201
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Yang X, Wang C, Nie H, Zhou J, He X, Ou C. Minichromosome maintenance gene family: potential therapeutic targets and prognostic biomarkers for lung squamous cell carcinoma. Aging (Albany NY) 2022; 14:9167-9185. [PMID: 36445337 PMCID: PMC9740372 DOI: 10.18632/aging.204399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022]
Abstract
The minichromosome maintenance (MCM) gene family comprises of ten members with key roles in eukaryotic DNA replication and are associated with the occurrence and progression of many tumors. However, whether the MCM family contributes to lung squamous cell carcinoma (LUSC) is unclear. In this study, we performed bioinformatic analysis to identify the roles of MCM genes in patients with LUSC. We also evaluated their differential gene expression, prognostic correlation, DNA methylation, functional enrichment of genetic alterations, and immunomodulation. According to the Tumor Immune Estimation Resource database, the expression of MCM2-10 mRNA was elevated in LUSC tissues. According to the Gene Expression Profiling Interactive Analysis database, MCM2-8 and MCM10 were considerably upregulated in LUSC tissues, and protein levels of all MCMs were increased in LUSC tissues. In addition, among the MCM family members, the expression of MCM3 and MCM7 showed the strongest correlation with the prognoses of patients with LUSC. To clarify the role and mechanisms of the MCM family, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment studies were performed. We detected a significant correlation between the expression patterns of MCM family members and infiltrating immune cells. In conclusion, our results improve the understanding of the aberrant expression of MCM family members in LUSC. These findings demonstrate the potential of the MCM family as therapeutic targets and biomarkers for the diagnosis and prognosis of LUSC.
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Affiliation(s)
- Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hui Nie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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202
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Patra P, Gao YQ. Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation. J Phys Chem B 2022; 126:9187-9206. [PMID: 36322688 DOI: 10.1021/acs.jpcb.2c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sequence-specific recognition of transcription factor (TF) binding motifs in the target site of DNA over the vast amount of non-target DNA is of primary importance for the transcriptional regulation of gene expression by the TFs. Binding of TFs to the target site of DNA relies not only on the direct contact formation but also on the structural and conformational features of DNA. Recognition of DNA structural features or shape readout by proteins is an important factor in the context of TF-DNA interaction. Based on the atomistic molecular simulation, here we report the sequence-dependent unique structural features, solvation, and ion-binding properties of biologically relevant AT- and GC-rich human TF binding motifs in DNA. Counterion and water distribution around the motif is found to be sensitive to the motif sequence, which is accompanied with the DNA shape features. The motif sequence affects the electrostatic potential along the grooves, and cytosine methylation alters the DNA shape features. Characteristic solvation properties of TF binding motif DNA fragments infer that an ionic environment and hydration influences are essential to describe TF-DNA interactions.
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Affiliation(s)
- Piya Patra
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen 518107, China
| | - Yi Qin Gao
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen 518107, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
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203
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Li G, Liu B, Yang J, Li X, Wang H, Wen H, He F. Acute Hypoxia Stress-Induced Apoptosis in Gill of Japanese Flounder ( Paralichthys olivaceus) by Modulating the Epas1/Bad Pathway. BIOLOGY 2022; 11:biology11111656. [PMID: 36421370 PMCID: PMC9687431 DOI: 10.3390/biology11111656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
The physiological responses and molecular mechanisms of apoptosis in Japanese flounder under hypoxic stress remain unclear. In the present study, we performed acute hypoxia stress on Japanese flounder (2.39 ± 0.84 mg/L) and detected gills responses in histomorphology and molecular mechanisms. The results showed that the volume of the interlamellar cell mass decreased and the gill lamellae prolonged, indicating the expansion of the respiratory surface area. Additionally, the fluorescence signal of apoptosis increased under hypoxic stress. In addition, the expression of two genes (EPAS1 and Bad) related to apoptosis increased about four-fold and two-fold, respectively, at 6 h of hypoxia. Meanwhile, the result of the dual-luciferase reporter assay showed that EPAS1 is a transcription factor, which could regulate (p < 0.05) the expression of the Bad gene, and we identified the binding site of EPAS1 was the AATGGAAAC sequence located near −766. DNA methylation assay showed that hypoxia affected the methylation status of CpG islands of EPAS1 and Bad genes. All results indicated that hypoxia could activate the EPAS1/Bad signal pathway to induce gill apoptosis of Japanese flounder. Our study provides new light on understanding the molecular mechanism of hypoxia-induced apoptosis in Japanese flounder.
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Affiliation(s)
| | | | | | | | | | | | - Feng He
- Correspondence: ; Tel.: +86-532-82031953
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204
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Dong Z, Zhou H. Pan-cancer landscape of aberrant DNA Methylation across childhood Cancers: Molecular Characteristics and Clinical relevance. Exp Hematol Oncol 2022; 11:89. [PMID: 36348462 PMCID: PMC9644499 DOI: 10.1186/s40164-022-00339-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Aberrant DNA methylation (DNAm) is an important epigenetic regulator in various cancers. Pan-cancer DNAm analyses have investigated the potential common mechanisms of DNAm in tumorigenesis. However, these pan-cancer studies focused on adult cancers rather than pediatric cancers, which may have distinct pathology and treatment responses. Here, we performed a pan-cancer analysis of genome-wide DNAm in over 2,000 samples from nine pediatric cancers to elucidate the DNAm landscape of pediatric cancers. We identified 217,586 differentially methylated CpG sites (DMCs) in pediatric cancers, with a tendency toward hypermethylation as opposed to hypomethylation (P = 0.02). Amongst them, 75.65% also presented DNAm alterations in adult cancers. In nine pediatric cancers, we defined 54 shared DMCs (SDMCs), which were also observed in at least one adult cancer type. Furthermore, methylation patterns in SDMCs influenced the transcription of several genes (MEIS1, MIA3, PCDHAC2, SH3BP4, and ATP8B1) involved in well-known cancer-related pathways and cancer hallmarks (FDR < 0.05). Moreover, SDMCs were significantly associated with patient survival, and this association was independent of sex, age, and tumor stage (P < 0.05). Interestingly, SDMCs could affect patient survival not only in the nine pediatric cancers that were used to identify SDMCs but also in other untested pediatric cancers (P < 0.05). Collectively, our data depicts a comprehensive landscape of aberrant DNA methylation in pediatric cancers, which is partly similar to that of adult cancers. We also suggest a potential clinical application of SDMCs as biomarkers for the prognosis of pediatric cancer.
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205
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Jing Zhang F, Zhang SW, Zhang S. Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3614-3623. [PMID: 34752400 DOI: 10.1109/tcbb.2021.3126623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Identification of transcription factor binding sites (TFBSs) is essential for revealing the rules of protein-DNA binding. Although some computational methods have been presented to predict TFBSs using epigenomic and sequence features, most of them ignore the common features among cross-cell types. It is still unclear to what extent the common features could help for this task. To this end, we proposed a new method (named Attention-augmented Convolutional Neural Network, or ACNN) to predict TFBSs. ACNN uses attention-augmented convolutional layers to capture global and local contexts in DNA sequences and employs the convolutional layers to capture features of histone modification markers. In addition, ACNN adopts the private and shared convolutional neural network (CNN) modules to learn specific and common features, respectively. To encourage the shared CNN module to learn the common features, adversarial training is applied in ACNN. The results on 253 ChIP-seq datasets show that ACNN outperforms other existing methods. The attention-augmented convolutional layers and adversarial training mechanism in ACNN can effectively improve the prediction performance. Moreover, in the case of limited labeled data, ACNN also performs better than a baseline method. We further visualize the convolution kernels as motifs to explain the interpretability of ACNN.
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206
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Li A, Koch Z, Ideker T. Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging. J Intern Med 2022; 292:733-744. [PMID: 35726002 DOI: 10.1111/joim.13533] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Numerous studies have shown that epigenetic age-an individual's degree of aging based on patterns of DNA methylation-can be computed and is associated with an array of factors including diet, lifestyle, genetics, and disease. One can expect that still further associations will emerge with additional aging research, but to what end? Prediction of age was an important first step, but-in our view-the focus must shift from chasing increasingly accurate age computations to understanding the links between the epigenome and the mechanisms and physiological changes of aging. Here, we outline emerging areas of epigenetic aging research that prioritize biological understanding and clinical application. First, we survey recent progress in epigenetic clocks, which are beginning to predict not only chronological age but aging outcomes such as all-cause mortality and onset of disease, or which integrate aging signals across multiple biological processes. Second, we discuss research that exemplifies how investigation of the epigenome is building a mechanistic theory of aging and informing clinical practice. Such examples include identifying methylation sites and the genes most strongly predictive of aging-a subset of which have shown strong potential as biomarkers of neurodegenerative disease and cancer; relating epigenetic clock predictions to hallmarks of aging; and using longitudinal studies of DNA methylation to characterize human disease, resulting in the discovery of epigenetic indications of type 1 diabetes and the propensity for psychotic experiences.
