1
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Torres-Berrío A, Estill M, Patel V, Ramakrishnan A, Kronman H, Minier-Toribio A, Issler O, Browne CJ, Parise EM, van der Zee YY, Walker DM, Martínez-Rivera FJ, Lardner CK, Durand-de Cuttoli R, Russo SJ, Shen L, Sidoli S, Nestler EJ. Mono-methylation of lysine 27 at histone 3 confers lifelong susceptibility to stress. Neuron 2024:S0896-6273(24)00413-6. [PMID: 38959894 DOI: 10.1016/j.neuron.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/05/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Histone post-translational modifications are critical for mediating persistent alterations in gene expression. By combining unbiased proteomics profiling and genome-wide approaches, we uncovered a role for mono-methylation of lysine 27 at histone H3 (H3K27me1) in the enduring effects of stress. Specifically, mice susceptible to early life stress (ELS) or chronic social defeat stress (CSDS) displayed increased H3K27me1 enrichment in the nucleus accumbens (NAc), a key brain-reward region. Stress-induced H3K27me1 accumulation occurred at genes that control neuronal excitability and was mediated by the VEFS domain of SUZ12, a core subunit of the polycomb repressive complex-2, which controls H3K27 methylation patterns. Viral VEFS expression changed the transcriptional profile of the NAc, led to social, emotional, and cognitive abnormalities, and altered excitability and synaptic transmission of NAc D1-medium spiny neurons. Together, we describe a novel function of H3K27me1 in the brain and demonstrate its role as a "chromatin scar" that mediates lifelong stress susceptibility.
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Affiliation(s)
- Angélica Torres-Berrío
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Lurie Center for Autism, Massachusetts General Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Molly Estill
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vishwendra Patel
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hope Kronman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angélica Minier-Toribio
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Orna Issler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caleb J Browne
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yentl Y van der Zee
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deena M Walker
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Freddyson J Martínez-Rivera
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Casey K Lardner
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romain Durand-de Cuttoli
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott J Russo
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2
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Alves VC, Figueiro-Silva J, Ferrer I, Carro E. Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer's disease. Cell Mol Life Sci 2023; 80:196. [PMID: 37405535 PMCID: PMC10322771 DOI: 10.1007/s00018-023-04845-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Modulation of brain olfactory (OR) and taste receptor (TASR) expression was recently reported in neurological diseases. However, there is still limited evidence of these genes' expression in the human brain and the transcriptional regulation mechanisms involved remain elusive. We explored the possible expression and regulation of selected OR and TASR in the human orbitofrontal cortex (OFC) of sporadic Alzheimer's disease (AD) and non-demented control specimens using quantitative real-time RT-PCR and ELISA. Global H3K9me3 amounts were measured on OFC total histone extracts, and H3K9me3 binding at each chemoreceptor locus was examined through native chromatin immunoprecipitation. To investigate the potential interactome of the repressive histone mark H3K9me3 in OFC specimens, native nuclear complex co-immunoprecipitation (Co-IP) was combined with reverse phase-liquid chromatography coupled to mass spectrometry analysis. Interaction between H3K9me3 and MeCP2 was validated by reciprocal Co-IP, and global MeCP2 levels were quantitated. We found that OR and TAS2R genes are expressed and markedly downregulated in OFC at early stages of sporadic AD, preceding the progressive reduction in their protein levels and the appearance of AD-associated neuropathology. The expression pattern did not follow disease progression suggesting transcriptional regulation through epigenetic mechanisms. We discovered an increase of OFC global H3K9me3 levels and a substantial enrichment of this repressive signature at ORs and TAS2Rs proximal promoter at early stages of AD, ultimately lost at advanced stages. We revealed the interaction between H3K9me3 and MeCP2 at early stages and found that MeCP2 protein is increased in sporadic AD. Findings suggest MeCP2 might be implicated in OR and TAS2R transcriptional regulation through interaction with H3K9me3, and as an early event, it may uncover a novel etiopathogenetic mechanism of sporadic AD.
