601
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Matsuda T, Irie T, Katsurabayashi S, Hayashi Y, Nagai T, Hamazaki N, Adefuin AMD, Miura F, Ito T, Kimura H, Shirahige K, Takeda T, Iwasaki K, Imamura T, Nakashima K. Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion. Neuron 2019; 101:472-485.e7. [PMID: 30638745 DOI: 10.1016/j.neuron.2018.12.010] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 10/23/2018] [Accepted: 12/05/2018] [Indexed: 02/07/2023]
Abstract
Minimal sets of transcription factors can directly reprogram somatic cells into neurons. However, epigenetic remodeling during neuronal reprogramming has not been well reconciled with transcriptional regulation. Here we show that NeuroD1 achieves direct neuronal conversion from mouse microglia both in vitro and in vivo. Exogenous NeuroD1 initially occupies closed chromatin regions associated with bivalent trimethylation of histone H3 at lysine 4 (H3K4me3) and H3K27me3 marks in microglia to induce neuronal gene expression. These regions are resolved to a monovalent H3K4me3 mark at later stages of reprogramming to establish the neuronal identity. Furthermore, the transcriptional repressors Scrt1 and Meis2 are induced as NeuroD1 target genes, resulting in a decrease in the expression of microglial genes. In parallel, the microglial epigenetic signature in promoter and enhancer regions is erased. These findings reveal NeuroD1 pioneering activity accompanied by global epigenetic remodeling for two sequential events: onset of neuronal property acquisition and loss of the microglial identity during reprogramming.
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Affiliation(s)
- Taito Matsuda
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Takashi Irie
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shutaro Katsurabayashi
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Yoshinori Hayashi
- Department of Aging Science and Pharmacology, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Tatsuya Nagai
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuhiko Hamazaki
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Aliya Mari D Adefuin
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Fumihito Miura
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Tadayuki Takeda
- Genome Network Analysis Support Facility (GeNAS), RIKEN Center for Life Science Technologies, Kanagawa, Japan
| | - Katsunori Iwasaki
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Takuya Imamura
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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602
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Leung KK, Nguyen A, Shi T, Tang L, Ni X, Escoubet L, MacBeth KJ, DiMartino J, Wells JA. Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome. Proc Natl Acad Sci U S A 2019; 116:695-700. [PMID: 30584089 PMCID: PMC6329958 DOI: 10.1073/pnas.1813666116] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor widely used to treat MDS and AML, yet the impact of AZA on the cell-surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell-surface proteome. Untreated AML cell lines showed substantial overlap at all three omics levels; however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteome analysis found no commonly regulated proteins. Gene set enrichment analysis of differentially regulated RNA and surface proteins showed a decrease in metabolic pathways and an increase in immune defense response pathways. As such, AZA treatment led to diverse effects at the individual gene and protein levels but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines, we discuss potential therapeutic strategies for AML in combination with AZA.
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Affiliation(s)
- Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Aaron Nguyen
- Epigenetics Thematic Center of Excellence, Celgene Corporation, San Francisco, CA 94158
| | - Tao Shi
- Department of Informatics and Predictive Sciences, Celgene Corporation, San Diego, CA 92121
| | - Lin Tang
- Department of Informatics and Predictive Sciences, Celgene Corporation, San Diego, CA 92121
| | - Xiaochun Ni
- Department of Informatics and Predictive Sciences, Celgene Corporation, Cambridge, MA 02140
| | - Laure Escoubet
- Department of Informatics and Predictive Sciences, Celgene Corporation, San Diego, CA 92121
| | - Kyle J MacBeth
- Epigenetics Thematic Center of Excellence, Celgene Corporation, San Francisco, CA 94158
| | - Jorge DiMartino
- Epigenetics Thematic Center of Excellence, Celgene Corporation, San Francisco, CA 94158
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143;
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603
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Glastad KM, Hunt BG, Goodisman MAD. Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:185-203. [PMID: 30285490 DOI: 10.1146/annurev-ento-011118-111914] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic inheritance is fundamentally important to cellular differentiation and developmental plasticity. In this review, we provide an introduction to the field of molecular epigenetics in insects. Epigenetic information is passed across cell divisions through the methylation of DNA, the modification of histone proteins, and the activity of noncoding RNAs. Much of our knowledge of insect epigenetics has been gleaned from a few model species. However, more studies of epigenetic information in traditionally nonmodel taxa will help advance our understanding of the developmental and evolutionary significance of epigenetic inheritance in insects. To this end, we also provide a brief overview of techniques for profiling and perturbing individual facets of the epigenome. Doing so in diverse cellular, developmental, and taxonomic contexts will collectively help shed new light on how genome regulation results in the generation of diversity in insect form and function.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, Georgia 30223, USA;
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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604
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Hsu JSJ, So M, Tang CSM, Karim A, Porsch RM, Wong C, Yu M, Yeung F, Xia H, Zhang R, Cherny SS, Chung PHY, Wong KKY, Sham PC, Ngo ND, Li M, Tam PKH, Lui VCH, Garcia-Barcelo MM. De novo mutations in Caudal Type Homeo Box transcription Factor 2 (CDX2) in patients with persistent cloaca. Hum Mol Genet 2019; 27:351-358. [PMID: 29177441 DOI: 10.1093/hmg/ddx406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/27/2017] [Indexed: 12/24/2022] Open
Abstract
The cloaca is an embryonic cavity that is divided into the urogenital sinus and rectum upon differentiation of the cloacal epithelium triggered by tissue-specific transcription factors including CDX2. Defective differentiation leads to persistent cloaca in humans (PC), a phenotype recapitulated in Cdx2 mutant mice. PC is linked to hypo/hyper-vitaminosis A. Although no gene has ever been identified, there is a strong evidence for a genetic contribution to PC. We applied whole-exome sequencing and copy-number-variants analyses to 21 PC patients and their unaffected parents. The damaging p.Cys132* and p.Arg237His de novo CDX2 variants were identified in two patients. These variants altered the expression of CYP26A1, a direct CDX2 target encoding the major retinoic acid (RA)-degrading enzyme. Other RA genes, including the RA-receptor alpha, were also mutated. Genes governing the development of cloaca-derived structures were recurrently mutated and over-represented in the basement-membrane components set (q-value < 1.65 × 10-6). Joint analysis of the patients' profile highlighted the extracellular matrix-receptor interaction pathway (MsigDBID: M7098, FDR: q-value < 7.16 × 10-9). This is the first evidence that PC is genetic, with genes involved in the RA metabolism at the lead. Given the CDX2 de novo variants and the role of RA, our observations could potentiate preventive measures. For the first time, a gene recapitulating PC in mouse models is found mutated in humans.