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Affiliation(s)
- Adam Li
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zane Koch
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
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207
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Pongor LS, Tlemsani C, Elloumi F, Arakawa Y, Jo U, Gross JM, Mosavarpour S, Varma S, Kollipara RK, Roper N, Teicher BA, Aladjem MI, Reinhold W, Thomas A, Minna JD, Johnson JE, Pommier Y. Integrative epigenomic analyses of small cell lung cancer cells demonstrates the clinical translational relevance of gene body methylation. iScience 2022; 25:105338. [DOI: 10.1016/j.isci.2022.105338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 10/31/2022] Open
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208
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Fuggle NR, Laskou F, Harvey NC, Dennison EM. A review of epigenetics and its association with ageing of muscle and bone. Maturitas 2022; 165:12-17. [PMID: 35841774 DOI: 10.1016/j.maturitas.2022.06.014] [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: 04/30/2022] [Revised: 06/21/2022] [Accepted: 06/30/2022] [Indexed: 10/31/2022]
Abstract
Ageing is defined as the 'increasing frailty of an organism with time that reduces the ability of that organism to deal with stress'. It has been suggested that epigenetics may underlie the observation that some individuals appear to age faster than others. Epigenetics is the study of changes which occur in an organism due to changes in expression of the genetic code rather than changes to the genetic code itself; that is, epigenetic mechanisms impact upon the function of DNA without changing the DNA sequence. It is important to recognise that epigenetic changes, in contrast to genetic changes, can vary according to different cell types and therefore can demonstrate significant tissue-specificity. There are different types of epigenetic mechanisms: histone modification, non-coding RNAs and DNA methylation. Epigenetic clocks have been developed using statistical techniques to identify the optimal combination of CpG sites (from methylation arrays) to correlate with chronological age. This review considers how epigenetic factors may affect rates of ageing of muscle and bone and provides an overview of current understanding in this area. We discuss studies using first-generation epigenetic clocks, as well as the second-generation iterations, which appear to show stronger associations with the ageing muscle phenotype. We also review epigenome-wide association studies that have been performed in various tissues examining relationships with osteoporosis and fracture. It is hoped that an understanding of this area will lead to interventions that might prevent or reduce rates of musculoskeletal ageing in later life.
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Affiliation(s)
- N R Fuggle
- MRC Lifecourse Epidemiology Centre, University of Southampton, SO16 6YD, United Kingdom of Great Britain and Northern Ireland
| | - F Laskou
- MRC Lifecourse Epidemiology Centre, University of Southampton, SO16 6YD, United Kingdom of Great Britain and Northern Ireland
| | - N C Harvey
- MRC Lifecourse Epidemiology Centre, University of Southampton, SO16 6YD, United Kingdom of Great Britain and Northern Ireland
| | - E M Dennison
- MRC Lifecourse Epidemiology Centre, University of Southampton, SO16 6YD, United Kingdom of Great Britain and Northern Ireland.
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209
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Sugimachi K, Araki H, Saito H, Masuda T, Miura F, Inoue K, Shimagaki T, Mano Y, Iguchi T, Morita M, Toh Y, Yoshizumi T, Ito T, Mimori K. Persistent epigenetic alterations in transcription factors after a sustained virological response in hepatocellular carcinoma. JGH Open 2022; 6:854-863. [PMID: 36514506 PMCID: PMC9730721 DOI: 10.1002/jgh3.12833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Background and Aim The risk of hepatocellular carcinoma (HCC) persists in a condition of sustained virologic response (SVR) after hepatitis C virus (HCV) eradication. Comprehensive molecular analyses were performed to test the hypothesis that epigenetic abnormalities present after an SVR play a role in hepatocarcinogenesis. Methods Whole-genome methylome and RNA sequencing were performed on HCV, SVR, and healthy liver tissue. Integrated analysis of the sequencing data focused on expression changes in transcription factors and their target genes, commonly found in HCV and SVR. Identified expression changes were validated in demethylated cultured HCC cell lines and an independent validation cohort. Results The coincidence rates of the differentially methylated regions between the HCV and SVR groups were 91% in the hypomethylated and 71% in the hypermethylated regions in tumorous tissues, and 37% in the hypomethylated and 36% in the hypermethylated regions in non-tumorous tissues. These results indicate that many epigenomic abnormalities persist even after an SVR was achieved. Integrated analysis identified 61 transcription factors and 379 other genes that had methylation abnormalities and gene expression changes in both groups. Validation cohort specified gene expression changes for 14 genes, and gene ontology pathway analysis revealed apoptotic signaling and inflammatory response were associated with these genes. Conclusion This study demonstrates that DNA methylation abnormalities, retained after HCV eradication, affect the expression of transcription factors and their target genes. These findings suggest that DNA methylation in SVR patients may be functionally important in carcinogenesis, and could serve as biomarkers to predict HCC occurrence.
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Affiliation(s)
- Keishi Sugimachi
- Department of Hepatobiliary‐Pancreatic SurgeryNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Hiromitsu Araki
- Department of Biochemistry, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan,Department of Business and Technology Management, Faculty of EconomicsKyushu UniversityFukuokaJapan
| | - Hideyuki Saito
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Takaaki Masuda
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Fumihito Miura
- Department of Biochemistry, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kentaro Inoue
- Department of Biochemistry, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan,Department of Surgery and Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Tomonari Shimagaki
- Department of Hepatobiliary‐Pancreatic SurgeryNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Yohei Mano
- Department of Hepatobiliary‐Pancreatic SurgeryNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Tomohiro Iguchi
- Department of Hepatobiliary‐Pancreatic SurgeryNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Masaru Morita
- Department of Gastroenterological SurgeryNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Yasushi Toh
- Department of Gastroenterological SurgeryNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takashi Ito
- Department of Biochemistry, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Koshi Mimori
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
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210
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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211
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Higham J, Kerr L, Zhang Q, Walker RM, Harris SE, Howard DM, Hawkins EL, Sandu AL, Steele JD, Waiter GD, Murray AD, Evans KL, McIntosh AM, Visscher PM, Deary IJ, Cox SR, Sproul D. Local CpG density affects the trajectory and variance of age-associated DNA methylation changes. Genome Biol 2022; 23:216. [PMID: 36253871 PMCID: PMC9575273 DOI: 10.1186/s13059-022-02787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Altered rates of aging inferred from these clocks are observed in human disease. However, the molecular mechanisms underpinning age-associated DNA methylation changes remain unknown. Local DNA sequence can program steady-state DNA methylation levels, but how it influences age-associated methylation changes is unknown. RESULTS We analyze longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs. We show that changes in methylation with age occur at 182,760 loci largely independently of variation in cell type proportions. These changes are especially apparent at 8322 low CpG density loci. Using SNP data from the same individuals, we demonstrate that methylation trajectories are affected by local sequence polymorphisms at 1487 low CpG density loci. More generally, we find that low CpG density regions are particularly prone to change and do so variably between individuals in people aged over 65. This differs from the behavior of these regions in younger individuals where they predominantly lose methylation. CONCLUSIONS Our results, which we reproduce in two independent groups of individuals, demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.
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Affiliation(s)
- Jonathan Higham
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Present address: Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Present address: School of Psychology, University of Exeter, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Emma L Hawkins
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca-Larisa Sandu
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - J Douglas Steele
- Division of Imaging Science and Technology, Medical School, University of Dundee, Dundee, UK
| | - Gordon D Waiter
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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212
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The Mutagenic Consequences of DNA Methylation within and across Generations. EPIGENOMES 2022; 6:epigenomes6040033. [PMID: 36278679 PMCID: PMC9624357 DOI: 10.3390/epigenomes6040033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic modification with wide-ranging consequences across the life of an organism. This modification can be stable, persisting through development despite changing environmental conditions. However, in other contexts, DNA methylation can also be flexible, underlying organismal phenotypic plasticity. One underappreciated aspect of DNA methylation is that it is a potent mutagen; methylated cytosines mutate at a much faster rate than other genetic motifs. This mutagenic property of DNA methylation has been largely ignored in eco-evolutionary literature, despite its prevalence. Here, we explore how DNA methylation induced by environmental and other factors could promote mutation and lead to evolutionary change at a more rapid rate and in a more directed manner than through stochastic genetic mutations alone. We argue for future research on the evolutionary implications of DNA methylation driven mutations both within the lifetime of organisms, as well as across timescales.
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213
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Nam AS, Dusaj N, Izzo F, Murali R, Myers RM, Mouhieddine TH, Sotelo J, Benbarche S, Waarts M, Gaiti F, Tahri S, Levine R, Abdel-Wahab O, Godley LA, Chaligne R, Ghobrial I, Landau DA. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat Genet 2022; 54:1514-1526. [PMID: 36138229 PMCID: PMC10068894 DOI: 10.1038/s41588-022-01179-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Somatic mutations in cancer genes have been detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, because mutated and wild-type cells are admixed, we have limited ability to link genotypes with phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing genotype, transcriptomes and methylomes in progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations result in myeloid over lymphoid bias, and an expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate, with dysregulated expression of lineage and leukemia stem cell markers. Mutated DNMT3A leads to preferential hypomethylation of polycomb repressive complex 2 targets and a specific CpG flanking motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics paves the road to defining the downstream consequences of mutations that drive clonal mosaicism.
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Affiliation(s)
- Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville Dusaj
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franco Izzo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Rekha Murali
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tarek H Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Waarts
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federico Gaiti
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sabrin Tahri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Irene Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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214
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Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. Nat Biotechnol 2022; 40:1520-1527. [PMID: 35606422 PMCID: PMC9546773 DOI: 10.1038/s41587-022-01307-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 04/04/2022] [Indexed: 01/02/2023]
Abstract
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, that accurately defines sequence recognition in terms of equilibrium binding constants or kinetic rates. This is achieved using a multi-layered maximum-likelihood framework that models both the molecular interactions and the data generation process. We show that ProBound quantifies transcription factor (TF) behavior with models that predict binding affinity over a range exceeding that of previous resources; captures the impact of DNA modifications and conformational flexibility of multi-TF complexes; and infers specificity directly from in vivo data such as ChIP-seq without peak calling. When coupled with an assay called KD-seq, it determines the absolute affinity of protein-ligand interactions. We also apply ProBound to profile the kinetics of kinase-substrate interactions. ProBound opens new avenues for decoding biological networks and rationally engineering protein-ligand interactions.
