveness and lung eosinophilia. Increased expression of Muc5ac, Il13, Il33, Il17a, Egfr, and Tff2 were observed in HDM-challenged Tet1-deficient mice compared to Tet1+/+ littermates. Further, transcriptomic analysis of lung RNA followed by pathway and protein network analysis showed that the IFN signaling pathway was significantly upregulated and the aryl hydrocarbon receptor (AhR) pathway was significantly downregulated in HDM-challenged Tet1-/- mice. This transcriptional regulation of the IFN and AhR pathways by Tet1 was also present in human bronchial epithelial cells at base line and following HDM challenges. Genes in these pathways were further associated with changes in DNA methylation, predicted binding of transcriptional factors with relevant functions in their promoters, and the presence of histone marks generated by histone enzymes that are known to interact with Tet1. Collectively, our data suggest that Tet1 inhibits HDM-induced allergic airway inflammation by direct regulation of the IFN and AhR pathways.
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Affiliation(s)
- J D Burleson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dylan Siniard
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Veda K Yadagiri
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Brandy P Ruff
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eric B Brandt
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hong Ji
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA. .,California National Primate Research Center, Davis, CA, USA.
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17
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Ray S, Ufot A, Assad N, Singh J, Durell SR, Porollo A, Tillo D, Vinson C. The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:486-492. [PMID: 30825655 DOI: 10.1016/j.bbagrm.2019.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/09/2019] [Accepted: 02/05/2019] [Indexed: 12/25/2022]
Abstract
The bZIP homodimers CEBPB and CREB1 bind DNA containing methylated cytosines differently. CREB1 binds stronger to the C/EBP half-site GCAA when the cytosine is methylated. For CEBPB, methylation of the same cytosine does not affect DNA binding. The X-ray structure of CREB1 binding the half site GTCA identifies an alanine in the DNA binding region interacting with the methyl group of T, structurally analogous to the methyl group of methylated C. This alanine is replaced with a valine in CEBPB. To explore the contribution of this amino acid to binding with methylated cytosine of the GCAA half-site, we made the reciprocal mutants CEBPB(V285A) and CREB1(A297V) and used protein binding microarrays (PBM) to examine binding to four types of double-stranded DNA (dsDNA): 1) DNA with cytosine in both strands (DNA(C|C)), 2) DNA with 5-methylcytosine (M) in one strand and cytosine in the second strand (DNA(M|C)), 3) DNA with 5-hydroxymethylcytosine (H) in one strand and cytosine in the second strand (DNA(H|C)), and 4) DNA with both cytosines in all CG dinucleotides containing 5-methylcytosine (DNA(5mCG)). When binding to DNA(C|C), CEBPB (V285A) preferentially binds the CRE consensus motif (TGACGTCA), similar to CREB1. The reciprocal mutant, CREB1(A297V) binds DNA with some similarity to CEBPB, with strongest binding to the methylated PAR site 8-mer TTACGTAA. These data demonstrate that V285 residue inhibits CEBPB binding to methylated cytosine of the GCAA half-site.
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Affiliation(s)
- Sreejana Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Aniekanabasi Ufot
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Nima Assad
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Jocelyn Singh
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Aleksey Porollo
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States of America; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, United States of America
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States of America.
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18
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Abstract
Senescence, a state of permanent cell cycle arrest, can be induced by DNA damage. This process, which was initially described in fibroblasts, is now recognized to occur in stem cells. It has been well characterized in cell lines, but there is currently very limited data available on human senescence in vivo. We recently reported that the expression of transposable elements (TE), including endogenous retroviruses, was up-regulated along with inflammatory genes in human senescent hematopoietic stem and progenitor cells (HSPCs) in vivo. The mechanism of regulation of TE expression is not completely understood, but changes in DNA methylation and chromatin modifications are known to alter their expression. In order to elucidate the molecular mechanisms for TE up-regulation after senescence of HSPCs, we employed whole-genome bisulfite sequencing in paired senescent and active human HSPCs in vivo from healthy subjects. We found that the senescent HSPCs exhibited hypomethylated regions in the genome, which were enriched for TEs. This is the first report characterizing the methylome of senescent human HSPCs.