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Affiliation(s)
- Victoria Cunha Alves
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
| | - Joana Figueiro-Silva
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
| | - Isidre Ferrer
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Institute of Neuropathology, Bellvitge University Hospital-IDIBELL, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Eva Carro
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Present Address: Neurobiology of Alzheimer’s Disease Unit, Functional Unit for Research Into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain
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3
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Torres-Berrío A, Estill M, Ramakrishnan A, Kronman H, Patel V, Minier-Toribio A, Issler O, Browne CJ, Parise EM, van der Zee Y, Walker D, Martínez-Rivera FJ, Lardner CK, Cuttoli RDD, Russo SJ, Shen L, Sidoli S, Nestler EJ. Monomethylation of Lysine 27 at Histone 3 Confers Lifelong Susceptibility to Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539829. [PMID: 37214877 PMCID: PMC10197593 DOI: 10.1101/2023.05.08.539829] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Histone post-translational modifications are critical for mediating persistent alterations in gene expression. By combining unbiased proteomics profiling, and genome-wide approaches, we uncovered a role for mono-methylation of lysine 27 at histone H3 (H3K27me1) in the enduring effects of stress. Specifically, mice exposed to early life stress (ELS) or to chronic social defeat stress (CSDS) in adulthood displayed increased enrichment of H3K27me1, and transient decreases in H3K27me2, in the nucleus accumbens (NAc), a key brain-reward region. Stress induction of H3K27me1 was mediated by the VEFS domain of SUZ12, a core subunit of the polycomb repressive complex-2, which is induced by chronic stress and controls H3K27 methylation patterns. Overexpression of the VEFS domain led to social, emotional, and cognitive abnormalities, and altered excitability of NAc D1 mediums spiny neurons. Together, we describe a novel function of H3K27me1 in brain and demonstrate its role as a "chromatin scar" that mediates lifelong stress susceptibility.
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4
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Imagawa E, Seyama R, Aoi H, Uchiyama Y, Marcarini BG, Furquim I, Honjo RS, Bertola DR, Kim CA, Matsumoto N. Imagawa-Matsumoto syndrome: SUZ12-related overgrowth disorder. Clin Genet 2023; 103:383-391. [PMID: 36645289 DOI: 10.1111/cge.14296] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/17/2023]
Abstract
The SUZ12 gene encodes a subunit of polycomb repressive complex 2 (PRC2) that is essential for development by silencing the expression of multiple genes. Germline heterozygous variants in SUZ12 have been found in Imagawa-Matsumoto syndrome (IMMAS) characterized by overgrowth and multiple dysmorphic features. Similarly, both EZH2 and EED also encode a subunit of PRC2 each and their pathogenic variants cause Weaver syndrome and Cohen-Gibson syndrome, respectively. Clinical manifestations of these syndromes significantly overlap, although their different prevalence rates have recently been noted: generalized overgrowth, intellectual disability, scoliosis, and excessive loose skin appear to be less prevalent in IMMAS than in the other two syndromes. We could not determine any apparent genotype-phenotype correlation in IMMAS. The phenotype of neurofibromatosis type 1 arising from NF1 deletion was also shown to be modified by the deletion of SUZ12, 560 kb away. This review deepens our understanding of the clinical and genetic characteristics of IMMAS together with other overgrowth syndromes related to PRC2. We also report on a novel IMMAS patient carrying a splicing variant (c.1023+1G>C) in SUZ12. This patient had a milder phenotype than other previously reported IMMAS cases, with no macrocephaly or overgrowth phenotypes, highlighting the clinical variation in IMMAS.
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Affiliation(s)
- Eri Imagawa
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Bruno Guimaraes Marcarini
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Isabel Furquim
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Rachel Sayuri Honjo
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Debora Romeo Bertola
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Chong Ae Kim
- Genetics Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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5
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Shirahama Y, Yamamoto K. The E2F6 Transcription Factor is Associated with the Mammalian SUZ12-Containing Polycomb Complex. Kurume Med J 2023; 67:171-183. [PMID: 36464274 DOI: 10.2739/kurumemedj.ms674006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Polycomb group protein (PcG) SUZ12 forms Polycomb repressive complexes together with histone methyltransferase EZH2. Although the complexes have been demonstrated to be involved in epigenetic maintenance of gene expression in a transcriptional repressive state, it is unclear how they are recruited to the target genes. Here we report that SUZ12 directly interacts with site-specific transcriptional repressor E2F6 and forms a complex together with EZH2. SUZ12 interacts with E2F6 selectively among the E2F family proteins and E2F6- containing SUZ12-EZH2 complex was biochemically purified from HEK293 cells stably expressing Flag-tagged SUZ12. Chromatin immunoprecipitation assays revealed the target genes of the E2F6-SUZ12-EZH2 complex. Contrary to expectation, the promoter regions of these genes are not or only weakly tri-methylated at histone H3-K27, and their expression is down-regulated by depletion of EZH2. Given that the transactivation function of SUZ12-EZH2 has been previously reported, the inhibitory effect on E2F6-mediated transcriptional repression by physical interaction can be considered a candidate mechanism of gene activation by these PcGs.