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Affiliation(s)
- H Tomas Rube
- Department of Bioengineering, University of California, Merced, Merced, CA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Basheer Becerra
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lucas A N Melo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Bach Viet Do
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Xiaoting Li
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Hammaad H Adam
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
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215
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Wang K, Dai R, Xia Y, Tian J, Jiao C, Mikhailova T, Zhang C, Chen C, Liu C. Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development. Epigenetics 2022; 17:1110-1127. [PMID: 34652256 PMCID: PMC9543113 DOI: 10.1080/15592294.2021.1993607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
DNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs was identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (>90%) of cGCPs was tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlights the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, the early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalogue of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies.
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Affiliation(s)
- Kangli Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rujia Dai
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Yan Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Jianghua Tian
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chuan Jiao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Tatiana Mikhailova
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Chunling Zhang
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, Ny, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA,Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, Ny, USA,CONTACT Chunyu Liu Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY13210, USA; Chao Chen Center for Medical Genetics, Central South University, Changsha, Hunan 410005, China
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216
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Kaplun DS, Kaluzhny DN, Prokhortchouk EB, Zhenilo SV. DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target. Acta Naturae 2022; 14:4-19. [PMID: 36694897 PMCID: PMC9844086 DOI: 10.32607/actanaturae.11822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA methylation is the most important epigenetic modification involved in the regulation of transcription, imprinting, establishment of X-inactivation, and the formation of a chromatin structure. DNA methylation in the genome is often associated with transcriptional repression and the formation of closed heterochromatin. However, the results of genome-wide studies of the DNA methylation pattern and transcriptional activity of genes have nudged us toward reconsidering this paradigm, since the promoters of many genes remain active despite their methylation. The differences in the DNA methylation distribution in normal and pathological conditions allow us to consider methylation as a diagnostic marker or a therapy target. In this regard, the need to investigate the factors affecting DNA methylation and those involved in its interpretation becomes pressing. Recently, a large number of protein factors have been uncovered, whose ability to bind to DNA depends on their methylation. Many of these proteins act not only as transcriptional activators or repressors, but also affect the level of DNA methylation. These factors are considered potential therapeutic targets for the treatment of diseases resulting from either a change in DNA methylation or a change in the interpretation of its methylation level. In addition to protein factors, a secondary DNA structure can also affect its methylation and can be considered as a therapy target. In this review, the latest research into the DNA methylation landscape in the genome has been summarized to discuss why some DNA regions avoid methylation and what factors can affect its level or interpretation and, therefore, can be considered a therapy target.
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Affiliation(s)
- D. S. Kaplun
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - D. N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - S. V. Zhenilo
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
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217
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Lu X, Yang S, Jie M, Wang S, Sun C, Wu L, Chang S, Pei P, Wang S, Zhang T, Wang L. Folate deficiency disturbs PEG10 methylation modifications in human spina bifida. Pediatr Res 2022; 92:987-994. [PMID: 34934172 DOI: 10.1038/s41390-021-01908-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/26/2021] [Accepted: 12/02/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Paternally expressed gene 10 (PEG10) is believed to be a key imprinted gene involved in placenta formation. However, its role in human folate-related spina bifida (SB) remains unclear. METHODS The methylation status of the germline differentially methylated region (gDMR) in the PEG10/sarcoglycan epsilon (SGCE) imprinted cluster was compared between SB patients and control samples. Moreover, the influence of ectopic PEG10 expression on apoptosis was assessed to explore the underlying mechanisms related to folate deficiency-induced aberrant gDMR methylation in SB. RESULTS The case group exhibited a significant increase in the methylation level of the gDMR and a marked reduction in the mRNA and protein expression of PEG10 compared with the control group. A prominent negative correlation was found between the folate level in brain tissue and gDMR methylation status (r = -0.62, P = 0.001). A cell model treated with a demethylating agent showed a significant elevation of PEG10 transcription level, as well as other imprinted genes in this cluster. In addition, the inhibition of PEG10 was found to be accompanied by aberrant activation of apoptosis in SB. CONCLUSIONS Our findings suggest that disturbed gDMR methylation of the PEG10/SGCE cluster due to folate deficiency is involved in SB through aberrant activation of apoptosis. IMPACT Disturbed genomic imprinting has been verified to be involved in neural tube defects (NTDs). However, little is known about the effect of ectopic expression of imprinted gene PEG10 on human NTDs. Aberrant methylation status of the germline differentially methylated region (gDMR) of PEG10/SGCE cluster due to folate deficiency has been found to result in the inhibition of PEG10 and has a marked association with an increased occurrence of spina bifida. Inhibited expression of PEG10 partly is found to be related to the abnormal activation of apoptosis in spina bifida.
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Affiliation(s)
- Xiaolin Lu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.,Institute of Basic Medicine, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100005, Beijing, China
| | - Shuyan Yang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Min Jie
- Department of Medical Genetics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Chunrong Sun
- Laboratory of Institute, Capital Institute of Pediatrics, Beijing, China
| | - Lihua Wu
- Department of Medical Genetics, Capital Institute of Pediatrics, 100020, Beijing, China
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Pei Pei
- Laboratory of Institute, Capital Institute of Pediatrics, Beijing, China
| | - Shuowen Wang
- Institute of Basic Medicine, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100005, Beijing, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China. .,Institute of Basic Medicine, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100005, Beijing, China.
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218
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MacKay H, Gunasekara CJ, Yam KY, Srisai D, Yalamanchili HK, Li Y, Chen R, Coarfa C, Waterland RA. Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index. SCIENCE ADVANCES 2022; 8:eabo3991. [PMID: 36170368 PMCID: PMC9519050 DOI: 10.1126/sciadv.abo3991] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Recent genome-wide association studies corroborate classical research on developmental programming indicating that obesity is primarily a neurodevelopmental disease strongly influenced by nutrition during critical ontogenic windows. Epigenetic mechanisms regulate neurodevelopment; however, little is known about their role in establishing and maintaining the brain's energy balance circuitry. We generated neuron and glia methylomes and transcriptomes from male and female mouse hypothalamic arcuate nucleus, a key site for energy balance regulation, at time points spanning the closure of an established critical window for developmental programming of obesity risk. We find that postnatal epigenetic maturation is markedly cell type and sex specific and occurs in genomic regions enriched for heritability of body mass index in humans. Our results offer a potential explanation for both the limited ontogenic windows for and sex differences in sensitivity to developmental programming of obesity and provide a rich resource for epigenetic analyses of developmental programming of energy balance.
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Affiliation(s)
- Harry MacKay
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chathura J. Gunasekara
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kit-Yi Yam
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Dollada Srisai
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Hari Krishna Yalamanchili
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Yumei Li
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert A. Waterland
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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219
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Zhao C, Biondic S, Vandal K, Björklund ÅK, Hagemann-Jensen M, Sommer TM, Canizo J, Clark S, Raymond P, Zenklusen DR, Rivron N, Reik W, Petropoulos S. Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids. Genome Res 2022; 32:1627-1641. [PMID: 35948369 PMCID: PMC9528977 DOI: 10.1101/gr.276665.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022]
Abstract
The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; ∼25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the trophectoderm (TE) lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation-DNA methylation and microRNAs (miRNAs)-likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.
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Affiliation(s)
- Cheng Zhao
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Savana Biondic
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Katherine Vandal
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Åsa K Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, SE-752 37 Uppsala, Sweden
| | | | - Theresa Maria Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jesica Canizo
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Stephen Clark
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Pascal Raymond
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Daniel R Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
- Center for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Sophie Petropoulos
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, 14186 Stockholm, Sweden
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
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220
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Fernandes V, Preeti K, Sood A, Nair KP, Khan S, Rao BSS, Khatri DK, Singh SB. Neuroepigenetic Changes in DNA Methylation Affecting Diabetes-Induced Cognitive Impairment. Cell Mol Neurobiol 2022:10.1007/s10571-022-01278-5. [PMID: 36138280 DOI: 10.1007/s10571-022-01278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
Chronic diabetic conditions have been associated with certain cerebral complications, that include neurobehavioral dysfunctional patterns and morphological alterations of neurons, especially the hippocampus. Neuroanatomical studies done by the authors have shown decreased total dendritic length, intersections, dendritic length per branch order and nodes in the CA1 hippocampal region of the diabetic brain as compared to its normal control group, indicating reduced dendritic arborization of the hippocampal CA1 neurons. Epigenetic alterations in the brain are well known to affect age-associated disorders, however its association with the evolving diabetes-induced damage in the brain is still not fully understood. DNA hypermethylation within the neurons, tend to silent the gene expression of several regulatory proteins. The findings in the study have shown an increase in global DNA methylation in palmitic acid-induced lipotoxic Neuro-2a cells as well as within the diabetic mice brain. Inhibiting DNA methylation, restored the levels of HSF1 and certain HSPs, suggesting plausible effect of DNMTs in maintaining the proteostasis and synaptic fidelity. Neuroinflammation, as exhibited by the astrocyte activation (GFAP), were further significantly decreased in the 5-azadeoxycytidine group (DNMT inhibitor). This was further evidenced by decrease in proinflammatory cytokines TNF⍺, IL-6, and mediators iNOS and Phospho-NFkB. Our results suggest that changes in DNA methylation advocate epigenetic dysregulation and its involvement in disrupting the synaptic exactitude in the hippocampus of diabetic mice model, providing an insight into the pathophysiology of diabetes-induced neuroepigenetic changes.