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19
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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20
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Ray S, Tillo D, Assad N, Ufot A, Deppmann C, Durell SR, Porollo A, Vinson C. Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA. Biochem Biophys Res Commun 2018; 501:905-912. [PMID: 29772230 DOI: 10.1016/j.bbrc.2018.05.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 05/13/2018] [Indexed: 11/15/2022]
Abstract
Zta is a bZIP transcription factor (TF) in the Epstein-Barr virus that binds unmethylated and methylated DNA sequences. Substitution of cysteine 189 of Zta to serine (Zta(C189S)) results in a virus that is unable to execute the lytic cycle, which was attributed to a change in binding to methylated DNA sequences. To learn more about the role of this position in defining sequence-specific DNA binding, we mutated cysteine 189 to four other amino acids, producing Zta(C189S), Zta(C189T), Zta(C189A), and Zta(C189V) mutants. Zta and mutants were used in protein binding microarray (PBM) experiments to evaluate sequence-specific DNA binding to four types of double-stranded DNA (dsDNA): 1) with cytosine in both strands (DNA(C|C)), 2) with 5-methylcytosine (5mC) in one strand and cytosine in the second strand (DNA(5mC|C)), 3) with 5-hydroxymethylcytosine (5hmC) in one strand and cytosine in the second strand (DNA(5hmC|C)), and 4) with both cytosines in all CG dinucleotides containing 5mC (DNA(5mCG)). Zta(C189S) and Zta(C189T) bound the TRE (AP-1) motif (TGAG/CTCA) more strongly than wild-type Zta, while binding to other sequences, including the C/EBP half site GCAA was reduced. Binding of Zta(C189S) and Zta(C189T) to DNA containing modified cytosines (DNA(5mC|C), DNA(5hmC|C), and DNA(5mCG)) was reduced compared to Zta. Zta(C189A) and Zta(C189V) had higher non-specific binding to all four types of DNA. Our data suggests that position C189 in Zta impacts sequence-specific binding to DNA containing modified and unmodified cytosine.
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Affiliation(s)
- Sreejana Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nima Assad
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aniekanabasi Ufot
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christopher Deppmann
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, 22903, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903, USA
| | - Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aleksey Porollo
- Center for Autoimmune Genomics and Etiology and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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21
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Bie L, Du L, Yuan Q, Gao J. How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study. J Mol Model 2018; 24:159. [PMID: 29892907 DOI: 10.1007/s00894-018-3678-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/15/2018] [Indexed: 12/23/2022]
Abstract
CpG methylation can regulate gene expression by altering the specific binding of protein and DNA. In order to understand how a single 5mC regulates protein-DNA interactions, we have compared the structures and dynamics of CEBP/βprotein-DNA complexes before and after methylation, and the results indicate that even a single 5mC can regulate protein-DNA recognition by steric-hindrance effect of methyl group and changing the hydrogen bond interactions. The interactions between the methyl group, mCpG motif, and the conserved residue arginine make the protein read out the variation of local environment, which further enhances the specific recognition and affects the base pair stacking. The stacking interactions can propagate along the backbone of DNA and lead to long-range allosteric effects, including obvious conformational variations for DNA base pairs.
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Affiliation(s)
- Lihua Bie
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Likai Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Qiaoxia Yuan
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Jun Gao
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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22
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Wortel IMN, van der Meer LT, Kilberg MS, van Leeuwen FN. Surviving Stress: Modulation of ATF4-Mediated Stress Responses in Normal and Malignant Cells. Trends Endocrinol Metab 2017; 28:794-806. [PMID: 28797581 PMCID: PMC5951684 DOI: 10.1016/j.tem.2017.07.003] [Citation(s) in RCA: 354] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 01/14/2023]
Abstract
Activating transcription factor 4 (ATF4) is a stress-induced transcription factor that is frequently upregulated in cancer cells. ATF4 controls the expression of a wide range of adaptive genes that allow cells to endure periods of stress, such as hypoxia or amino acid limitation. However, under persistent stress conditions, ATF4 promotes the induction of apoptosis. Recent advances point to a role for post-translational modifications (PTMs) and epigenetic mechanisms in balancing these pro- and anti-survival effects of ATF4. We review here how PTMs and epigenetic modifiers associated with ATF4 may be exploited by cancer cells to cope with cellular stress conditions that are intrinsically associated with tumor growth. Identification of mechanisms that modulate ATF4-mediated transcription and its effects on cellular metabolism may uncover new targets for cancer treatment.
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Affiliation(s)
- Inge M N Wortel
- Laboratory of Pediatric Oncology, Radboud Institute for Molecular Life Science, Radboud university medical center, Nijmegen, The Netherlands; Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Laurens T van der Meer
- Laboratory of Pediatric Oncology, Radboud Institute for Molecular Life Science, Radboud university medical center, Nijmegen, The Netherlands
| | - Michael S Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610-0245, USA.
| | - Frank N van Leeuwen
- Laboratory of Pediatric Oncology, Radboud Institute for Molecular Life Science, Radboud university medical center, Nijmegen, The Netherlands.