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Affiliation(s)
- Yuko Shirahama
- Department of Medical Biochemistry, Kurume University School of Medicine
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine
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6
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Wu X, Liu H, Lian B, Jiang X, Chen C, Tang T, Ding X, Hu J, Zhao S, Zhang S, Wu J. Genome-wide analysis of epigenetic and transcriptional changes in the pathogenesis of RGSV in rice. FRONTIERS IN PLANT SCIENCE 2023; 13:1090794. [PMID: 36714706 PMCID: PMC9874293 DOI: 10.3389/fpls.2022.1090794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Rice grassy stunt virus (RGSV), a typical negative single-stranded RNA virus, invades rice and generates several disease signs, including dwarfing, tillering, and sterility. Previous research has revealed that RGSV-encoded proteins can force the host's ubiquitin-proteasome system to utilize them for viral pathogenesis. However, most of the studies were limited to a single omics level and lacked multidimensional data collection and correlation analysis on the mechanisms of RGSV-rice interactions. Here, we performed a comprehensive association analysis of genome-wide methylation sequencing, transcriptome sequencing, and histone H3K9me3 modification in RGSV-infested as well as non-infested rice leaves, and the levels of all three cytosine contexts (CG, CHG and CHH) were found to be slightly lower in RGSV-infected rice leaves than in normal rice. Large proportions of DMRs were distributed in the promoter and intergenic regions, and most DMRs were enriched in the CHH context, where the number of CHH hypo-DMRs was almost twice as high as that of hyper-DMRs. Among the genes with down-regulated expression and hypermethylation, we analyzed and identified 11 transcripts involved in fertility, plant height and tillering, and among the transcribed up-regulated and hypermethylated genes, we excavated 7 transcripts related to fertility, plant height and tillering. By analyzing the changes of histone H3K9me3 modification before and after virus infestation, we found that the distribution of H3K9me3 modification in the whole rice genome was prevalent, mainly concentrated in the gene promoter and gene body regions, which was distinctly different from the characteristics of animals. Combined with transcriptomic data, H3K9me3 mark was found to favor targeting highly expressed genes. After RGSV infection, H3K9me3 modifications in several regions of CTK and BR hormone signaling-related genes were altered, providing important targets for subsequent studies.
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Affiliation(s)
- Xiaoqing Wu
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongfei Liu
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bi Lian
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xue Jiang
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng Chen
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianxin Tang
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinlun Ding
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Hu
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shanshan Zhao
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuai Zhang
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
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7
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Wen Z, He K, Zhan M, Li Y, Liu F, He X, Wei Y, Zhao W, Zhang Y, Xue Y, Xia Y, Wang F, Xia Z, Xin Y, Wu Y, Duan X, Xiao J, Shen F, Feng Y, Xiang G, Lu L. Distinct binding pattern of EZH2 and JARID2 on RNAs and DNAs in hepatocellular carcinoma development. Front Oncol 2022; 12:904633. [PMID: 36578923 PMCID: PMC9792092 DOI: 10.3389/fonc.2022.904633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/14/2022] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most malignant cancers worldwide, with high mortality. However, the molecular regulatory mechanisms of liver cancer, especially transcriptional and post-transcriptional mechanisms, should be further studied. Here we used chromatin and cross-linking immunoprecipitation with high throughput sequencing methods (ChIP-seq and CLIP-seq) to capture the global binding profiles on RNAs and DNAs of Enhancer of zeste homolog 2 (EZH2) and its partner Jumonji And AT-Rich Interaction Domain Containing 2 (JARID2) in liver carcinoma cell lines (HepG2) and normal liver cell line (THLE-2), respectively. We also integrated HCC transcriptome data from the TCGA to analyze the expression pattern of bound genes. We found that EZH2 and JARID2 both showed distinct binding profiles between HepG2 and THLE-2 cells. By binding to the primary RNAs, bound transcripts of EZH2 and JARID2 in HepG2 showed significantly increased transcriptional levels in HCC patients. By performing gene set enrichment analysis (GSEA), the bound transcripts were also highly related to HCC development. We also found EZH2 and JARID2 could specifically bind to several long noncoding RNAs (lncRNAs), including H19. By exploring the DNA binding profile, we detected a dramatically repressed DNA binding ability of EZH2 in HepG2 cells. We also found that the EZH2-bound genes showed slightly increased transcriptional levels in HepG2 cells. Integrating analysis of the RNA and DNA binding profiles suggests EZH2 and JARID2 shift their binding ability from DNA to RNA in HepG2 cells to promote cancer development in HCC. Our study provided a comprehensive and distinct binding profile on RNAs and DNAs of EZH2 and JARID2 in liver cancer cell lines, suggesting their potential novel functional manners to promote HCC development.