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Affiliation(s)
- Valencia Fernandes
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kumari Preeti
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Anika Sood
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kala P Nair
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Sabiya Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - B S Shankaranarayana Rao
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
| | - Shashi Bala Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
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221
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Laufer BI, Hasegawa Y, Zhang Z, Hogrefe CE, Del Rosso LA, Haapanen L, Hwang H, Bauman MD, Van de Water J, Taha AY, Slupsky CM, Golub MS, Capitanio JP, VandeVoort CA, Walker CK, LaSalle JM. Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models. Nat Commun 2022; 13:5538. [PMID: 36130949 PMCID: PMC9492781 DOI: 10.1038/s41467-022-33162-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Maternal obesity during pregnancy is associated with neurodevelopmental disorder (NDD) risk. We utilized integrative multi-omics to examine maternal obesity effects on offspring neurodevelopment in rhesus macaques by comparison to lean controls and two interventions. Differentially methylated regions (DMRs) from longitudinal maternal blood-derived cell-free fetal DNA (cffDNA) significantly overlapped with DMRs from infant brain. The DMRs were enriched for neurodevelopmental functions, methylation-sensitive developmental transcription factor motifs, and human NDD DMRs identified from brain and placenta. Brain and cffDNA methylation levels from a large region overlapping mir-663 correlated with maternal obesity, metabolic and immune markers, and infant behavior. A DUX4 hippocampal co-methylation network correlated with maternal obesity, infant behavior, infant hippocampal lipidomic and metabolomic profiles, and maternal blood measurements of DUX4 cffDNA methylation, cytokines, and metabolites. We conclude that in this model, maternal obesity was associated with changes in the infant brain and behavior, and these differences were detectable in pregnancy through integrative analyses of cffDNA methylation with immune and metabolic factors.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Yu Hasegawa
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Zhichao Zhang
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Casey E Hogrefe
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Laura A Del Rosso
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - Lori Haapanen
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Hyeyeon Hwang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
| | - Melissa D Bauman
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
| | - Judy Van de Water
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Internal Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Ameer Y Taha
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Nutrition, University of California Davis, Davis, CA, 95616, USA
| | - Mari S Golub
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
| | - John P Capitanio
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Psychology, University of California Davis, Davis, CA, 95616, USA
| | - Catherine A VandeVoort
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Cheryl K Walker
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA
- California National Primate Research Center, University of California Davis, Davis, CA, 95616, USA
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA
- Department of Obstetrics and Gynecology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, School of Medicine, University of California Davis, Sacramento, CA, 95817, USA.
- Perinatal Origins of Disparities Center, University of California Davis, Davis, CA, 95616, USA.
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222
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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 PMCID: PMC9485127 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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223
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Pantier R, Chhatbar K, Alston G, Lee HY, Bird A. High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro. STAR Protoc 2022; 3:101490. [PMID: 35776646 PMCID: PMC9243297 DOI: 10.1016/j.xpro.2022.101490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
High-throughput sequencing SELEX (HT-SELEX) is a powerful technique for unbiased determination of preferred target motifs of DNA-binding proteins in vitro. The procedure depends upon selection of DNA binding sites from a random library of oligonucleotides by purifying protein-DNA complexes and amplifying bound DNA using the polymerase chain reaction. Here, we describe an optimized step-by-step protocol for HT-SELEX compatible with Illumina sequencing. We also introduce a bioinformatic pipeline (eme_selex) facilitating the detection of promiscuous DNA binding by analyzing the enrichment of all possible k-mers. For complete details on the use and execution of this protocol, please refer to Pantier et al. (2021).
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Affiliation(s)
- Raphaël Pantier
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK.
| | - Kashyap Chhatbar
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK; Informatics Forum, School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - Grace Alston
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Heng Yang Lee
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Adrian Bird
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK.
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224
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Cui K, Yao X, Wei Z, yang Y, Liu X, Huang Z, Huo H, Tang J, Xie Y. Poor prognosis, hypomethylation, and immune infiltrates are associated with downregulation of INMT in head and neck squamous cell carcinoma. Front Genet 2022; 13:917344. [PMID: 36186458 PMCID: PMC9520724 DOI: 10.3389/fgene.2022.917344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Indiolethylamine-N-methyltransferase (INMT) is a methyltransferase responsible for transferring methyl groups from methyl donor SAM to its substrate. S-adenosyl-l-methionine (SAM), obtained from the methionine cycle, is a naturally occurring sulfonium compound that is vital to cellular metabolism. The expression of INMT is down-regulated in many tumorous tissues, and it may contribute to tumor invasion and metastasis. Nevertheless, the expression of INMT and its relationship to methylation and immune infiltrates in head and neck squamous cell carcinoma (HNSC) remains a mystery. Thus, we evaluated expression, clinicopathological features, prognosis, several critical pathways, DNA methylation, and immune cell infiltration for the first time.Methods: Analysis of the clinicopathological characteristics of INMT expression, several tumor-related bioinformatics databases were utilized. In addition, the role of INMT expression was analyzed for prognosis. Several INMT-related pathways were enriched on the LinkedOmics website. In addition, we have analyzed the methylation of INMT in HNSC in detail by using several methylation databases. Lastly, the relationship between INMT gene expression and immune infiltration was analyzed with ssGSEA, Timer, and TISIDB.Results: In HNSC, mRNA and protein levels were significantly lower than in normal tissues. The low expression of INMT was statistically associated with T stage, histological grade, gender, smoking history, and alcohol consumption. HNSC patients with low INMT expression have a poorer OS (overall survival) compared to those with high levels of expression. In addition, the multivariate analysis revealed INMT expression to be a remarkable independent predictor of prognosis in HNSC patients. An analysis of gene enrichment showed that several pathways were enriched in INMT, including the Ras signaling pathway, the cGMP-PKG signaling pathway, and others. Moreover, methylation patterns of INMT detected in a variety of methylation databases are closely associated with mRNA expression and prognosis. Finally, INMT was significantly correlated with immune infiltration levels.Conclusion: HNSC with low levels of INMT exhibits poor survival, hypomethylation, and immune infiltration. For HNSC, this study presented evidence that INMT is both a biomarker of poor prognosis and a target of immunotherapy.
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Affiliation(s)
- Kun Cui
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi, China
| | - Xi Yao
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhengbo Wei
- Department of Head and Neck Tumor Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Yujia yang
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi, China
| | - Xinli Liu
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhongheng Huang
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Department of Head and Neck Tumor Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Huimin Huo
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi, China
| | - Jinping Tang
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Department of Head and Neck Tumor Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Ying Xie
- Guangxi Key Laboratory of High‐Incidence Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi, China
- Life Sciences Institute of Guangxi Medical University, Nanning, Guangxi, China
- *Correspondence: Ying Xie,
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225
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Chen S, Wang Y, Li D, Wang H, Zhao X, Yang J, Chen L, Guo M, Zhao J, Chen C, Zhou Y, Liang G, Xu L. Mechanisms Controlling MicroRNA Expression in Tumor. Cells 2022; 11:cells11182852. [PMID: 36139427 PMCID: PMC9496884 DOI: 10.3390/cells11182852] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are widely present in many organisms and regulate the expression of genes in various biological processes such as cell differentiation, metabolism, and development. Numerous studies have shown that miRNAs are abnormally expressed in tumor tissues and are closely associated with tumorigenesis. MiRNA-based cancer gene therapy has consistently shown promising anti-tumor effects and is recognized as a new field in cancer treatment. So far, some clinical trials involving the treatment of malignancies have been carried out; however, studies of miRNA-based cancer gene therapy are still proceeding slowly. Therefore, furthering our understanding of the regulatory mechanisms of miRNA can bring substantial benefits to the development of miRNA-based gene therapy or other combination therapies and the clinical outcome of patients with cancer. Recent studies have revealed that the aberrant expression of miRNA in tumors is associated with promoter sequence mutation, epigenetic alteration, aberrant RNA modification, etc., showing the complexity of aberrant expression mechanisms of miRNA in tumors. In this paper, we systematically summarized the regulation mechanisms of miRNA expression in tumors, with the aim of providing assistance in the subsequent elucidation of the role of miRNA in tumorigenesis and the development of new strategies for tumor prevention and treatment.
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Affiliation(s)
- Shipeng Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Ya Wang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Dongmei Li
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Hui Wang
- The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Xu Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Jing Yang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Longqing Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Ya Zhou
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Medical Physics, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (G.L.); (L.X.)
| | - Guiyou Liang
- Department of Cardiovascular Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550031, China
- Department of Cardiovascular Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (G.L.); (L.X.)
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (G.L.); (L.X.)