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Affiliation(s)
- Jacob S J Hsu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Manting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anwarul Karim
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Robert M Porsch
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Carol Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Michelle Yu
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Fanny Yeung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, Guandong, China
| | - Ruizhong Zhang
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, Guandong, China
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick H Y Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth K Y Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ngoc Diem Ngo
- Department of Human Genetics, National Hospital of Pediatrics, Hà N?i, Vietnam
| | - Miaoxin Li
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul K H Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vincent C H Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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605
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5-Methylcytosine and Its Oxidized Derivatives. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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606
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Barbour JA, Wong JWH. Dysregulation of Cis-Regulatory Elements in Cancer. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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607
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Ma Q, Xu Z, Lu H, Xu Z, Zhou Y, Yuan B, Ci W. Distal regulatory elements identified by methylation and hydroxymethylation haplotype blocks from mouse brain. Epigenetics Chromatin 2018; 11:75. [PMID: 30594220 PMCID: PMC6311040 DOI: 10.1186/s13072-018-0248-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
Background 5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TET enzymes. Results We applied TAB-seq and oxBS-seq to selectively detect 5hmC and 5mC at base resolution in the mouse cortex, olfactory bulb and cerebellum tissues. We found that majority of the called 5hmC CpG sites frequently have 5mC modification simultaneously and are enriched in gene body regions of neuron development-related genes in brain tissues. Strikingly, by a systematic search of regions that show highly coordinated methylation and hydroxymethylation (MHBs and hMHBs), we found that MHBs significantly overlapped with hMHBs in gene body regions. Moreover, using a metric called methylation haplotype load, we defined a subset of 1361 tissue-specific MHBs and 3818 shared MHBs. Shared MHBs with low MHL correspond with developmental enhancers, and tissue-specific MHBs resemble the regulatory elements for tissue identity. Conclusions Our results provide new insights into the role of coordinately oxidized 5mC to 5hmC as distal regulatory elements may involve in regulating tissue identity. Electronic supplementary material The online version of this article (10.1186/s13072-018-0248-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qin Ma
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengzheng Xu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huan Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziying Xu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Zhou
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bifeng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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608
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Abstract
Senescence, a state of permanent cell cycle arrest, can be induced by DNA damage. This process, which was initially described in fibroblasts, is now recognized to occur in stem cells. It has been well characterized in cell lines, but there is currently very limited data available on human senescence in vivo. We recently reported that the expression of transposable elements (TE), including endogenous retroviruses, was up-regulated along with inflammatory genes in human senescent hematopoietic stem and progenitor cells (HSPCs) in vivo. The mechanism of regulation of TE expression is not completely understood, but changes in DNA methylation and chromatin modifications are known to alter their expression. In order to elucidate the molecular mechanisms for TE up-regulation after senescence of HSPCs, we employed whole-genome bisulfite sequencing in paired senescent and active human HSPCs in vivo from healthy subjects. We found that the senescent HSPCs exhibited hypomethylated regions in the genome, which were enriched for TEs. This is the first report characterizing the methylome of senescent human HSPCs.
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609
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Lea AJ, Vockley CM, Johnston RA, Del Carpio CA, Barreiro LB, Reddy TE, Tung J. Genome-wide quantification of the effects of DNA methylation on human gene regulation. eLife 2018; 7:e37513. [PMID: 30575519 PMCID: PMC6303109 DOI: 10.7554/elife.37513] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Changes in DNA methylation are involved in development, disease, and the response to environmental conditions. However, not all regulatory elements are functionally methylation-dependent (MD). Here, we report a method, mSTARR-seq, that assesses the causal effects of DNA methylation on regulatory activity at hundreds of thousands of fragments (millions of CpG sites) simultaneously. Using mSTARR-seq, we identify thousands of MD regulatory elements in the human genome. MD activity is partially predictable using sequence and chromatin state information, and distinct transcription factors are associated with higher activity in unmethylated versus methylated DNA. Further, pioneer TFs linked to higher activity in the methylated state appear to drive demethylation of experimentally methylated sites. MD regulatory elements also predict methylation-gene expression relationships across individuals, where they are 1.6x enriched among sites with strong negative correlations. mSTARR-seq thus provides a map of MD regulatory activity in the human genome and facilitates interpretation of differential methylation studies.
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Affiliation(s)
- Amanda J Lea
- Department of BiologyDuke UniversityNorth CarolinaUnited States
| | - Christopher M Vockley
- Center for Genomic and Computational BiologyDuke University Medical SchoolNorth CarolinaUnited States
- Department of Biostatistics and BioinformaticsDuke University Medical SchoolNorth CarolinaUnited States
| | - Rachel A Johnston
- Department of Evolutionary AnthropologyDuke UniversityNorth CarolinaUnited States
| | | | - Luis B Barreiro
- Department of PediatricsSainte-Justine Hospital Research Centre, University of MontrealMontrealCanada
| | - Timothy E Reddy
- Center for Genomic and Computational BiologyDuke University Medical SchoolNorth CarolinaUnited States
- Department of Biostatistics and BioinformaticsDuke University Medical SchoolNorth CarolinaUnited States
- Program in Computational Biology and BioinformaticsDuke UniversityNorth CarolinaUnited States
| | - Jenny Tung
- Department of BiologyDuke UniversityNorth CarolinaUnited States
- Department of Evolutionary AnthropologyDuke UniversityNorth CarolinaUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Duke University Population Research InstituteDuke UniversityNorth CarolinaUnited States
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610
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Liu Y, Shen J, Yang X, Sun Q, Yang X. Folic Acid Reduced Triglycerides Deposition in Primary Chicken Hepatocytes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13162-13172. [PMID: 30484310 DOI: 10.1021/acs.jafc.8b05193] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Abdominal fat or fatty liver cause huge economic losses in the poultry industry, and nonalcoholic fatty liver disease (NAFLD) is also a global health issue in humans. More than 90% of de novo lipogenesis in humans and chickens is undertaken by the liver, which is proved to be full of lipids in new-born chickens. Folic acid was thought to have correlation with lipid metabolism. Primary hepatocytes from new-born chickens were employed as a natural model of early stage fatty liver in vitro and further to explore whether folic acid could prevent fatty liver in the current study. We found that folic acid addition reduced triglyceride deposition by suppressing de novo fatty acid synthesis and coordinately promoting triglyceride hydrolysis and exportation in primary chicken hepatocytes from new-born chickens. In addition, lipogenesis suppression was through the PI3K/AKT/SREBP pathway mediated by weakening insulin/IGF signal. Our data suggested that folic acid may be considered as a precautionary strategy for abdominal fat deposition in broilers or fatty liver in laying hens and humans. In addition, mechanism regulation also implied that an IGF2 inhibitor and PI3K inhibitor may be used for the NAFLD precautionary measure to reduce TG deposition.
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Affiliation(s)
- Yanli Liu
- College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Jing Shen
- College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Xin Yang
- College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Qingzhu Sun
- College of Animal Science and Technology , Northwest A&F University , Yangling , China
| | - Xiaojun Yang
- College of Animal Science and Technology , Northwest A&F University , Yangling , China
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611
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Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 2018; 362:362/6413/eaav1898. [PMID: 30361341 DOI: 10.1126/science.aav1898] [Citation(s) in RCA: 627] [Impact Index Per Article: 104.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.
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612
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Xiong T, Rohm D, Workman RE, Roundtree L, Novina CD, Timp W, Ostermeier M. Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria. PLoS One 2018; 13:e0209408. [PMID: 30562388 PMCID: PMC6298699 DOI: 10.1371/journal.pone.0209408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/05/2018] [Indexed: 12/22/2022] Open
Abstract
Mammalian gene expression is a complex process regulated in part by CpG methylation. The ability to target methylation for de novo gene regulation could have therapeutic and research applications. We have previously developed a dCas9-MC/MN protein for targeting CpG methylation. dCas9-MC/MN is composed of an artificially split M.SssI methyltransferase (MC/MN), with the MC fragment fused to a nuclease-null CRISPR/Cas9 (dCas9). Guide RNAs directed dCas9-MC/MN to methylate target sites in E. coli and human cells but also caused some low-level off-target methylation. Here, in E. coli, we show that shortening the dCas9-MC linker increases methylation of CpG sites located at select distances from the dCas9 binding site. Although a shortened linker decreased methylation of other CpGs proximal to the target site, it did not reduce off-target methylation of more distant CpG sites. Instead, targeted mutagenesis of the methyltransferase's DNA binding domain, designed to reduce DNA affinity, significantly and preferentially reduced methylation of such sites.
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Affiliation(s)
- Tina Xiong
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Dahlia Rohm
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rachael E. Workman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Lauren Roundtree
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Carl D. Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
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613
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Laisné M, Gupta N, Kirsh O, Pradhan S, Defossez PA. Mechanisms of DNA Methyltransferase Recruitment in Mammals. Genes (Basel) 2018; 9:genes9120617. [PMID: 30544749 PMCID: PMC6316769 DOI: 10.3390/genes9120617] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is an essential epigenetic mark in mammals. The proper distribution of this mark depends on accurate deposition and maintenance mechanisms, and underpins its functional role. This, in turn, depends on the precise recruitment and activation of de novo and maintenance DNA methyltransferases (DNMTs). In this review, we discuss mechanisms of recruitment of DNMTs by transcription factors and chromatin modifiers—and by RNA—and place these mechanisms in the context of biologically meaningful epigenetic events. We present hypotheses and speculations for future research, and underline the fundamental and practical benefits of better understanding the mechanisms that govern the recruitment of DNMTs.