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Affiliation(s)
- Zhili Wen
- Department of Gastroenterology, Second Affiliated Hospital, Nanchang University, Nanchang, China
- Infectious Hospital, Nanchang University, Nanchang, China
| | - Ke He
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Meixiao Zhan
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yong Li
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Fei Liu
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xu He
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yanli Wei
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhao
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yu Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Yaqiang Xue
- Center for Genome Analysis, ABLife Inc., Wuhan, China
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, China
| | - Yong Xia
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Fenfen Wang
- Department of Gastroenterology, Second Affiliated Hospital, Nanchang University, Nanchang, China
| | - Zhenglin Xia
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yongjie Xin
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yeye Wu
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Xiaopeng Duan
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Jing Xiao
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Feng Shen
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Yuliang Feng
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Guoan Xiang
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Ligong Lu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
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8
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Farley SJ, Grishok A, Zeldich E. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain. Epigenetics Chromatin 2022; 15:39. [PMID: 36463299 PMCID: PMC9719135 DOI: 10.1186/s13072-022-00471-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability is a well-known hallmark of Down Syndrome (DS) that results from the triplication of the critical region of human chromosome 21 (HSA21). Major studies were conducted in recent years to gain an understanding about the contribution of individual triplicated genes to DS-related brain pathology. Global transcriptomic alterations and widespread changes in the establishment of neural lineages, as well as their differentiation and functional maturity, suggest genome-wide chromatin organization alterations in trisomy. High Mobility Group Nucleosome Binding Domain 1 (HMGN1), expressed from HSA21, is a chromatin remodeling protein that facilitates chromatin decompaction and is associated with acetylated lysine 27 on histone H3 (H3K27ac), a mark correlated with active transcription. Recent studies causatively linked overexpression of HMGN1 in trisomy and the development of DS-associated B cell acute lymphoblastic leukemia (B-ALL). HMGN1 has been shown to antagonize the activity of the Polycomb Repressive Complex 2 (PRC2) and prevent the deposition of histone H3 lysine 27 trimethylation mark (H3K27me3), which is associated with transcriptional repression and gene silencing. However, the possible ramifications of the increased levels of HMGN1 through the derepression of PRC2 target genes on brain cell pathology have not gained attention. In this review, we discuss the functional significance of HMGN1 in brain development and summarize accumulating reports about the essential role of PRC2 in the development of the neural system. Mechanistic understanding of how overexpression of HMGN1 may contribute to aberrant brain cell phenotypes in DS, such as altered proliferation of neural progenitors, abnormal cortical architecture, diminished myelination, neurodegeneration, and Alzheimer's disease-related pathology in trisomy 21, will facilitate the development of DS therapeutic approaches targeting chromatin.
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Affiliation(s)
- Sean J. Farley
- grid.189504.10000 0004 1936 7558Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Alla Grishok
- grid.189504.10000 0004 1936 7558Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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9
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Williams G, Chambers D, Rahman R, Molina-Holgado F. Transcription Profile and Pathway Analysis of the Endocannabinoid Receptor Inverse Agonist AM630 in the Core and Infiltrative Boundary of Human Glioblastoma Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072049. [PMID: 35408449 PMCID: PMC9000751 DOI: 10.3390/molecules27072049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/01/2022] [Accepted: 03/11/2022] [Indexed: 01/02/2023]
Abstract
Background: We have previously reported that the endocannabinoid receptor inverse agonist AM630 is a potent inhibitor of isocitrade dehydrogenase-1 wild-type glioblastoma (GBM) core tumour cell proliferation. To uncover the mechanism behind the anti-tumour effects we have performed a transcriptional analysis of AM630 activity both in the tumour core cells (U87) and the invasive margin cells (GIN-8), the latter representing a better proxy of post-surgical residual disease. Results: The core and invasive margin cells exhibited markedly different gene expression profiles and only the core cells had high expression of a potential AM630 target, the CB1 receptor. Both cell types had moderate expression of the HTR2B serotonin receptor, a reported AM630 target. We found that the AM630 driven transcriptional response was substantially higher in the central cells than in the invasive margin cells, with the former driving the up regulation of immune response and the down regulation of cell cycle and metastatic pathways and correlating with transcriptional responses driven by established anti-neoplastics as well as serotonin receptor antagonists. Conclusion: Our results highlight the different gene sets involved in the core and invasive margin cell lines derived from GBM and an associated marked difference in responsiveness to AM630. Our findings identify AM630 as an anti-neoplastic drug in the context of the core cells, showing a high correlation with the activity of known antiproliferative drugs. However, we reveal a key set of similarities between the two cell lines that may inform therapeutic intervention.