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226
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Uddin MDM, Nguyen NQH, Yu B, Brody JA, Pampana A, Nakao T, Fornage M, Bressler J, Sotoodehnia N, Weinstock JS, Honigberg MC, Nachun D, Bhattacharya R, Griffin GK, Chander V, Gibbs RA, Rotter JI, Liu C, Baccarelli AA, Chasman DI, Whitsel EA, Kiel DP, Murabito JM, Boerwinkle E, Ebert BL, Jaiswal S, Floyd JS, Bick AG, Ballantyne CM, Psaty BM, Natarajan P, Conneely KN. Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease. Nat Commun 2022; 13:5350. [PMID: 36097025 PMCID: PMC9468335 DOI: 10.1038/s41467-022-33093-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022] Open
Abstract
Age-related changes to the genome-wide DNA methylation (DNAm) pattern observed in blood are well-documented. Clonal hematopoiesis of indeterminate potential (CHIP), characterized by the age-related acquisition and expansion of leukemogenic mutations in hematopoietic stem cells (HSCs), is associated with blood cancer and coronary artery disease (CAD). Epigenetic regulators DNMT3A and TET2 are the two most frequently mutated CHIP genes. Here, we present results from an epigenome-wide association study for CHIP in 582 Cardiovascular Health Study (CHS) participants, with replication in 2655 Atherosclerosis Risk in Communities (ARIC) Study participants. We show that DNMT3A and TET2 CHIP have distinct and directionally opposing genome-wide DNAm association patterns consistent with their regulatory roles, albeit both promoting self-renewal of HSCs. Mendelian randomization analyses indicate that a subset of DNAm alterations associated with these two leading CHIP genes may promote the risk for CAD.
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Affiliation(s)
- M D Mesbah Uddin
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ngoc Quynh H Nguyen
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Akhil Pampana
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Tetsushi Nakao
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jan Bressler
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Michael C Honigberg
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Romit Bhattacharya
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Gabriel K Griffin
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Varuna Chander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Genetics and Genomics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Genetics and Genomics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, 02118, USA
- Framingham Heart Study, Boston University and NHLBI/NIH, Framingham, MA, 01702, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Daniel I Chasman
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27516, USA
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, 27516, USA
| | - Douglas P Kiel
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, 02131, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joanne M Murabito
- Framingham Heart Study, Boston University and NHLBI/NIH, Framingham, MA, 01702, USA
- Department of Medicine, Section of General Internal Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, 02118, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 20815, USA
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, 98101, USA
| | - Pradeep Natarajan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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227
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DNA Methylation in Regulatory T Cell Differentiation and Function: Challenges and Opportunities. Biomolecules 2022; 12:biom12091282. [PMID: 36139121 PMCID: PMC9496199 DOI: 10.3390/biom12091282] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
As a bona fide epigenetic marker, DNA methylation has been linked to the differentiation and function of regulatory T (Treg) cells, a subset of CD4 T cells that play an essential role in maintaining immune homeostasis and suppressing autoimmunity and antitumor immune response. DNA methylation undergoes dynamic regulation involving maintenance of preexisting patterns, passive and active demethylation, and de novo methylation. Scattered evidence suggests that these processes control different stages of Treg cell lifespan ranging from lineage induction to cell fate maintenance, suppression of effector T cells and innate immune cells, and transdifferentiation. Despite significant progress, it remains to be fully explored how differential DNA methylation regulates Treg cell fate and immunological function. Here, we review recent progress and discuss the questions and challenges for further understanding the immunological roles and mechanisms of dynamic DNA methylation in controlling Treg cell differentiation and function. We also explore the opportunities that these processes offer to manipulate Treg cell suppressive function for therapeutic purposes by targeting DNA methylation.
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228
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Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Rażew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP. Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function. SCIENCE ADVANCES 2022; 8:eabm2427. [PMID: 36070377 PMCID: PMC9451156 DOI: 10.1126/sciadv.abm2427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor-binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germ line. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), respectively, illuminating TET function in transcriptional responses and pluripotency support.
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Affiliation(s)
- Mirunalini Ravichandran
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 1301, San Francisco, CA 94143, USA
- Universität Stuttgart, Abteilung Biochemie, Institute für Biochemie und Technische Biochemie, Allmandring 31, Stuttgart D-70569, Germany
| | - Dominik Rafalski
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Claudia I. Davies
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | | | - Xinsheng Nan
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | | | - Annika Kotter
- Johannes-Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Staudingerweg 5, 55128 Mainz, Germany
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Andrew H. Wang
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Marek Wojciechowski
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Michał Rażew
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Issam M. Mayyas
- University of Otago, Department of Pathology, Dunedin 9016, New Zealand
| | - Olga Kardailsky
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Uwe Schwartz
- University of Regensburg, Computational Core Unit, 93053 Regensburg, Germany
| | - Krzysztof Zembrzycki
- Institute of Fundamental Technological Research, Department of Biosystems and Soft Matter PAS, Pawińskiego 5B, Warsaw, Poland
| | - Ian M. Morison
- University of Otago, Department of Pathology, Dunedin 9016, New Zealand
| | - Mark Helm
- Johannes-Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Staudingerweg 5, 55128 Mainz, Germany
| | - Dieter Weichenhan
- German Cancer Research Center (DKFZ), Division of Cancer Epigenomics, Heidelberg, Germany
| | - Renata Z. Jurkowska
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Christoph Plass
- German Cancer Research Center (DKFZ), Division of Cancer Epigenomics, Heidelberg, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, James-Franck Str. 1, 85748 Garching, Germany
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS (IBB), Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Timothy A. Hore
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Tomasz P. Jurkowski
- Universität Stuttgart, Abteilung Biochemie, Institute für Biochemie und Technische Biochemie, Allmandring 31, Stuttgart D-70569, Germany
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
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Song H, Liu Y, Tan Y, Zhang Y, Jin W, Chen L, Wu S, Yan J, Li J, Chen Z, Chen S, Wang K. Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia. Blood 2022; 140:1132-1144. [PMID: 35653587 PMCID: PMC9461475 DOI: 10.1182/blood.2021014945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genetic alternations can occur at noncoding regions, but how they contribute to cancer pathogenesis is poorly understood. Here, we established a mutational landscape of cis-regulatory regions (CREs) in acute promyelocytic leukemia (APL) based on whole-genome sequencing analysis of paired tumor and germline samples from 24 patients and epigenetic profiling of 16 patients. Mutations occurring in CREs occur preferentially in active enhancers bound by the complex of master transcription factors in APL. Among significantly enriched mutated CREs, we found a recurrently mutated region located within the third intron of WT1, an essential regulator of normal and malignant hematopoiesis. Focusing on noncoding mutations within this WT1 intron, an analysis on 169 APL patients revealed that somatic mutations were clustered into a focal hotspot region, including one site identified as a germline polymorphism contributing to APL risk. Significantly decreased WT1 expression was observed in APL patients bearing somatic and/or germline noncoding WT1 variants. Furthermore, biallelic WT1 inactivation was recurrently found in APL patients with noncoding WT1 variants, which resulted in the complete loss of WT1. The high incidence of biallelic inactivation suggested the tumor suppressor activity of WT1 in APL. Mechanistically, noncoding WT1 variants disrupted MYB binding on chromatin and suppressed the enhancer activity and WT1 expression through destroying the chromatin looping formation. Our study highlights the important role of noncoding variants in the leukemogenesis of APL.
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Affiliation(s)
- Huan Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yabin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shishuang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsong Yan
- Department of Hematology, the Second Hospital of Dalian Medical University, Dalian, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
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Aivalioti MM, Bartholdy BA, Pradhan K, Bhagat TD, Zintiridou A, Jeong JJ, Thiruthuvanathan VJ, Pujato M, Paranjpe A, Zhang C, Levine RL, Viny AD, Wickrema A, Verma A, Will B. PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation. Blood Cancer Discov 2022; 3:444-467. [PMID: 35820129 PMCID: PMC9894728 DOI: 10.1158/2643-3230.bcd-21-0226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/05/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022] Open
Abstract
Cytosine hypermethylation in and around DNA-binding sites of master transcription factors, including PU.1, occurs in aging hematopoietic stem cells following acquired loss-of-function mutations of DNA methyl-cytosine dioxygenase ten-eleven translocation-2 (TET2), albeit functional relevance has been unclear. We show that Tet2-deficient mouse hematopoietic stem and progenitor cells undergo malignant transformation upon compromised gene regulation through heterozygous deletion of an upstream regulatory region (UREΔ/WT) of the PU.1 gene. Although compatible with multilineage blood formation at young age, Tet2-deficient PU.1 UREΔ/WT mice develop highly penetrant, transplantable acute myeloid leukemia (AML) during aging. Leukemic stem and progenitor cells show hypermethylation at putative PU.1-binding sites, fail to activate myeloid enhancers, and are hallmarked by a signature of genes with impaired expression shared with human AML. Our study demonstrates that Tet2 and PU.1 jointly suppress leukemogenesis and uncovers a methylation-sensitive PU.1-dependent gene network as a unifying molecular vulnerability associated with AML. SIGNIFICANCE We identify moderately impaired PU.1 mRNA expression as a biological modality predisposing Tet2-deficient hematopoietic stem and progenitor cells to malignant transformation. Our study furthermore uncovers a methylation-sensitive PU.1 gene network as a common feature of myeloid leukemia potentially allowing for the identification of patients at risk for malignant transformation. See related commentary by Schleicher and Pietras, p. 378. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Graduate Programs in the Biomedical Sciences, Albert Einstein College of Medicine, Bronx, New York
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Kith Pradhan
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Tushar D Bhagat
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Jong Jin Jeong
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Victor J Thiruthuvanathan
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chi Zhang
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Ross L Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron D Viny
- Department of Genetics and Development, Columbia University, New York, New York
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Amit Verma
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
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231
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DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation. J Biol Chem 2022; 298:102462. [PMID: 36067881 PMCID: PMC9530848 DOI: 10.1016/j.jbc.2022.102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
Specific DNA methylation at CpG and non-CpG sites is essential for chromatin regulation. The DNA methyltransferase DNMT3A interacts with target sites surrounded by variable DNA sequences with its TRD and RD loops, but the functional necessity of these interactions is unclear. We investigated CpG and non-CpG methylation in a randomized sequence context using WT DNMT3A and several DNMT3A variants containing mutations at DNA-interacting residues. Our data revealed that the flanking sequence of target sites between the −2 and up to the +8 position modulates methylation rates >100-fold. Non-CpG methylation flanking preferences were even stronger and favor C(+1). R836 and N838 in concert mediate recognition of the CpG guanine. R836 changes its conformation in a flanking sequence-dependent manner and either contacts the CpG guanine or the +1/+2 flank, thereby coupling the interaction with both sequence elements. R836 suppresses activity at CNT sites but supports methylation of CAC substrates, the preferred target for non-CpG methylation of DNMT3A in cells. N838 helps to balance this effect and prevent the preference for C(+1) from becoming too strong. Surprisingly, we found L883 reduces DNMT3A activity despite being highly conserved in evolution. However, mutations at L883 disrupt the DNMT3A-specific DNA interactions of the RD loop, leading to altered flanking sequence preferences. Similar effects occur after the R882H mutation in cancer cells. Our data reveal that DNMT3A forms flexible and interdependent interaction networks with the CpG guanine and flanking residues that ensure recognition of the CpG and efficient methylation of the cytosine in contexts of variable flanking sequences.