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Affiliation(s)
- Marthe Laisné
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | - Nikhil Gupta
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | - Olivier Kirsh
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | | | - Pierre-Antoine Defossez
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
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614
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Feng W, Zhou L, Wang H, Hu Z, Wang X, Fu J, Wang A, Liu JF. Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells. J Cell Biochem 2018; 120:10118-10127. [PMID: 30537176 DOI: 10.1002/jcb.28295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
Abstract
DNA methylation plays essential roles in regulating the activity of genes and may contribute to understanding the potential epigenetic biomarkers response to viruses. To explore the function of DNA methylation of protein kinase C and casein kinase substrate in neurons 1 (PACSNI1) promoter, herein we performed the bisulfite sequencing polymerase chain reaction and Western blot analysis to verify hypermethylation and downregulation of PACSIN1 expression in peripheral blood mononuclear cells of pig as the vitro model. Promoter methylation could reduce the transcriptional activity of the PACSIN1 gene potentially by affecting the binding of transcription factor Sp1. In addition, downregulation of the PACSIN1 gene expression could facilitate the production of interleukin-6 (IL-6), IL-8, tumor necrosis factor α, and NECAP2. The comprehensive analysis of PACSIN1 methylation and its function will help us to understand the gene to be served as an important candidate gene in pig for disease resistance breeding and aid in the identification of potential epigenetic biomarkers associated with responsiveness to viruses.
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Affiliation(s)
- Wen Feng
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal Genetics, Breeding and Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengzheng Hu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaomei Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianlian Fu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Aiguo Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
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615
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Lussier AA, Bodnar TS, Mingay M, Morin AM, Hirst M, Kobor MS, Weinberg J. Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues. Front Genet 2018; 9:610. [PMID: 30568673 PMCID: PMC6290329 DOI: 10.3389/fgene.2018.00610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022] Open
Abstract
Background: Prenatal alcohol exposure (PAE) can alter the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE resulted in blood alcohol levels of ~80-150 mg/dl throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal days (P) 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing. Results: PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental period at a false-discovery rate (FDR) < 0.05. In addition, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR < 0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses. Conclusions: Persistent DNA methylation changes in the hypothalamus may be associated with the long-term physiological and neurobehavioral alterations in observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology of neurodevelopmental and mental health disorders, as they share numerous phenotypes and comorbidities.
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Affiliation(s)
- Alexandre A Lussier
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Tamara S Bodnar
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Mingay
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre M Morin
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency Research Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
| | - Joanne Weinberg
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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616
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Tobi EW, van den Heuvel J, Zwaan BJ, Lumey L, Heijmans BT, Uller T. Selective Survival of Embryos Can Explain DNA Methylation Signatures of Adverse Prenatal Environments. Cell Rep 2018; 25:2660-2667.e4. [DOI: 10.1016/j.celrep.2018.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/18/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022] Open
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617
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Effect of hypermethylation in ovarian cancer: Computational approach. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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618
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Parker HR, Orjuela S, Martinho Oliveira A, Cereatti F, Sauter M, Heinrich H, Tanzi G, Weber A, Komminoth P, Vavricka S, Albanese L, Buffoli F, Robinson MD, Marra G. The proto CpG island methylator phenotype of sessile serrated adenomas/polyps. Epigenetics 2018; 13:1088-1105. [PMID: 30398409 PMCID: PMC6342079 DOI: 10.1080/15592294.2018.1543504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sessile serrated adenomas/polyps (SSA/Ps) are the putative precursors of the ~20% of colon cancers with the CpG island methylator phenotype (CIMP). To investigate the epigenetic phenotype of these precancers, we prospectively collected fresh-tissue samples of 17 SSA/Ps and 15 conventional adenomas (cADNs), each with a matched sample of normal mucosa. Their DNA was subjected to bisulfite next-generation sequencing to assess methylation levels at ~2.7 million CpGs located predominantly in gene regulatory regions and spanning 80.5Mb; RNA was sequenced to define the samples' transcriptomes. Compared with normal mucosa, SSA/Ps and cADNs exhibited markedly remodeled methylomes. In cADNs, hypomethylated regions were far more numerous (18,417 vs 4288 in SSA/Ps) and rarely affected CpG islands/shores. SSA/Ps seemed to have escaped this wave of demethylation. Cytosine hypermethylation in SSA/Ps was more pervasive (hypermethylated regions: 22,147 vs 15,965 in cADNs; hypermethylated genes: 4938 vs 3443 in cADNs) and more extensive (region for region), and it occurred mainly within CpG islands and shores. Given its resemblance to the CIMP typical of SSA/Ps' putative descendant colon cancers, we refer to the SSA/P methylation phenotype as proto-CIMP. Verification studies of six hypermethylated regions in an independent series of precancers demonstrated DNA methylation markers' high potential for predicting the diagnosis of SSA/Ps and cADNs. Surprisingly, proto-CIMP in SSA/Ps was associated with upregulated gene expression; downregulation was more common in cADNs. In conclusion, the epigenetic landscape of SSA/Ps differs markedly from that of cADNs. These differences are a potentially rich source of novel tissue-based and noninvasive biomarkers.
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Affiliation(s)
- Hannah R Parker
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland
| | - Stephany Orjuela
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland.,b Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics , University of Zurich , Zurich , Switzerland
| | | | - Fabrizio Cereatti
- c Gastroenterology and Endoscopy Unit , Hospital of Cremona , Cremona , Italy
| | - Matthias Sauter
- d Division of Gastroenterology , Triemli Hospital , Zurich , Switzerland
| | - Henriette Heinrich
- d Division of Gastroenterology , Triemli Hospital , Zurich , Switzerland
| | - Giulia Tanzi
- e Division of Pathology , Hospital of Cremona , Cremona , Italy
| | - Achim Weber
- f Institute of Surgical Pathology , University of Zurich , Zurich , Switzerland
| | - Paul Komminoth
- g Division of Pathology , Triemli Hospital , Zurich , Switzerland
| | - Stephan Vavricka
- d Division of Gastroenterology , Triemli Hospital , Zurich , Switzerland
| | - Luca Albanese
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland
| | - Federico Buffoli
- c Gastroenterology and Endoscopy Unit , Hospital of Cremona , Cremona , Italy
| | - Mark D Robinson
- b Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics , University of Zurich , Zurich , Switzerland
| | - Giancarlo Marra
- a Institute of Molecular Cancer Research , University of Zurich , Zurich , Switzerland
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619
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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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620
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Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature 2018; 563:579-583. [PMID: 30429608 DOI: 10.1038/s41586-018-0703-0] [Citation(s) in RCA: 517] [Impact Index Per Article: 86.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
The use of liquid biopsies for cancer detection and management is rapidly gaining prominence1. Current methods for the detection of circulating tumour DNA involve sequencing somatic mutations using cell-free DNA, but the sensitivity of these methods may be low among patients with early-stage cancer given the limited number of recurrent mutations2-5. By contrast, large-scale epigenetic alterations-which are tissue- and cancer-type specific-are not similarly constrained6 and therefore potentially have greater ability to detect and classify cancers in patients with early-stage disease. Here we develop a sensitive, immunoprecipitation-based protocol to analyse the methylome of small quantities of circulating cell-free DNA, and demonstrate the ability to detect large-scale DNA methylation changes that are enriched for tumour-specific patterns. We also demonstrate robust performance in cancer detection and classification across an extensive collection of plasma samples from several tumour types. This work sets the stage to establish biomarkers for the minimally invasive detection, interception and classification of early-stage cancers based on plasma cell-free DNA methylation patterns.