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Affiliation(s)
- Gareth Williams
- Wolfson-CARD, Kings College, London SE1 UL, UK; (G.W.); (D.C.)
| | - David Chambers
- Wolfson-CARD, Kings College, London SE1 UL, UK; (G.W.); (D.C.)
| | - Ruman Rahman
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Francisco Molina-Holgado
- Wolfson-CARD, Kings College, London SE1 UL, UK; (G.W.); (D.C.)
- School of Life & Health Sciences, University of Roehampton, London SW15 4JD, UK
- Correspondence:
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10
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Mroczek A, Zawitkowska J, Kowalczyk J, Lejman M. Comprehensive Overview of Gene Rearrangements in Childhood T-Cell Acute Lymphoblastic Leukaemia. Int J Mol Sci 2021; 22:E808. [PMID: 33467425 PMCID: PMC7829804 DOI: 10.3390/ijms22020808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Acute lymphoblastic leukaemia (ALL) is a relevant form of childhood neoplasm, as it accounts for over 80% of all leukaemia cases. T-cell ALL constitutes a genetically heterogeneous cancer derived from T-lymphoid progenitors. The diagnosis of T-ALL is based on morphologic, immunophenotypic, cytogenetic, and molecular features, thus the results are used for patient stratification. Due to the expression of surface and intracellular antigens, several subtypes of T-ALL can be distinguished. Although the aetiology of T-ALL remains unclear, a wide spectrum of rearrangements and mutations affecting crucial signalling pathways has been described so far. Due to intensive chemotherapy regimens and supportive care, overall cure rates of more than 80% in paediatric T-ALL patients have been accomplished. However, improved knowledge of the mechanisms of relapse, drug resistance, and determination of risk factors are crucial for patients in the high-risk group. Even though some residual disease studies have allowed the optimization of therapy, the identification of novel diagnostic and prognostic markers is required to individualize therapy. The following review summarizes our current knowledge about genetic abnormalities in paediatric patients with T-ALL. As molecular biology techniques provide insights into the biology of cancer, our study focuses on new potential therapeutic targets and predictive factors which may improve the outcome of young patients with T-ALL.
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Affiliation(s)
- Anna Mroczek
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Joanna Zawitkowska
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Jerzy Kowalczyk
- Department of Paediatric Haematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; (A.M.); (J.Z.); (J.K.)
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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11
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Oppel F, Ki DH, Zimmerman MW, Ross KN, Tao T, Shi H, He S, Aster JC, Look AT. suz12 inactivation in p53- and nf1-deficient zebrafish accelerates the onset of malignant peripheral nerve sheath tumors and expands the spectrum of tumor types. Dis Model Mech 2020; 13:dmm.042341. [PMID: 32651197 PMCID: PMC7473648 DOI: 10.1242/dmm.042341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is an epigenetic regulator of gene expression that possesses histone methyltransferase activity. PRC2 trimethylates lysine 27 of histone H3 proteins (H3K27me3) as a chromatin modification associated with repressed transcription of genes frequently involved in cell proliferation or self-renewal. Loss-of-function mutations in the PRC2 core subunit SUZ12 have been identified in a variety of tumors, including malignant peripheral nerve sheath tumors (MPNSTs). To determine the consequences of SUZ12 loss in the pathogenesis of MPNST and other cancers, we used CRISPR-Cas9 to disrupt the open reading frame of each of two orthologous suz12 genes in zebrafish: suz12a and suz12b. We generated these knockout alleles in the germline of our previously described p53 (also known as tp53)- and nf1-deficient zebrafish model of MPNSTs. Loss of suz12 significantly accelerated the onset and increased the penetrance of MPNSTs compared to that in control zebrafish. Moreover, in suz12-deficient zebrafish, we detected additional types of tumors besides MPNSTs, including leukemia with histological characteristics of lymphoid malignancies, soft tissue sarcoma and pancreatic adenocarcinoma, which were not detected in p53/nf1-deficient control fish, and are also contained in the human spectrum of SUZ12-deficient malignancies identified in the AACR Genie database. The suz12-knockout tumors displayed reduced or abolished H3K27me3 epigenetic marks and upregulation of gene sets reported to be targeted by PRC2. Thus, these zebrafish lines with inactivation of suz12 in combination with loss of p53/nf1 provide a model of human MPNSTs and multiple other tumor types, which will be useful for mechanistic studies of molecular pathogenesis and targeted therapy with small molecule inhibitors. Summary: In p53- and nf1-deficient zebrafish, onset of MPNSTs, as well as diverse other tumors, is accelerated by loss of the suz12 tumor suppressor, accompanied by global reduction in H3K27me3 marks and increased Ras-Mapk signaling.