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232
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Lin L, Wang S, Zhang J, Song X, Zhang D, Cheng W, Cui M, Long Y, Xing Z. Integrative analysis of transcriptome and metabolome reveals the effect of DNA methylation of chalcone isomerase gene in promoter region on Lithocarpus polystachyus Rehd flavonoids. Synth Syst Biotechnol 2022; 7:928-940. [PMID: 35664927 PMCID: PMC9149025 DOI: 10.1016/j.synbio.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/26/2022] [Accepted: 05/16/2022] [Indexed: 11/01/2022] Open
Abstract
Metabolite biosynthesis is regulated by gene expression, which is altered by DNA methylation in the promoter region. Chalcone isomerase (CHI) gene encodes a key enzyme in the Lithocarpus polystachyus Rehd flavonoid pathway, and the expression of L. polystachyus CHI (LpCHI) is closely related to the synthesis of flavonoid metabolites. In this study, we analyzed the DNA methylation site of the LpCHI promoter and its effect on gene expression and metabolite accumulation. The proportions of three types of LpCHI promoter DNA methylation are 7.5%, 68.75%, 18.75%, determined by bisulfite sequencing. Transcriptome sequencing shows that LpCHI is strongly up-regulated in LpCHI promoter methylation Type A but down-regulated in LpCHI promoter methylation Type B and Type C. The expression of LpCHI shows no significant difference between Type B and Type C. Moreover, nine kinds of differentially expressed transcription factors (DETFs) bind to seven CpG-sites of the LpCHI promoter region to regulate LpCHI expression. The results of metabolomics show that differentially accumulated flavonoids are higher in LpCHI promoter methylation Type A than in LpCHI promoter methylation Type B and Type C. Additionally, a positive correlation was found between the LpCHI expression and flavonoids accumulation. These results show that the effect of CpG site-specificity on gene transcription is great than that of overall promoter DNA methylation on gene transcription. The mechanisms of flavonoid genes regulating metabolite accumulation are further revealed.
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233
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Vega-Benedetti AF, Loi E, Zavattari P. DNA methylation alterations caused by Leishmania infection may generate a microenvironment prone to tumour development. Front Cell Infect Microbiol 2022; 12:984134. [PMID: 36105147 PMCID: PMC9465093 DOI: 10.3389/fcimb.2022.984134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/10/2022] [Indexed: 01/10/2023] Open
Abstract
DNA methylation is an epigenetic signature consisting of a methyl group at the 5’ cytosine of CpG dinucleotides. Modifications in DNA methylation pattern have been detected in cancer and infectious diseases and may be associated with gene expression changes. In cancer development DNA methylation aberrations are early events whereas in infectious diseases these epigenetic changes may be due to host/pathogen interaction. In particular, in leishmaniasis, a parasitic disease caused by the protozoan Leishmania, DNA methylation alterations have been detected in macrophages upon infection with Leishmania donovani and in skin lesions from patients with cutaneous leishmaniasis. Interestingly, different types of cancers, such as cutaneous malignant lesions, lymphoma and hepatocellular carcinoma, have been diagnosed in patients with a history of leishmaniasis. In fact, it is known that there exists an association between cancer and infectious diseases. Leishmania infection may increase susceptibility to develop cancer, but the mechanisms involved are not entirely clear. Considering these aspects, in this review we discuss the hypothesis that DNA methylation alterations induced by Leishmania may trigger tumorigenesis in long term infection since these epigenetic modifications may enhance and accumulate during chronic leishmaniasis.
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234
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Marchal C, Defossez PA, Miotto B. Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38. Epigenetics 2022; 17:2122-2143. [PMID: 36000449 DOI: 10.1080/15592294.2022.2111135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation on CpGs regulates transcription in mammals, both by decreasing the binding of methylation-repelled factors and by increasing the binding of methylation-attracted factors. Among the latter, zinc finger proteins have the potential to bind methylated CpGs in a sequence-specific context. The protein ZBTB38 is unique in that it has two independent sets of zinc fingers, which recognize two different methylated consensus sequences in vitro. Here, we identify the binding sites of ZBTB38 in a human cell line, and show that they contain the two methylated consensus sequences identified in vitro. In addition, we show that the distribution of ZBTB38 sites is highly unusual: while 10% of the ZBTB38 sites are also bound by CTCF, the other 90% of sites reside in closed chromatin and are not bound by any of the other factors mapped in our model cell line. Finally, a third of ZBTB38 sites are found upstream of long and active CpG islands. Our work therefore validates ZBTB38 as a methyl-DNA binder in vivo and identifies its unique distribution in the genome.
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Affiliation(s)
- Claire Marchal
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | | | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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235
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C. Silva T, Young JI, Zhang L, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease. Nat Commun 2022; 13:4852. [PMID: 35982059 PMCID: PMC9388493 DOI: 10.1038/s41467-022-32475-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/01/2022] [Indexed: 01/17/2023] Open
Abstract
To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA methylation in two large independent blood-based studies in AD, the ADNI and AIBL studies, and identified 5 CpGs, mapped to the SPIDR, CDH6 genes, and intergenic regions, that are significantly associated with AD diagnosis. A cross-tissue analysis that combined these blood DNA methylation datasets with four brain methylation datasets prioritized 97 CpGs and 10 genomic regions that are significantly associated with both AD neuropathology and AD diagnosis. An out-of-sample validation using the AddNeuroMed dataset showed the best performing logistic regression model includes age, sex, immune cell type proportions, and methylation risk score based on prioritized CpGs in cross-tissue analysis (AUC = 0.696, 95% CI: 0.616 - 0.770, P-value = 2.78 × 10-5). Our study offers new insights into epigenetics in AD and provides a valuable resource for future AD biomarker discovery.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lanyu Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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Liu B, Wen H, Yang J, Li X, Li G, Zhang J, Wu S, Butts IAE, He F. Hypoxia Affects HIF-1/LDH-A Signaling Pathway by Methylation Modification and Transcriptional Regulation in Japanese Flounder (Paralichthys olivaceus). BIOLOGY 2022; 11:biology11081233. [PMID: 36009861 PMCID: PMC9405012 DOI: 10.3390/biology11081233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
Abstract
Simple Summary With global climate change and increased aquaculture production, fishes in natural waters or aquaculture systems are easily subjected to hypoxic stress. However, our understanding about their responsive mechanisms to hypoxia is still limited. Japanese flounder (Paralichthys olivaceus) is a widely cultivated marine economical flatfish, whose hypoxic responsive mechanisms are not fully researched. In this study, responses to hypoxia were investigated at blood physiological, biochemical, hormonal, and molecular levels. Responsive mechanisms of the HIF-1/LDH-A signaling pathway in epigenetic modification and transcriptional regulation were also researched. These results are important for enriching the theory of environmental responsive mechanisms and guiding aquaculture. Abstract Japanese flounder (Paralichthys olivaceus) responsive mechanisms to hypoxia are still not fully understood. Therefore, we performed an acute hypoxic treatment (dissolved oxygen at 2.07 ± 0.08 mg/L) on Japanese flounder. It was confirmed that the hypoxic stress affected the physiological phenotype through changes in blood physiology (RBC, HGB, WBC), biochemistry (LDH, ALP, ALT, GLU, TC, TG, ALB), and hormone (cortisol) indicators. Hypoxia inducible factor-1 (HIF-1), an essential oxygen homeostasis mediator in organisms consisting of an inducible HIF-1α and a constitutive HIF-1β, and its target gene LDH-A were deeply studied. Results showed that HIF-1α and LDH-A genes were co-expressed and significantly affected by hypoxic stress. The dual-luciferase reporter assay confirmed that transcription factor HIF-1 transcriptionally regulated the LDH-A gene, and its transcription binding sequence was GGACGTGA located at −2343~−2336. The DNA methylation status of HIF-1α and LDH-A genes were detected to understand the mechanism of environmental stress on genes. It was found that hypoxia affected the HIF-1α gene and LDH-A gene methylation levels. The study uncovered HIF-1/LDH-A signaling pathway responsive mechanisms of Japanese flounder to hypoxia in epigenetic modification and transcriptional regulation. Our study is significant to further the understanding of environmental responsive mechanisms as well as providing a reference for aquaculture.