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Affiliation(s)
- Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rajat Singhania
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gordon Fehringer
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael H A Roehrl
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dianne Chadwick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Philip C Zuzarte
- Genome Technologies, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ting Ting Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olena Kis
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiago da Silva Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yadon Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David Roulois
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,UMR_S 1236, Univ Rennes 1, Inserm, Etablissement Français du sang Bretagne, Rennes, France
| | - Ilias Ettayebi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhuo Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Signy Chow
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tracy Murphy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mark Mansour
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Catherine O'Brien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Natasha Leighl
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe L Bedard
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Neil Fleshner
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Steven Gallinger
- Fred Litwin Centre for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada. .,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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621
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Transcriptional Landscape of PARs in Epithelial Malignancies. Int J Mol Sci 2018; 19:ijms19113451. [PMID: 30400241 PMCID: PMC6275037 DOI: 10.3390/ijms19113451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/22/2018] [Accepted: 10/27/2018] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of cell receptors, act as important regulators of diverse signaling pathways. Our understanding of the impact of GPCRs in tumors is emerging, yet there is no therapeutic platform based on GPCR driver genes. As cancer progresses, it disrupts normal epithelial organization and maintains the cells outside their normal niche. The dynamic and flexible microenvironment of a tumor contains both soluble and matrix-immobilized proteases that contribute to the process of cancer advancement. An example is the activation of cell surface protease-activated receptors (PARs). Mammalian PARs are a subgroup of GPCRs that form a family of four members, PAR1–4, which are uniquely activated by proteases found in the microenvironment. PAR1 and PAR2 play central roles in tumor biology, and PAR3 acts as a coreceptor. The significance of PAR4 in neoplasia is just beginning to emerge. PAR1 has been shown to be overexpressed in malignant epithelia, in direct correlation with tumor aggressiveness, but there is no expression in normal epithelium. In this review, the involvement of key transcription factors such as Egr1, p53, Twist, AP2, and Sp1 that control PAR1 expression levels specifically, as well as hormone transcriptional regulation by both estrogen receptors (ER) and androgen receptors (AR) are discussed. The cloning of the human protease-activated receptor 2; Par2 (hPar2) promoter region and transcriptional regulation of estrogen (E2) via binding of the E2–ER complex to estrogen response elements (ERE) are shown. In addition, evidence that TEA domain 4 (TEAD4) motifs are present within the hPar2 promoter is presented since the YAP oncogene, which plays a central part in tumor etiology, acts via the TEAD4 transcription factor. As of now, no information is available on regulation of the hPar3 promoter. With regard to hPar4, only data showing CpG methylation promoter regulation is available. Characterization of the PAR transcriptional landscape may identify powerful targets for cancer therapies.
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622
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Sardina JL, Collombet S, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T. Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate. Cell Stem Cell 2018; 23:727-741.e9. [DOI: 10.1016/j.stem.2018.08.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/07/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
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623
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Lin KN, Grandhi TSP, Goklany S, Rege K. Chemotherapeutic Drug-Conjugated Microbeads Demonstrate Preferential Binding to Methylated Plasmid DNA. Biotechnol J 2018; 13:e1700701. [DOI: 10.1002/biot.201700701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Kevin N. Lin
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University; Tempe AZ 85287 USA
| | - Taraka Sai Pavan Grandhi
- Biomedical Engineering, School of Biological and Health Systems Engineering, Arizona State University; Tempe AZ 85287 USA
| | - Sheba Goklany
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University; Tempe AZ 85287 USA
| | - Kaushal Rege
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University; Tempe AZ 85287 USA
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624
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Hudson NO, Whitby FG, Buck-Koehntop BA. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J Biol Chem 2018; 293:19835-19843. [PMID: 30355731 DOI: 10.1074/jbc.ra118.005147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/16/2018] [Indexed: 02/05/2023] Open
Abstract
Methyl-CpG-binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 Å resolution. From the structure, methyl-selective binding is preferentially localized at the 5' mCpG site of the bound DNA, which is facilitated through a series of base-specific interactions from residues within the α-helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined, these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding of how ZF-containing proteins can interpret this essential epigenetic mark.
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Affiliation(s)
| | - Frank G Whitby
- Biochemistry, University of Utah, Salt Lake City, Utah 84112
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625
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Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat Biotechnol 2018; 36:nbt.4204. [PMID: 30295673 PMCID: PMC6453757 DOI: 10.1038/nbt.4204] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/03/2018] [Indexed: 12/17/2022]
Abstract
Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.
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Affiliation(s)
- Emily K. Schutsky
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E. DeNizio
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica Yun Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Emily B. Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Young Hwang
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
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626
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Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018; 23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys₂His₂ zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.
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Affiliation(s)
- Nicholas O Hudson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
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627
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Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells. Cancers (Basel) 2018; 10:cancers10100371. [PMID: 30301163 PMCID: PMC6210734 DOI: 10.3390/cancers10100371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 01/18/2023] Open
Abstract
Breast cancer prognosis and response to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively). Although much is known about ERα gene (ESR1) regulation after hormonal stimulation, how it is regulated in hormone-free condition is not fully understood. We used ER-/PR-positive breast cancer cells to investigate the role of PR in ESR1 regulation in the absence of hormones. We show that PR binds to the low-methylated ESR1 promoter and maintains both gene expression and DNA methylation of the ESR1 locus in hormone-deprived breast cancer cells. Depletion of PR reduces ESR1 expression, with a concomitant increase in gene promoter methylation. The high amount of methylation in the ESR1 promoter of PR-depleted cells persists after the stable re-expression of PR and inhibits PR binding to this genomic region. As a consequence, the rescue of PR expression in PR-depleted cells is insufficient to restore ESR1 expression. Consistently, DNA methylation impedes PR binding to consensus progesterone responsive elements. These findings contribute to understanding the complex crosstalk between PR and ER and suggest that the analysis of ESR1 promoter methylation in breast cancer cells can help to design more appropriate targeted therapies for breast cancer patients.
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628
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Liu Y, Huang R, Liu Y, Song W, Wang Y, Yang Y, Dong S, Yang X. Insights from multidimensional analyses of the pan-cancer DNA methylome heterogeneity and the uncanonical CpG-gene associations. Int J Cancer 2018; 143:2814-2827. [PMID: 30121964 DOI: 10.1002/ijc.31810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/18/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022]
Abstract
Although the DNA methylome profiles have been available in large cancer cohorts such as The Cancer Genome Atlas (TCGA), integrative analysis of the DNA methylome architectures in a pan-cancer manner remains limited. In the present study, we aimed to systematically dissect the insightful features related to the inter-tumoral DNA methylome heterogeneity in a pan-cancer context of 21 cancers in TCGA. First, pan-cancer clustering of the DNA methylomes revealed convergence of cancers and, meanwhile, new classifications of cancer subtypes, which are often associated to prognostic differences. Next, within each type of cancer, we showed that the transcription factor (TF) genes tend to bear more dynamic promoter DNA methylation profiles than the other genes, which serves as a potential source of the transcriptome heterogeneity in cancers. Finally, we found unanticipated significant numbers of the non-canonical promoter CpG sites that are positively correlated with the gene expression. Distribution patterns of these CpG sites in the CpG islands, ChIP-seq, DNaseI-seq, PMD regions and histone modification landscapes suggested against a pervasive mechanism of transcriptional activation due to mCpG-dependent binding of TFs, which is not in complete agreement with previous hypothesis. In summary, our deep mining of the highly heterogeneous DNA methylome data in a pan-cancer context generated novel insights into the architecture of cancer epigenetics and provided a series of resources for further investigations in the related fields of cancer genomics and epigenetics.