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23
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Garcia-Gomez A, Li T, Kerick M, Català-Moll F, Comet NR, Rodríguez-Ubreva J, de la Rica L, Branco MR, Martín J, Ballestar E. TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells. Nucleic Acids Res 2017; 45:10002-10017. [PMID: 28973458 PMCID: PMC5622316 DOI: 10.1093/nar/gkx666] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022] Open
Abstract
The plasticity of myeloid cells is illustrated by a diversity of functions including their role as effectors of innate immunity as macrophages (MACs) and bone remodelling as osteoclasts (OCs). TET2, a methylcytosine dioxygenase highly expressed in these cells and frequently mutated in myeloid leukemias, may be a key contributor to this plasticity. Through transcriptomic and epigenomic analyses, we investigated 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and gene expression changes in two divergent terminal myeloid differentiation processes, namely MAC and OC differentiation. MACs and OCs undergo highly similar 5hmC and 5mC changes, despite their wide differences in gene expression. Many TET2- and thymine-DNA glycosylase (TDG)-dependent 5mC and 5hmC changes directly activate the common terminal myeloid differentiation programme. However, the acquisition of differential features between MACs and OCs also depends on TET2/TDG. In fact, 5mC oxidation precedes differential histone modification changes between MACs and OCs. TET2 and TDG downregulation impairs the acquisition of such differential histone modification and expression patterns at MAC-/OC-specific genes. We prove that the histone H3K4 methyltransferase SETD1A is differentially recruited between MACs and OCs in a TET2-dependent manner. We demonstrate a novel role of these enzymes in the establishment of specific elements of identity and function in terminal myeloid differentiation.
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Affiliation(s)
- Antonio Garcia-Gomez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Tianlu Li
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Martin Kerick
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de La Salud (PTS), Granada, Spain
| | - Francesc Català-Moll
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Natalia R Comet
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lorenzo de la Rica
- Barts and The London School of Medicine and Dentistry, Centre for Neuroscience & Trauma, Blizard Institute, 4 Newark Street, London E1 2AT, UK
| | - Miguel R Branco
- Barts and The London School of Medicine and Dentistry, Centre for Neuroscience & Trauma, Blizard Institute, 4 Newark Street, London E1 2AT, UK
| | - Javier Martín
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de La Salud (PTS), Granada, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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24
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5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes. Proc Natl Acad Sci U S A 2017; 114:E7812-E7821. [PMID: 28847947 DOI: 10.1073/pnas.1708044114] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
5-hydroxymethylcytosine (5hmC) occurs at maximal levels in postmitotic neurons, where its accumulation is cell-specific and correlated with gene expression. Here we demonstrate that the distribution of 5hmC in CG and non-CG dinucleotides is distinct and that it reflects the binding specificity and genome occupancy of methylcytosine binding protein 2 (MeCP2). In expressed gene bodies, accumulation of 5hmCG acts in opposition to 5mCG, resulting in "functional" demethylation and diminished MeCP2 binding, thus facilitating transcription. Non-CG hydroxymethylation occurs predominantly in CA dinucleotides (5hmCA) and it accumulates in regions flanking active enhancers. In these domains, oxidation of 5mCA to 5hmCA does not alter MeCP2 binding or expression of adjacent genes. We conclude that the role of 5-hydroxymethylcytosine in postmitotic neurons is to functionally demethylate expressed gene bodies while retaining the role of MeCP2 in chromatin organization.
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25
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Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X. MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Nucleic Acids Res 2017; 45:2396-2407. [PMID: 27903915 PMCID: PMC5389568 DOI: 10.1093/nar/gkw1184] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5΄-CACGTG-3΄. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms. Crystallization of MAX with a 5caC modified E-box oligonucleotide revealed that MAX Arg36 recognizes 5caC using a 5caC–Arg–Guanine triad, with the next nearest residue to the carboxylate group being Arg60. In an analysis of >800 primary multiple myelomas, MAX alterations occurred at a frequency of ∼3%, more than half of which were single nucleotide substitutions affecting a basic clamp-like interface important for DNA interaction. Among these, arginines 35, 36 and 60 were the most frequently altered. In vitro binding studies showed that whereas mutation of Arg36 (R36W) or Arg35 (R35H/L) completely abolished DNA binding, mutation of Arg60 (R60Q) significantly reduced DNA binding, but retained a preference for the 5caC modified E-box. Interestingly, MAX alterations define a subset of myeloma patients with lower MYC expression and a better overall prognosis. Together these data indicate that MAX can act as a direct epigenetic sensor of E-box cytosine modification states and that local CpG modification and MAX variants converge to modulate the MAX-MYC transcriptional network.