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Affiliation(s)
- Binghua Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Jun Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Xiaohui Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Guangling Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Jingru Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Shuxian Wu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Ian AE Butts
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
- Correspondence:
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Nishizaki SS, Boyle AP. SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. BMC Bioinformatics 2022; 23:317. [PMID: 35927613 PMCID: PMC9351228 DOI: 10.1186/s12859-022-04865-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
MOTIVATION Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor's motif. RESULTS SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease. AVAILABILITY AND IMPLEMENTATION SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe .
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Affiliation(s)
- Sierra S Nishizaki
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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238
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Lee JU, Soo Chang H, Kyung Kim M, Park SL, Kim JH, Park JS, Park CS. Genome-wide DNA methylation profile of peripheral blood lymphocytes from subjects with nonsteroidal anti-inflammatory drug-induced respiratory diseases. Pharmacogenet Genomics 2022; 32:226-234. [PMID: 35696287 DOI: 10.1097/fpc.0000000000000475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Significant changes in CpG methylation have been identified in nasal polyps, which are the main targets of nonsteroidal anti-inflammatory drug-exacerbated respiratory disease (NERD); however, these polyps are composed of various cellular components. In the present study, whole-genome CpG methylation in peripheral blood lymphocytes (PBLs) was analyzed to define the epigenetic changes in lymphocytes, which are the primary immune cells involved in NERD. MATERIALS AND METHODS Genomic DNA from peripheral blood mononuclear cells from 27 NERD and 24 aspirin-tolerant asthma (ATA) was subjected to bisulfate conversion and a methylation array. Quantitative CpG methylation, the β-values as a quantitative measure of DNA methylation, in lymphocytes were calculated after adjustments for cellular composition. RESULTS Fifty-six hypermethylated and three hypomethylated differentially methylated CpGs (DMCs) in PBLs in the NERD compared with ATA. The top 10 CpG loci predicted the methylation risk score, with a positive predictive value of 91.3%, a negative predictive value of 81.5% and an accuracy of 84.3%. As demonstrated in the nasal polyps, 30 DMCs were predicted to bind to the following 10 transcription factors, ranked in descending order: AP-2alphaA, TFII-1, STAT4, FOXP3, GR, c-Est-1, E2F-1, XBP1, ENKTF-1 and NF-1. Gene ontology analysis identified 13 categories such as regulation of T-helper 17 cell differentiation, including SMAD7 and NFKBIZ. PBLs in NERD contained no DMCs in genes associated with the prostaglandin and leukotriene pathways, which were found in ATA. CONCLUSION PBLs in NERD form a unique pattern of DNA CpG methylation, and the combined analysis may provide predictive values for NERD.
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Affiliation(s)
- Jong-Uk Lee
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
| | - Hun Soo Chang
- Department of Anatomy and BK21 FOUR Project, College of Medicine, Soonchunhyang University, Cheonan
| | - Min Kyung Kim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University
| | - Seung-Lee Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University
| | - Jung Hyun Kim
- Department of Internal Medicine, Korean Armed Forces Capital Hospital, Seongnam
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
- PulmoBioPark Co., Ltd., Soonchunhyang University Bucheon Hospital, Bucheon, Korea
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239
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Stolz P, Mantero AS, Tvardovskiy A, Ugur E, Wange LE, Mulholland CB, Cheng Y, Wierer M, Enard W, Schneider R, Bartke T, Leonhardt H, Elsässer SJ, Bultmann S. TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation. Nucleic Acids Res 2022; 50:8491-8511. [PMID: 35904814 PMCID: PMC9410877 DOI: 10.1093/nar/gkac642] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/25/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent the regulatory functions of TET1 can be attributed to its catalytic activity remains unclear. Here, we use genome engineering and quantitative multi-omics approaches to dissect the precise catalytic vs. non-catalytic functions of TET1 in murine embryonic stem cells (mESCs). Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. In particular, we show that TET1 is critical for the establishment of H3K9me3 and H4K20me3 at endogenous retroviral elements (ERVs) and their silencing that is independent of its canonical role in DNA demethylation. Furthermore, we provide evidence that this repression of ERVs depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.
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Affiliation(s)
- Paul Stolz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Lucas E Wange
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Yuying Cheng
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Sebastian Bultmann
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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240
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Zheng M, Guo T, Yang B, Zhang Z, Huang L. Origin, evolution, and tissue-specific functions of the porcine repetitive element 1. Genet Sel Evol 2022; 54:54. [PMID: 35896967 PMCID: PMC9327148 DOI: 10.1186/s12711-022-00745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Background The porcine repetitive element 1 (PRE1) is the most abundant short interspersed nuclear element (SINE) in the Sus scrofa genome and it has been suggested that some PRE1 can have regulatory functions. The million copies of PRE1 in the porcine genome have accumulated abundant CpG dinucleotides and unique structural variations, such as direct repeats and patterns of sequence degeneration. The aims of this study were to analyse these structural variations to trace the origin and evolutionary pattern of PRE1 and to investigate potential methylation-related functions of PRE1 based on methylation patterns of PRE1 CpG dinucleotides in different tissues. Results We investigated the evolutionary trajectory of PRE1 and found that PRE1 originated from the ancestral CHRS-S1 family through three main successive partial duplications. We found that the partial duplications and deletions of PRE1 were likely due to RNA splicing events during retrotransposition. Functionally, correlation analysis showed that the methylation levels of 103 and 261 proximal PRE1 were, respectively, negatively and positively correlated with the expression levels of neighboring genes (Spearman correlation, P < 0.01). Further epigenomic analysis revealed that, in the testis, demethylation of proximal PRE1 in the HORMAD1 and HACD3 genes had tissue-specific enhancer and promoter functions, while in the muscle, methylation of proximal PRE1 repeats in the TCEA3 gene had an enhancer function. Conclusions The characteristic sequences of PRE1 reflect unique patterns of origin and evolution and provide a structural basis for diverse regulatory functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00745-3.
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Affiliation(s)
- Min Zheng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Tianfu Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
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241
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de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol 2022; 23:163. [PMID: 35883107 PMCID: PMC9316731 DOI: 10.1186/s13059-022-02728-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Background Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed. Results Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. Conclusions These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02728-5.
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Affiliation(s)
- Alex de Mendoza
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia. .,School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Trung Viet Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sam Buckberry
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Matthew R Grimmer
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA.,Integrated Genetics and Genomics, University of California, Davis, 451 Health Sciences Dr, Davis, CA, 95616, USA.,Department of Neurological Surgery, University of California, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Sabine Stolzenburg
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Ozren Bogdanovic
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.,School of BioScience, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
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242
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Ning S, He C, Guo Z, Zhang H, Mo Z. [VIPR1 promoter methylation promotes transcription factor AP-2 α binding to inhibit VIPR1 expression and promote hepatocellular carcinoma cell growth in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:957-965. [PMID: 35869757 DOI: 10.12122/j.issn.1673-4254.2022.07.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the transcriptional regulation mechanism and biological function of low expression of vasoactive intestinal peptide receptor 1 (VIPR1) in hepatocellular carcinoma (HCC). METHODS We constructed plasmids carrying wild-type VIPR1 promoter or two mutant VIPR1 promoter sequences for transfection of the HCC cell lines Hep3B and Huh7, and examined the effect of AP-2α expression on VIPR1 promoter activity using dual-luciferase reporter assay. Pyrosequencing was performed to detect the changes in VIPR1 promoter methylation level in HCC cells treated with a DNA methyltransferase inhibitor (DAC). Chromatin immunoprecipitation was used to evaluate the binding ability of AP-2α to VIPR1 promoter. Western blotting was used to assess the effect of AP-2α knockdown on VIPR1 expression and examine the differential expression of VIPR1 in the two cell lines. The effects of VIPR1 overexpression and knockdown on the proliferation, cell cycle and apoptosis of HCC cells were analyzed using CCK8 assay and flow cytometry. We also observed the growth of HCC xenograft with lentivirus-mediated over-expression of VIPR1 in nude mice. RESULTS Compared with the wild-type VIPR1 promoter group, co-transfection with the vector carrying two promoter mutations and the AP-2α-over-expressing plasmid obviously restored the luciferase activity in HCC cells (P < 0.05). DAC treatment of the cells significantly decreased the methylation level of VIPR1 promoter and inhibited the binding of AP-2α to VIPR1 promoter (P < 0.01). The HCC cells with AP-2α knockdown showed increased VIPR1 expression, which was lower in Huh7 cells than in Hep3B cells. VIPR1 overexpression in HCC cells caused significant cell cycle arrest in G2/M phase (P < 0.01), promoted cell apoptosis (P < 0.001), and inhibited cell proliferation (P < 0.001), while VIPR1 knockdown produced the opposite effects. In the tumor-bearing nude mice, VIPR1 overexpression in the HCC cells significantly suppressed the increase of tumor volume (P < 0.001) and weight (P < 0.05). CONCLUSION VIPR1 promoter methylation in HCC promotes the binding of AP-2α and inhibits VIPR1 expression, while VIPR1 overexpression causes cell cycle arrest, promotes cell apoptosis, and inhibits cell proliferation and tumor growth.