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Affiliation(s)
- Yang Liu
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China
| | - Rongyao Huang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Liu
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
| | - Wanlu Song
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
| | - Yuting Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China
| | - Yang Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengcheng Dong
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
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629
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Gatzmann F, Falckenhayn C, Gutekunst J, Hanna K, Raddatz G, Carneiro VC, Lyko F. The methylome of the marbled crayfish links gene body methylation to stable expression of poorly accessible genes. Epigenetics Chromatin 2018; 11:57. [PMID: 30286795 PMCID: PMC6172769 DOI: 10.1186/s13072-018-0229-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022] Open
Abstract
Background The parthenogenetic marbled crayfish (Procambarus virginalis) is a novel species that has rapidly invaded and colonized various different habitats. Adaptation to different environments appears to be independent of the selection of genetic variants, but epigenetic programming of the marbled crayfish genome remains to be understood. Results Here, we provide a comprehensive analysis of DNA methylation in marbled crayfish. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue invariant, suggesting a function that is unrelated to cell fate specification. Indeed, integrative analysis of DNA methylation, chromatin accessibility and mRNA expression patterns revealed that gene body methylation correlated with limited chromatin accessibility and stable gene expression, while low-methylated genes often resided in chromatin with higher accessibility and showed increased expression variation. Interestingly, marbled crayfish also showed reduced gene body methylation and higher gene expression variability when compared with their noninvasive mother species, Procambarus fallax. Conclusions Our results provide novel insights into invertebrate gene body methylation and its potential role in adaptive gene regulation. Electronic supplementary material The online version of this article (10.1186/s13072-018-0229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fanny Gatzmann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Cassandra Falckenhayn
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Vitor Coutinho Carneiro
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
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630
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Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Res 2018; 78:5538-5547. [PMID: 30275053 PMCID: PMC6169995 DOI: 10.1158/0008-5472.can-18-0454] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/04/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
Abstract
Understanding sex differences in colon cancer is essential to advance disease prevention, diagnosis, and treatment. Males have a higher risk of developing colon cancer and a lower survival rate than women. However, the molecular features that drive these sex differences are poorly understood. In this study, we use both transcript-based and gene regulatory network methods to analyze RNA-seq data from The Cancer Genome Atlas for 445 patients with colon cancer. We compared gene expression between tumors in men and women and observed significant sex differences in sex chromosome genes only. We then inferred patient-specific gene regulatory networks and found significant regulatory differences between males and females, with drug and xenobiotics metabolism via cytochrome P450 pathways more strongly targeted in females. This finding was validated in a dataset of 1,193 patients from five independent studies. While targeting, the drug metabolism pathway did not change overall survival for males treated with adjuvant chemotherapy, females with greater targeting showed an increase in 10-year overall survival probability, 89% [95% confidence interval (CI), 78-100] survival compared with 61% (95% CI, 45-82) for women with lower targeting, respectively (P = 0.034). Our network analysis uncovers patterns of transcriptional regulation that differentiate male and female colon cancer and identifies differences in regulatory processes involving the drug metabolism pathway associated with survival in women who receive adjuvant chemotherapy. This approach can be used to investigate the molecular features that drive sex differences in other cancers and complex diseases.Significance: A network-based approach reveals that sex-specific patterns of gene targeting by transcriptional regulators are associated with survival outcome in colon cancer. This approach can be used to understand how sex influences progression and response to therapies in other cancers. Cancer Res; 78(19); 5538-47. ©2018 AACR.
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Affiliation(s)
- Camila M Lopes-Ramos
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Marieke L Kuijjer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Charles S Fuchs
- Yale Cancer Center, New Haven, Connecticut
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut
- Smilow Cancer Hospital, New Haven, Connecticut
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
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631
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Abstract
The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive regulator of promoter activity. However, whole-genome analysis of 5mC reveals widespread tissue- and cell type-specific patterns and pervasive dynamics during mammalian development. Here we review recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments as well as discuss the molecular mechanisms that connect transcriptional regulation and 5mC. Beyond the newly appreciated dynamics, regulatory roles for 5mC have been suggested in new biological contexts, such as learning and memory or aging. The use of new single-cell measurement techniques and precise editing tools will enable functional analyses of 5mC in gene expression, clarifying its role in various biological processes.
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Affiliation(s)
- Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, W12 0NN London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, W12 0NN London, UK
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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632
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The interaction landscape between transcription factors and the nucleosome. Nature 2018; 562:76-81. [PMID: 30250250 PMCID: PMC6173309 DOI: 10.1038/s41586-018-0549-5] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 08/06/2018] [Indexed: 01/01/2023]
Abstract
Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.
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633
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Goodman SJ, Roubinov DS, Bush NR, Park M, Farré P, Emberly E, Hertzman C, Essex MJ, Kobor MS, Boyce WT. Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood. Dev Sci 2018; 22:e12739. [PMID: 30176105 PMCID: PMC6433477 DOI: 10.1111/desc.12739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/08/2018] [Indexed: 12/21/2022]
Abstract
A growing body of research has documented associations between adverse childhood environments and DNA methylation, highlighting epigenetic processes as potential mechanisms through which early external contexts influence health across the life course. The present study tested a complementary hypothesis: indicators of children's early internal, biological, and behavioral responses to stressful challenges may also be linked to stable patterns of DNA methylation later in life. Children's autonomic nervous system reactivity, temperament, and mental health symptoms were prospectively assessed from infancy through early childhood, and principal components analysis (PCA) was applied to derive composites of biological and behavioral reactivity. Buccal epithelial cells were collected from participants at 15 and 18 years of age. Findings revealed an association between early life biobehavioral inhibition/disinhibition and DNA methylation across many genes. Notably, reactive, inhibited children were found to have decreased DNA methylation of the DLX5 and IGF2 genes at both time points, as compared to non‐reactive, disinhibited children. Results of the present study are provisional but suggest that the gene's profile of DNA methylation may constitute a biomarker of normative or potentially pathological differences in reactivity. Overall, findings provide a foundation for future research to explore relations among epigenetic processes and differences in both individual‐level biobehavioral risk and qualities of the early, external childhood environment.
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Affiliation(s)
- Sarah J Goodman
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Nicole R Bush
- Psychiatry, University of California, San Francisco, California.,Pediatrics, University of California, San Francisco, California
| | - Mina Park
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Pau Farré
- Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Eldon Emberly
- Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Clyde Hertzman
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
| | - Marilyn J Essex
- Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - W Thomas Boyce
- Psychiatry, University of California, San Francisco, California.,Pediatrics, University of California, San Francisco, California.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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634
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Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. eLife 2018; 7:36187. [PMID: 30188322 PMCID: PMC6126923 DOI: 10.7554/elife.36187] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023] Open
Abstract
Vascular endothelial cell (EC) function depends on appropriate organ-specific molecular and cellular specializations. To explore genomic mechanisms that control this specialization, we have analyzed and compared the transcriptome, accessible chromatin, and DNA methylome landscapes from mouse brain, liver, lung, and kidney ECs. Analysis of transcription factor (TF) gene expression and TF motifs at candidate cis-regulatory elements reveals both shared and organ-specific EC regulatory networks. In the embryo, only those ECs that are adjacent to or within the central nervous system (CNS) exhibit canonical Wnt signaling, which correlates precisely with blood-brain barrier (BBB) differentiation and Zic3 expression. In the early postnatal brain, single-cell RNA-seq of purified ECs reveals (1) close relationships between veins and mitotic cells and between arteries and tip cells, (2) a division of capillary ECs into vein-like and artery-like classes, and (3) new endothelial subtype markers, including new validated tip cell markers.
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Affiliation(s)
- Mark F Sabbagh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jacob S Heng
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Amir Rattner
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Loyal A Goff
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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635
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Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1423. [PMID: 29694718 PMCID: PMC6202284 DOI: 10.1002/wsbm.1423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/23/2018] [Accepted: 03/11/2018] [Indexed: 01/17/2023]
Abstract
Sequence-specific transcription factors (TFs) bind short DNA sequences in the genome to regulate the expression of target genes. In the last decade, numerous technical advances have enabled the determination of the DNA-binding specificities of many of these factors. Large-scale screens of many TFs enabled the creation of databases of TF DNA-binding specificities, typically represented as position weight matrices (PWMs). Although great progress has been made in determining and predicting binding specificities systematically, there are still many surprises to be found when studying a particular TF's interactions with DNA in detail. Paralogous TFs' binding specificities can differ in subtle ways, in a manner that is not immediately apparent from looking at their PWMs. These differences affect gene regulatory outputs and enable TFs to rewire transcriptional networks over evolutionary time. This review discusses recent observations made in the study of TF-DNA interactions that highlight the importance of continued in-depth analysis of TF-DNA interactions and their inherent complexity. This article is categorized under: Biological Mechanisms > Regulatory Biology.