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Affiliation(s)
- Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin G Barwick
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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26
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Shu S, Xu Y, Xie L, Ouyang Y. The role of C/EBPβ phosphorylation in modulating membrane phospholipids repairing in LPS-induced human lung/bronchial epithelial cells. Gene 2017; 629:76-85. [PMID: 28760550 PMCID: PMC7125708 DOI: 10.1016/j.gene.2017.07.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 06/22/2017] [Accepted: 07/27/2017] [Indexed: 11/19/2022]
Abstract
Acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is a common critical emergency with high mortality in clinical practice. The key mechanism of ALI/ARDS is that the excessive inflammatory response damages the integrity of alveolar and bronchial cell membrane and thus affects their basic function. Phospholipids are the main component of cell membranes. Phospholipase A2 (PLA2), which catalyzes the cleavage of membrane phospholipids, is the most important inflammatory mediator of ALI. However, clara cell secretory protein 1 (CCSP1), an endogenous PLA2 inhibitor can increase the self-defense of membrane phospholipids. Thus, CCSP1 up-regulation and PLA2 inhibition constitutes an effective method for ensuring the stability of membrane phospholipids and for the treatment of ALI/ARDS. In the present study, we developed an in vitro model of ALI via lipopolysaccharide (LPS) stimulation of a human bronchial epithelial cell line, BEAS-2B, and assessed the mRNA and protein levels of CCSP1 and PLA2 in the model cells. The results demonstrated LPS induction inhibited the transcription and protein expression of CCSP1, but only the protein level of membrane associated PLA2 was increased, suggesting that in the in vitro ALI model, abnormally regulated CCSP1 transcription plays a crucial role in the damage of cell membrane. To find out the reason that CCSP1 expression was decreased in the ALI model, we predicted, by means of bioinformatics, putative transcription factors which would bind to CCSP1 promoter, examined their background and expression, and found that a transcription factor, CCAAT/enhancer binding protein β (C/EBP β), was correlated with the transcription of CCSP1 in the in vitro ALI model, and its phosphorylation in the model was decreased. CHIP-PCR and luciferase reporter assay revealed that C/EBP β bound to CCSP1 promoter and facilitated its transcription. Therefore, we conclude that there is a C/EBP β/CCSP1/PLA2 pathway in the in vitro ALI model. The study of underlying mechanism show that the activity of C/EBP β depends on its phosphorylation:LPS stimulation reduced C/EBP β phosphorylation and suppressed the transcription of CCSP1 in BEAS-2B cells, which resulted in enhanced PLA2 and the consequent membrane damage. And further study shows that overexpression of CDK2(Cyclindependent kinase 2), promoted the phosphorylation of C/EBP β and inhibited PLA2 through the C/EBP β/CCSP1/PLA2 pathway, so as to attenuate membrane damage. The significance of this study lies in that artificial C/EBP β phosphorylation regulation may ease the membrane damage in ALI and improve membrane repair. CDK2 over-expression promotes C/EBPβ phosphorylation and improves membrane repair through C/EBPβ/CCSP/PLA2 pathway in ALI.
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Affiliation(s)
- Shiyu Shu
- Anesthesiology Department, Children's Hospital of FudanUniversity,Shanghai,201102, China.
| | - Yan Xu
- Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014,China
| | - Ling Xie
- Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014,China
| | - Yufang Ouyang
- Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014,China
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27
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Ding B, Wan LZ, Zhang YQ. Biosafety Evaluation of Three Sodium Lauryl N-Amino Acids Synthesized from Silk Industrial Waste in Mice. J SURFACTANTS DETERG 2017. [DOI: 10.1007/s11743-017-1995-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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28
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Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci U S A 2017; 114:E1633-E1640. [PMID: 28193886 DOI: 10.1073/pnas.1618353114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Accurate enhancer identification is critical for understanding the spatiotemporal transcriptional regulation during development as well as the functional impact of disease-related noncoding genetic variants. Computational methods have been developed to predict the genomic locations of active enhancers based on histone modifications, but the accuracy and resolution of these methods remain limited. Here, we present an algorithm, regulatory element prediction based on tissue-specific local epigenetic marks (REPTILE), which integrates histone modification and whole-genome cytosine DNA methylation profiles to identify the precise location of enhancers. We tested the ability of REPTILE to identify enhancers previously validated in reporter assays. Compared with existing methods, REPTILE shows consistently superior performance across diverse cell and tissue types, and the enhancer locations are significantly more refined. We show that, by incorporating base-resolution methylation data, REPTILE greatly improves upon current methods for annotation of enhancers across a variety of cell and tissue types. REPTILE is available at https://github.com/yupenghe/REPTILE/.