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Affiliation(s)
- S Ning
- School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, China
| | - C He
- Faculty of Basic Medical Sciences, Guilin Medical University, Guilin 541199, China
| | - Z Guo
- School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, China
| | - H Zhang
- School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, China
| | - Z Mo
- School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541199, China
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243
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Isbel L, Grand RS, Schübeler D. Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat Rev Genet 2022; 23:728-740. [PMID: 35831531 DOI: 10.1038/s41576-022-00512-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/11/2022]
Abstract
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.
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Affiliation(s)
- Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Sciences, University of Basel, Basel, Switzerland.
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244
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Hernandez-Corchado A, Najafabadi HS. Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding. Genome Biol 2022; 23:151. [PMID: 35799193 PMCID: PMC9264634 DOI: 10.1186/s13059-022-02713-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background While methylation of CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of most transcription factors (TFs), recent in vitro studies have revealed a more complex picture, suggesting that over a third of TFs may preferentially bind to methylated sequences. Expanding these in vitro observations to in vivo TF binding preferences is challenging since the effect of methylation of individual CpG sites cannot be easily isolated from the confounding effects of DNA accessibility and regional DNA methylation. Thus, in vivo methylation preferences of most TFs remain uncharacterized. Results We introduce joint accessibility-methylation-sequence (JAMS) models, which connect the strength of the binding signal observed in ChIP-seq to the DNA accessibility of the binding site, regional methylation level, DNA sequence, and base-resolution cytosine methylation. We show that JAMS models quantitatively explain TF occupancy, recapitulate cell type-specific TF binding, and have high positive predictive value for identification of TFs affected by intra-motif methylation. Analysis of 2209 ChIP-seq experiments results in high-confidence JAMS models for 260 TFs, revealing a negative association between in vivo TF occupancy and intra-motif methylation for 45% of studied TFs, as well as 16 TFs that are predicted to bind to methylated sites, including 11 novel methyl-binding TFs mostly from the multi-zinc finger family. Conclusions Our study substantially expands the repertoire of in vivo methyl-binding TFs, but also suggests that most TFs that prefer methylated CpGs in vitro present themselves as methylation agnostic in vivo, potentially due to the balancing effect of competition with other methyl-binding proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02713-y.
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Affiliation(s)
- Aldo Hernandez-Corchado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.,McGill Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada. .,McGill Genome Centre, Montreal, QC, H3A 0G1, Canada.
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245
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Quantitative detection of CpG methylation level on G-quadruplex and i-motif-forming DNA by recombinase polymerase amplification. Anal Bioanal Chem 2022; 414:6223-6231. [PMID: 35788871 DOI: 10.1007/s00216-022-04192-3] [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: 04/20/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 11/01/2022]
Abstract
Detection of CpG methylation levels holds immense potential for application in medical diagnosis of various diseases. In this study, we report the development of a recombinase polymerase amplification (RPA)-based CpG methylation level sensing system on G-quadruplex (G4) and intercalated motif (i-motif)-forming regions, which are stabilized by CpG methylation. This detection system is based on the principle that DNA polymerase is stalled at the methylated G4 and i-motif-forming region, which results in a decrease in the initial elongation efficiency of RPA. This reduction in turn affects the onset of amplification depending on the extent of CpG methylation; therefore, the methylation level is quantified by RPA. We demonstrate that the onset of amplification was delayed by CpG methylation when PCR products containing the vascular endothelial growth factor (VEGF) G4 and i-motif-forming region were used as the template. Furthermore, onset of amplification was delayed with the increase in CpG methylation of the VEGF region on genomic DNA. These results demonstrate that the sensing system is capable of directly detecting the methylation level at a constant temperature (39 °C) within 30 min without performing bisulfite conversion or affinity capture of methylated DNA.
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246
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Boytsov A, Abramov S, Makeev VJ, Kulakovskiy IV. Positional weight matrices have sufficient prediction power for analysis of noncoding variants. F1000Res 2022; 11:33. [PMID: 35811788 PMCID: PMC9237556 DOI: 10.12688/f1000research.75471.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
The position weight matrix, also called the position-specific scoring matrix, is the commonly accepted model to quantify the specificity of transcription factor binding to DNA. Position weight matrices are used in thousands of projects and software tools in regulatory genomics, including computational prediction of the regulatory impact of single-nucleotide variants. Yet, recently Yan et al. reported that "the position weight matrices of most transcription factors lack sufficient predictive power" if applied to the analysis of regulatory variants studied with a newly developed experimental method, SNP-SELEX. Here, we re-analyze the rich experimental dataset obtained by Yan et al. and show that appropriately selected position weight matrices in fact can adequately quantify transcription factor binding to alternative alleles.
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Affiliation(s)
- Alexandr Boytsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - Sergey Abramov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - Vsevolod J. Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - Ivan V. Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
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Bhattacharya N, Indra AK, Ganguli-Indra G. Selective Ablation of BCL11A in Epidermal Keratinocytes Alters Skin Homeostasis and Accelerates Excisional Wound Healing In Vivo. Cells 2022; 11:cells11132106. [PMID: 35805190 PMCID: PMC9265695 DOI: 10.3390/cells11132106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
Transcriptional regulator BCL11A plays a crucial role in coordinating a suite of developmental processes including skin morphogenesis, barrier functions and lipid metabolism. There is little or no reports so far documenting the role of BCL11A in postnatal adult skin homeostasis and in the physiological process of tissue repair and regeneration. The current study establishes for the first time the In Vivo role of epidermal BCL11A in maintaining adult epidermal homeostasis and as a negative regulator of cutaneous wound healing. Conditional ablation of Bcl11a in skin epidermal keratinocytes (Bcl11aep−/−mice) enhances the keratinocyte proliferation and differentiation program, suggesting its critical role in epidermal homeostasis of adult murine skin. Further, loss of keratinocytic BCL11A promotes rapid closure of excisional wounds both in a cell autonomous manner likely via accelerating wound re-epithelialization and in a non-cell autonomous manner by enhancing angiogenesis. The epidermis specific Bcl11a knockout mouse serves as a prototype to gain mechanistic understanding of various downstream pathways converging towards the manifestation of an accelerated healing phenotype upon its deletion.
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Affiliation(s)
- Nilika Bhattacharya
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA;
| | - Arup K. Indra
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA;
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- Linus Pauling Science Center, Oregon State University, Corvallis, OR 97331, USA
- OHSU Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
- Department of Dermatology, OHSU, Portland, OR 97239, USA
- Correspondence: (A.K.I.); (G.G.-I.)
| | - Gitali Ganguli-Indra
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA;
- OHSU Knight Cancer Institute, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
- Correspondence: (A.K.I.); (G.G.-I.)
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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Joshi K, Liu S, Breslin S J P, Zhang J. Mechanisms that regulate the activities of TET proteins. Cell Mol Life Sci 2022; 79:363. [PMID: 35705880 DOI: 10.1007/s00018-022-04396-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023]
Abstract
The ten-eleven translocation (TET) family of dioxygenases consists of three members, TET1, TET2, and TET3. All three TET enzymes have Fe+2 and α-ketoglutarate (α-KG)-dependent dioxygenase activities, catalyzing the 1st step of DNA demethylation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Gene knockout studies demonstrated that all three TET proteins are involved in the regulation of fetal organ generation during embryonic development and normal tissue generation postnatally. TET proteins play such roles by regulating the expression of key differentiation and fate-determining genes via (1) enzymatic activity-dependent DNA methylation of the promoters and enhancers of target genes; and (2) enzymatic activity-independent regulation of histone modification. Interacting partner proteins and post-translational regulatory mechanisms regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are involved in the pathogenesis of human diseases, specifically cancers. Here, we summarize the research on the interaction partners and post-translational modifications of TET proteins. We also discuss the molecular mechanisms by which these partner proteins and modifications regulate TET functioning and target gene expression. Such information will help in the design of medications useful for targeted therapy of TET-mutant-related diseases.
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Affiliation(s)
- Kanak Joshi
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Shanhui Liu
- School of Life Sciences, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Peter Breslin S J
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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Zhang Q, Zhang J, Lei T, Liang Z, Dong X, Sun L, Zhao Y. Sirt6-mediated epigenetic modification of DNA accessibility is essential for Pou2f3-induced thymic tuft cell development. Commun Biol 2022; 5:544. [PMID: 35668088 PMCID: PMC9170729 DOI: 10.1038/s42003-022-03484-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThymic epithelial cells (TECs) are essential for the production of self-tolerant T cells. The newly identified thymic tuft cells are regulated by Pou2f3 and represent important elements for host type 2 immunity. However, epigenetic involvement in thymic tuft cell development remains unclear. We performed single-cell ATAC-seq of medullary TEC (mTEC) and established single-cell chromatin accessibility profiling of mTECs. The results showed that mTEC III cells can be further divided into three groups (Late Aire 1, 2, and 3) and that thymic tuft cells may be derived from Late Aire 2 cells. Pou2f3 is expressed in both Late Aire 2 cells and thymic tuft cells, while Pou2f3-regulated genes are specifically expressed in thymic tuft cells with simultaneous opening of chromatin accessibility, indicating the involvement of epigenetic modification in this process. Using the epigenetic regulator Sirt6-defect mouse model, we found that Sirt6 deletion increased Late Aire 2 cells and decreased thymic tuft cells and Late Aire 3 cells without affecting Pou2f3 expression. However, Sirt6 deletion reduced the chromatin accessibility of Pou2f3-regulated genes in thymic tuft cells, which may be caused by Sirt6–mediated regulation of Hdac9 expression. These data indicate that epigenetic regulation is indispensable for Pou2f3-mediated thymic tuft cell development.
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