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Affiliation(s)
- Julia M. Rogers
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, 02138, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, 02138, USA,Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
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636
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The role of epigenetics in cardiovascular health and ageing: A focus on physical activity and nutrition. Mech Ageing Dev 2018; 174:76-85. [DOI: 10.1016/j.mad.2017.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 02/06/2023]
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637
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Lead induces the up-regulation of the protein arginine methyltransferase 5 possibly by its promoter demethylation. Biochem J 2018; 475:2653-2666. [PMID: 30054435 DOI: 10.1042/bcj20180009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 01/10/2023]
Abstract
The studies on lead (Pb) exposure linking to epigenetic modulations are caused by its differential actions on global DNA methylation and histone modifications. These epigenetic changes may result in increased accessibility of the transcription factors to promoter DNA-binding elements leading to activation and expression of the gene. The protein arginine methyltransferase 5 (PRMT5) and its partner methylosome protein 50 (MEP50) together catalyze the mono- and symmetric dimethylation of arginine residues in many histone and non-histone protein substrates. Moreover, it is overexpressed in many forms of cancer. In the present study, the effects of Pb on the PRMT5 and MEP50 expression and formation of the symmetrically dimethylated arginine (SDMA), the catalytic product of the PRMT5-MEP50 complex were analyzed in vitro after exposing the A549 and MCF-7 cells. The results show that exposure to 0.1 and 1 µM of Pb strongly enhanced the expression of both PRMT5 and MEP50 transcript and protein leading to increased SDMA levels globally with H4R3 being increasingly symmetrically dimethylated in a dose-dependent manner after 48 h of Pb exposure in both cell types. The methylation-specific PCR also revealed that the CpG island present on the PRMT5 promoter proximal region was increasingly demethylated as the dose of Pb increased in a 48-h exposure window in both cells, with MCF-7 being more responsive to Pb-mediated PRMT5 promoter demethylation. The bisulfite sequencing confirmed this effect. The findings therefore indicate that Pb exposure increasing the PRMT5 expression might be one of the contributing epigenetic factors in the lead-mediated disease processes as PRMT5 has a versatile role in cellular functions and oncogenesis.
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638
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The effect of maternal care on gene expression and DNA methylation in a subsocial bee. Nat Commun 2018; 9:3468. [PMID: 30150650 PMCID: PMC6110825 DOI: 10.1038/s41467-018-05903-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Developmental plasticity describes the influence of environmental factors on phenotypic variation. An important mediator of developmental plasticity in many animals is parental care. Here, we examine the consequences of maternal care on offspring after the initial mass provisioning of brood in the small carpenter bee, Ceratina calcarata. Removal of the mother during larval development leads to increased aggression and avoidance in adulthood. This corresponds with changes in expression of over one thousand genes, alternative splicing of hundreds of genes, and significant changes to DNA methylation. We identify genes related to metabolic and neuronal functions that may influence developmental plasticity and aggression. We observe no genome-wide association between differential DNA methylation and differential gene expression or splicing, though indirect relationships may exist between these factors. Our results provide insight into the gene regulatory context of DNA methylation in insects and the molecular avenues through which variation in maternal care influences developmental plasticity.
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639
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Chen F, Zhang Q, Deng X, Zhang X, Chen C, Lv D, Li Y, Li D, Zhang Y, Li P, Diao Y, Kang L, Owen GI, Chen J, Li Z. Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues. Epigenetics 2018; 13:721-741. [PMID: 30009687 DOI: 10.1080/15592294.2018.1500057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The relationship between CpG content and DNA methylation has attracted considerable interest in recent years. Direct or indirect methods have been developed to investigate their regulatory functions based on various hypotheses, large cohort studies, and meta-analyses. However, all of these analyses were performed at units of CpG blocks and, thus, the influence of finer genome structure has been neglected. Herein, we present a novel algorithm of base-pair resolution to systematically investigate the relationship between CpG contents and DNA methylation. By introducing the concept of 'complementary index' we examined the methylomes of 34 adult and 7 embryonic tissues and successfully fitted the relationship of DNA methylation and CpG density into a nonlinear mathematical model. A further algorithm was developed to locate the regions where CpG density does not match expectations from the model, termed 'conflict of gap' (COG) regions. Interestingly, COGs are highly concordant in human and mouse and their distributions display a tissue-specific pattern. Based on COG methylation patterns we correctly classified tissues according to their function or origin. We demonstrate that COGs based on our method can reveal more and deeper information than traditional differential methylation region (DMR) approaches. We also found that when COGs are located near to transcription start site (TSS), these regions can determine which promoters will be utilized for initiating gene transcription. Furthermore, COGs located far from the TSS perform as enhancers in terms of histone modification, sequence conservation, transcription factor binding, and DNase I-hypersensitivity.
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Affiliation(s)
- Fushun Chen
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Qingzheng Zhang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Xiaodi Deng
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Xia Zhang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Chengjun Chen
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Dekang Lv
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Yulong Li
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Dan Li
- b The Second Hospital of Dalian Medical University , Dalian , China
| | - Yu Zhang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Peiying Li
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Yunpeng Diao
- c Department of Pharmacy , Dalian Medical University , Dalian , China
| | - Lan Kang
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
| | - Gareth I Owen
- d Faculty of Biological Sciences , Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Jun Chen
- b The Second Hospital of Dalian Medical University , Dalian , China
| | - Zhiguang Li
- a Center of Genome and Personalized Medicine , Institute of Cancer Stem Cell, Dalian Medical University , Dalian , China
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640
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Oyinlade O, Wei S, Kammers K, Liu S, Wang S, Ma D, Huang ZY, Qian J, Zhu H, Wan J, Xia S. Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions. Epigenetics 2018; 13:751-768. [PMID: 30058478 DOI: 10.1080/15592294.2018.1504592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent studies have revealed an unexpected role of DNA methylation at promoter regions in transcription activation. However, whether DNA methylation at enhancer regions activates gene expression and influences cellular functions remains to be determined. In this study, by employing the transcription factor krÜppel-like factor 4 (KLF4) that binds to methylated CpGs (mCpGs), we investigated the molecular outcomes of the recruitment of KLF4 to mCpGs at enhancer regions in human glioblastoma cells. First, by integrating KLF4 ChIP-seq, whole-genome bisulfite sequence, and H3K27ac ChIP-seq datasets, we found 1,299 highly methylated (β >0.5) KLF4 binding sites, three-quarters of which were located at putative enhancer regions, including gene bodies and intergenic regions. In the meantime, by proteomics, we identified 16 proteins as putative targets upregulated by KLF4-mCpG binding at enhancer regions. By chromosome conformation capture (3C) analysis, we demonstrated that KLF4 bound to methylated CpGs at the enhancer regions of the B-cell lymphocyte kinase (BLK) and Lim domain only protein 7 (LMO7) genes, and activated their expression via 3D chromatin loop formation with their promoter regions. Expression of mutant KLF4, which lacks KLF4 ability to bind methylated DNA, or removal of DNA methylation in enhancer regions by a DNA methyltransferase inhibitor abolished chromatin loop formation and gene expression, suggesting the essential role of DNA methylation in enhancer-promoter interactions. Finally, we performed functional assays and showed that BLK was involved in glioblastoma cell migration. Together, our study established the concept that DNA methylation at enhancer regions interacts with transcription factors to activate gene expression and influence cellular functions.