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29
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Syed KS, He X, Tillo D, Wang J, Durell SR, Vinson C. 5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) Enhance the DNA Binding of CREB1 to the C/EBP Half-Site Tetranucleotide GCAA. Biochemistry 2016; 55:6940-6948. [PMID: 27951657 DOI: 10.1021/acs.biochem.6b00796] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In human and mouse stem cells and brain, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) can occur outside of CG dinucleotides. Using protein binding microarrays (PBMs) containing 60-mer DNA probes, we evaluated the effect of 5mC and 5hmC on one DNA strand on the double-stranded DNA binding of the mouse B-ZIP transcription factors (TFs) CREB1, ATF1, and JUND. 5mC inhibited binding of CREB1 to the canonical CRE half-site |GTCA but enhanced binding to the C/EBP half-site |GCAA. 5hmC inhibited binding of CREB1 to all 8-mers except TGAT|GCAA, where binding is enhanced. We observed similar DNA binding patterns with ATF1, a closely related B-ZIP domain. In contrast, both 5mC and 5hmC inhibited binding of JUND. These results identify new DNA sequences that are well-bound by CREB1 and ATF1 only when they contain 5mC or 5hmC. Analysis of two X-ray structures examines the consequences of 5mC and 5hmC on DNA binding by CREB and FOS|JUN.
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Affiliation(s)
- Khund Sayeed Syed
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Ximiao He
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Desiree Tillo
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Jun Wang
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Stewart R Durell
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Charles Vinson
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
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30
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Bell CG. Insights in human epigenomic dynamics through comparative primate analysis. Genomics 2016; 108:115-125. [DOI: 10.1016/j.ygeno.2016.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
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31
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Khund-Sayeed S, He X, Holzberg T, Wang J, Rajagopal D, Upadhyay S, Durell SR, Mukherjee S, Weirauch MT, Rose R, Vinson C. 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4. Integr Biol (Camb) 2016; 8:936-45. [PMID: 27485769 DOI: 10.1039/c6ib00079g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We evaluated DNA binding of the B-HLH family members TCF4 and USF1 using protein binding microarrays (PBMs) containing double-stranded DNA probes with cytosine on both strands or 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) on one DNA strand and cytosine on the second strand. TCF4 preferentially bound the E-box motif (CAN|NTG) with strongest binding to the 8-mer CAG|GTGGT. 5mC uniformly decreases DNA binding of both TCF4 and USF1. The bulkier 5hmC also inhibited USF1 binding to DNA. In contrast, 5hmC dramatically enhanced TCF4 binding to E-box motifs ACAT|GTG and ACAC|GTG, being better bound than any 8-mer containing cytosine. Examination of X-ray structures of the closely related TCF3 and USF1 bound to DNA suggests TCF3 can undergo a conformational shift to preferentially bind to 5hmC while the USF1 basic region is bulkier and rigid precluding a conformation shift to bind 5hmC. These results greatly expand the regulatory DNA sequence landscape bound by TCF4.
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Affiliation(s)
- Syed Khund-Sayeed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA.
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Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M. Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression. Nucleic Acids Res 2016; 44:6756-69. [PMID: 27131363 PMCID: PMC5001587 DOI: 10.1093/nar/gkw316] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 04/13/2016] [Indexed: 01/31/2023] Open
Abstract
To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.
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Affiliation(s)
- Maxim Ivanov
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia Institute of Mathematics and Statistics, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Volker Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Isabel Barragan
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Von Eulers väg 8 IV, 17177 Stockholm, Sweden
| | - Philip Ewels
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Max Käller
- Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Tomas Axelsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory, Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, 17121 Stockholm, Sweden
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
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33
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Hashimoto H, Zhang X, Vertino PM, Cheng X. The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations. J Biol Chem 2015; 290:20723-20733. [PMID: 26152719 DOI: 10.1074/jbc.r115.656884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how the patterns of epigenetic modifications of DNA are generated, recognized, and erased. This includes covalent cytosine methylation of DNA and its associated oxidation states. An array of AdoMet-dependent methyltransferases, Fe(II)- and α-ketoglutarate-dependent dioxygenases, base excision glycosylases, and sequence-specific transcription factors is responsible for changing, maintaining, and interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases 5-methylcytosine and thymine (5-methyluracil).
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Affiliation(s)
- Hideharu Hashimoto
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Xing Zhang
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Paula M Vertino
- Departments of Radiation Oncology, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Xiaodong Cheng
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322.
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