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Affiliation(s)
- Olutobi Oyinlade
- a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA.,b Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA
| | - Shuang Wei
- a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA.,c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA.,g Department of Respiratory and Critical Care Medicine, Tongji Hospital , Tongji Medical College Huazhong University of Science and Technology , Wuhan , China
| | - Kai Kammers
- d Division of Biostatistics and Bioinformatics,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine , Johns Hopkins University , Baltimore , Maryland , USA
| | - Sheng Liu
- i Department of Medical and Molecular Genetics , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Shuyan Wang
- a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA.,c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA
| | - Ding Ma
- a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA.,c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA
| | - Zhi-Yong Huang
- h Department of General Surgery, Tongji Hospital , Tongji Medical College Huazhong University of Science and Technology , Wuhan , China
| | - Jiang Qian
- e Wilmer Eye Institute,Johns Hopkins School of Medicine , Johns Hopkins University , Baltimore , Maryland , USA
| | - Heng Zhu
- b Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA.,f Center for High Throughput Biology, Johns Hopkins School of Medicine , Johns Hopkins University , Baltimore , Maryland , USA
| | - Jun Wan
- i Department of Medical and Molecular Genetics , Indiana University School of Medicine , Indianapolis , IN , USA.,j Center for Computational Biology and Bioinformatics , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Shuli Xia
- a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA.,c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA
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641
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Catuogno S, Esposito CL, Ungaro P, de Franciscis V. Nucleic Acid Aptamers Targeting Epigenetic Regulators: An Innovative Therapeutic Option. Pharmaceuticals (Basel) 2018; 11:ph11030079. [PMID: 30149585 PMCID: PMC6161095 DOI: 10.3390/ph11030079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
Epigenetic mechanisms include DNA methylation, posttranslational modifications of histones, chromatin remodeling factors, and post transcriptional gene regulation by noncoding RNAs. All together, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Targeting enzymatic regulators responsible for DNA and chromatin modifications hold promise for modulating the transcriptional regulation of genes that are involved in cancer, as well as in chronic noncommunicable metabolic diseases like obesity, diabetes, and cardiovascular diseases. Increasingly studies are emerging, leading to the identification of specific and effective molecules targeting epigenetic pathways involved in disease onset. In this regard, RNA interference, which uses small RNAs to reduce gene expression and nucleic acid aptamers are arising as very promising candidates in therapeutic approach. Common to all these strategies is the imperative challenge of specificity. In this regard, nucleic acid aptamers have emerged as an attractive class of carrier molecules due to their ability to bind with high affinity to specific ligands, their high chemical flexibility as well as tissue penetration capability. In this review, we will focus on the recent progress in the field of aptamers used as targeting moieties able to recognize and revert epigenetics marks involved in diseases onset.
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Affiliation(s)
- Silvia Catuogno
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Carla Lucia Esposito
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Paola Ungaro
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Vittorio de Franciscis
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
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642
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Hui T, Cao Q, Wegrzyn-Woltosz J, O'Neill K, Hammond CA, Knapp DJHF, Laks E, Moksa M, Aparicio S, Eaves CJ, Karsan A, Hirst M. High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations. Stem Cell Reports 2018; 11:578-592. [PMID: 30078558 PMCID: PMC6093082 DOI: 10.1016/j.stemcr.2018.07.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023] Open
Abstract
Increasing evidence of functional and transcriptional heterogeneity in phenotypically similar cells examined individually has prompted interest in obtaining parallel methylome data. We describe the development and application of such a protocol to index-sorted murine and human hematopoietic cells that are highly enriched in their content of functionally defined stem cells. Utilizing an optimized single-cell bisulfite sequencing protocol, we obtained quantitative DNA methylation measurements of up to 5.7 million CpGs in single hematopoietic cells. In parallel, we developed an analytical strategy (PDclust) to define single-cell DNA methylation states through pairwise comparisons of single-CpG methylation measurements. PDclust revealed that a single-cell epigenetic state can be described by a small (<1%) stochastically sampled fraction of CpGs and that these states are reflective of cell identity and state. Using relationships revealed by PDclust, we derive near complete methylomes for epigenetically distinct subpopulations of hematopoietic cells enriched for functional stem cell content.
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Affiliation(s)
- Tony Hui
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Qi Cao
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Joanna Wegrzyn-Woltosz
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Colin A Hammond
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - David J H F Knapp
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Emma Laks
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada.
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643
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Johnson TE, Lee JH, Myler LR, Zhou Y, Mosley TJ, Yang SH, Uprety N, Kim J, Paull TT. Homeodomain Proteins Directly Regulate ATM Kinase Activity. Cell Rep 2018; 24:1471-1483. [PMID: 30089259 PMCID: PMC6127865 DOI: 10.1016/j.celrep.2018.06.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM) is a serine/threonine kinase that coordinates the response to DNA double-strand breaks and oxidative stress. NKX3.1, a prostate-specific transcription factor, was recently shown to directly stimulate ATM kinase activity through its highly conserved homeodomain. Here, we show that other members of the homeodomain family can also regulate ATM kinase activity. We found that six representative homeodomain proteins (NKX3.1, NKX2.2, TTF1, NKX2.5, HOXB7, and CDX2) physically and functionally interact with ATM and with the Mre11-Rad50-Nbs1 (MRN) complex that activates ATM in combination with DNA double-strand breaks. The binding between homeodomain proteins and ATM stimulates oxidation-induced ATM activation in vitro but inhibits ATM kinase activity in the presence of MRN and DNA and in human cells. These findings suggest that many tissue-specific homeodomain proteins may regulate ATM activity during development and differentiation and that this is a unique mechanism for the control of the DNA damage response.
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Affiliation(s)
- Tanya E Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ji-Hoon Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yi Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Trenell J Mosley
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soo-Hyun Yang
- College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nadima Uprety
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA.
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644
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Pathak R, Feil R. Environmental effects on chromatin repression at imprinted genes and endogenous retroviruses. Curr Opin Chem Biol 2018; 45:139-147. [DOI: 10.1016/j.cbpa.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/05/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
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645
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Grasse S, Lienhard M, Frese S, Kerick M, Steinbach A, Grimm C, Hussong M, Rolff J, Becker M, Dreher F, Schirmer U, Boerno S, Ramisch A, Leschber G, Timmermann B, Grohé C, Lüders H, Vingron M, Fichtner I, Klein S, Odenthal M, Büttner R, Lehrach H, Sültmann H, Herwig R, Schweiger MR. Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance. Genome Med 2018; 10:55. [PMID: 30029672 PMCID: PMC6054719 DOI: 10.1186/s13073-018-0562-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/21/2018] [Indexed: 12/31/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related deaths worldwide and is primarily treated with radiation, surgery, and platinum-based drugs like cisplatin and carboplatin. The major challenge in the treatment of NSCLC patients is intrinsic or acquired resistance to chemotherapy. Molecular markers predicting the outcome of the patients are urgently needed. Methods Here, we employed patient-derived xenografts (PDXs) to detect predictive methylation biomarkers for platin-based therapies. We used MeDIP-Seq to generate genome-wide DNA methylation profiles of 22 PDXs, their parental primary NSCLC, and their corresponding normal tissues and complemented the data with gene expression analyses of the same tissues. Candidate biomarkers were validated with quantitative methylation-specific PCRs (qMSP) in an independent cohort. Results Comprehensive analyses revealed that differential methylation patterns are highly similar, enriched in PDXs and lung tumor-specific when comparing differences in methylation between PDXs versus primary NSCLC. We identified a set of 40 candidate regions with methylation correlated to carboplatin response and corresponding inverse gene expression pattern even before therapy. This analysis led to the identification of a promoter CpG island methylation of LDL receptor-related protein 12 (LRP12) associated with increased resistance to carboplatin. Validation in an independent patient cohort (n = 35) confirmed that LRP12 methylation status is predictive for therapeutic response of NSCLC patients to platin therapy with a sensitivity of 80% and a specificity of 84% (p < 0.01). Similarly, we find a shorter survival time for patients with LRP12 hypermethylation in the TCGA data set for NSCLC (lung adenocarcinoma). Conclusions Using an epigenome-wide sequencing approach, we find differential methylation patterns from primary lung cancer and PDX-derived cancers to be very similar, albeit with a lower degree of differential methylation in primary tumors. We identify LRP12 DNA methylation as a powerful predictive marker for carboplatin resistance. These findings outline a platform for the identification of epigenetic therapy resistance biomarkers based on PDX NSCLC models. Electronic supplementary material The online version of this article (10.1186/s13073-018-0562-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabrina Grasse
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Martin Kerick
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Present Address: Department of Cell Biology and Immunology, Institute for Parasitology and Biomedicine, Granada, Spain
| | - Anne Steinbach
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, Germany
| | - Christina Grimm
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Michelle Hussong
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, CMMC, Cologne, Germany
| | - Jana Rolff
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Michael Becker
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Felix Dreher
- Alacris Theranostics GmbH Berlin, Berlin, Germany
| | - Uwe Schirmer
- Cancer Genome Research Group, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research, Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna Ramisch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Iduna Fichtner
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Sebastian Klein
- Institute of Pathology, University of Cologne, Cologne, Germany.,Else Kröner Forschungskolleg Clonal Evolution in Cancer, University Hospital Cologne, Weyertal 115b, 50931, Cologne, Germany
| | | | | | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH Berlin, Berlin, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research, Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michal R Schweiger
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany. .,Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Center for Molecular Medicine Cologne, CMMC, Cologne, Germany.
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646
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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647
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Zhang J, Han X, Gao C, Xing Y, Qi Z, Liu R, Wang Y, Zhang X, Yang YG, Li X, Sun B, Tian X. 5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:187-199. [PMID: 30010036 PMCID: PMC6076378 DOI: 10.1016/j.gpb.2018.06.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 02/06/2023]
Abstract
Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls (mean decrease accuracy >3.2, P < 3.68E−19) using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient’s cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.
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Affiliation(s)
- Ji Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Xiao Han
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunchun Gao
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yurong Xing
- Physical Examination Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zheng Qi
- Department of Anesthesiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ruijuan Liu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Yueqin Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China
| | - Yun-Gui Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangnan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Baofa Sun
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, School of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China.
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648
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Soulsbury CD, Lipponen A, Wood K, Mein CA, Hoffman JI, Lebigre C. Age- and quality-dependent DNA methylation correlate with melanin-based coloration in a wild bird. Ecol Evol 2018; 8:6547-6557. [PMID: 30038756 PMCID: PMC6053554 DOI: 10.1002/ece3.4132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022] Open
Abstract
Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) as well as by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin-based traits are known to relate to condition and there is a well-characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that genetic quality could influence trait expression via differential methylation and differential gene expression. We therefore conducted a pilot study examining DNA methylation at a candidate gene (agouti-related neuropeptide: AgRP) in the black grouse Lyrurus tetrix. We specifically tested whether CpG methylation covaries with age and multilocus heterozygosity (a proxy of genetic quality) and from there whether the expression of a melanin-based ornament (ultraviolet-blue chroma) correlates with DNA methylation. Consistent with expectations, we found clear evidence for age- and heterozygosity-specific patterns of DNA methylation, with two CpG sites showing the greatest DNA methylation in highly heterozygous males at their peak age of reproduction. Furthermore, DNA methylation at three CpG sites was significantly positively correlated with ultraviolet-blue chroma. Ours is the first study to our knowledge to document age- and quality-dependent variation in DNA methylation and to show that dynamic sexual trait expression across the lifespan of an organism is associated with patterns of DNA methylation. Although we cannot demonstrate causality, our work provides empirical support for a mechanism that could potentially link key individual factors to variation in sexual trait expression in a wild vertebrate.
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Affiliation(s)
| | - Anssi Lipponen
- Department of Biological and Environmental ScienceUniversity of JyväskyläFinland
- A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Kristie Wood
- The Genome Centre, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Charles A. Mein
- The Genome Centre, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
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649
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Marjonen H, Auvinen P, Kahila H, Tšuiko O, Kõks S, Tiirats A, Viltrop T, Tuuri T, Söderström-Anttila V, Suikkari AM, Salumets A, Tiitinen A, Kaminen-Ahola N. rs10732516 polymorphism at the IGF2/H19 locus associates with genotype-specific effects on placental DNA methylation and birth weight of newborns conceived by assisted reproductive technology. Clin Epigenetics 2018; 10:80. [PMID: 29946374 PMCID: PMC6006593 DOI: 10.1186/s13148-018-0511-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Assisted reproductive technology (ART) has been associated with low birth weight of fresh embryo transfer (FRESH) derived and increased birth weight of frozen embryo transfer (FET)-derived newborns. Owing to that, we focused on imprinted insulin-like growth factor 2 (IGF2)/H19 locus known to be important for normal growth. This locus is regulated by H19 imprinting control region (ICR) with seven binding sites for the methylation-sensitive zinc finger regulatory protein (CTCF). A polymorphism rs10732516 G/A in the sixth binding site for CTCF, associates with a genotype-specific trend to the DNA methylation. Due to this association, 62 couples with singleton pregnancies derived from FRESH (44 IVF/18 ICSI), 24 couples from FET (15 IVF/9 ICSI), and 157 couples with spontaneously conceived pregnancies as controls were recruited in Finland and Estonia for genotype-specific examination. DNA methylation levels at the H19 ICR, H19 DMR, and long interspersed nuclear elements in placental tissue were explored by MassARRAY EpiTYPER (n = 122). Allele-specific changes in the methylation level of H19 ICR in placental tissue (n = 26) and white blood cells (WBC, n = 8) were examined by bisulfite sequencing. Newborns' (n = 243) anthropometrics was analyzed by using international growth standards. Results A consistent trend of genotype-specific decreased methylation level was observed in paternal allele of rs10732516 paternal A/maternal G genotype, but not in paternal G/maternal A genotype, at H19 ICR in ART placentas. This hypomethylation was not detected in WBCs. Also genotype-specific differences in FRESH-derived newborns' birth weight and head circumference were observed (P = 0.04, P = 0.004, respectively): FRESH-derived newborns with G/G genotype were heavier (P = 0.04) and had larger head circumference (P = 0.002) compared to newborns with A/A genotype. Also, the placental weight and birth weight of controls, FRESH- and FET-derived newborns differed significantly in rs10732516 A/A genotype (P = 0.024, P = 0.006, respectively): the placentas and newborns of FET-derived pregnancies were heavier compared to FRESH-derived pregnancies (P = 0.02, P = 0.004, respectively). Conclusions The observed DNA methylation changes together with the phenotypic findings suggest that rs10732516 polymorphism associates with the effects of ART in a parent-of-origin manner. Therefore, this polymorphism should be considered when the effects of environmental factors on embryonic development are studied.
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Affiliation(s)
- Heidi Marjonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Pauliina Auvinen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Hanna Kahila
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Olga Tšuiko
- Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Sulev Kõks
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Airi Tiirats
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Paediatric ICU, Tartu University Hospital, Tartu, Estonia
| | - Triin Viltrop
- Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Viveca Söderström-Anttila
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- The Family Federation of Finland, Fertility Clinic, Helsinki, Finland
| | | | - Andres Salumets
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Aila Tiitinen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nina Kaminen-Ahola
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
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Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 2018; 52:77-85. [PMID: 29925040 DOI: 10.1016/j.gde.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022]
Abstract
The discovery of induced pluripotent stem cells (iPSCs) has solidified the concept of transcription factors as major players in controlling cell identity and provided a tractable tool to study how somatic cell identity can be dismantled and pluripotency established. A number of landmark studies have established hallmarks and roadmaps of iPSC formation by describing relative kinetics of transcriptional, protein and epigenetic changes, including alterations in DNA methylation and histone modifications. Recently, technological advancements such as single-cell analyses, high-resolution genome-wide chromatin assays and more efficient reprogramming systems have been used to challenge and refine our understanding of the reprogramming process. Here, we will outline novel insights into the molecular mechanisms underlying iPSC formation, focusing on how the core reprogramming factors OCT4, KLF4, SOX2 and MYC (OKSM) drive changes in gene expression, chromatin state and 3D genome topology. In addition, we will discuss unexpected consequences of reprogramming factor expression in in vitro and in vivo systems that may point towards new applications of iPSC technology.
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Affiliation(s)
- Effie Apostolou
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA.
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