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Affiliation(s)
- Felix Oppel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dong H Ki
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth N Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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12
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Finkle JD, Bagheri N. Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights. Bioinformatics 2020; 35:4671-4678. [PMID: 30994899 PMCID: PMC6853664 DOI: 10.1093/bioinformatics/btz256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/07/2019] [Accepted: 04/11/2019] [Indexed: 12/02/2022] Open
Abstract
Motivation To understand the regulatory pathways underlying diseases, studies often investigate the differential gene expression between genetically or chemically differing cell populations. Differential expression analysis identifies global changes in transcription and enables the inference of functional roles of applied perturbations. This approach has transformed the discovery of genetic drivers of disease and possible therapies. However, differential expression analysis does not provide quantitative predictions of gene expression in untested conditions. We present a hybrid approach, termed Differential Expression in Python (DiffExPy), that uniquely combines discrete, differential expression analysis with in silico differential equation simulations to yield accurate, quantitative predictions of gene expression from time-series data. Results To demonstrate the distinct insight provided by DiffExpy, we applied it to published, in vitro, time-series RNA-seq data from several genetic PI3K/PTEN variants of MCF10a cells stimulated with epidermal growth factor. DiffExPy proposed ensembles of several minimal differential equation systems for each differentially expressed gene. These systems provide quantitative models of expression for several previously uncharacterized genes and uncover new regulation by the PI3K/PTEN pathways. We validated model predictions on expression data from conditions that were not used for model training. Our discrete, differential expression analysis also identified SUZ12 and FOXA1 as possible regulators of specific groups of genes that exhibit late changes in expression. Our work reveals how DiffExPy generates quantitatively predictive models with testable, biological hypotheses from time-series expression data. Availability and implementation DiffExPy is available on GitHub (https://github.com/bagherilab/diffexpy). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justin D Finkle
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes, Northwestern University, Evanston, IL 60208, USA
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13
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Qi FF, Yang Y, Zhang H, Chen H. Long non-coding RNAs: Key regulators in oxaliplatin resistance of colorectal cancer. Biomed Pharmacother 2020; 128:110329. [PMID: 32502843 DOI: 10.1016/j.biopha.2020.110329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies in the world with high relapse and mortality rates. Although oxaliplatin (OXA), a platinum-based anticancer drug, is widely used in CRC treatment, the resulting chemoresistance dramatically attenuates the drug efficacy and increases the failure rate of this therapy. Thus, the study on OXA-induced chemoresistance is extremely urgent. In recent years, emerging evidence has shown that lncRNAs play irreplaceable roles in drug resistance. However, we only have a limited knowledge of the lncRNAs that are closely related to oxaliplatin resistance in CRC. In present study, we identify and characterize these lncRNAs, including their functions, underlying mechanisms and possible applications.
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Affiliation(s)
- Fang-Fang Qi
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Yunyao Yang
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Haowen Zhang
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi 330006, PR China; Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, Jiangxi 330006, PR China.
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14
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Doni Jayavelu N, Jajodia A, Mishra A, Hawkins RD. Candidate silencer elements for the human and mouse genomes. Nat Commun 2020; 11:1061. [PMID: 32103011 PMCID: PMC7044160 DOI: 10.1038/s41467-020-14853-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/08/2020] [Indexed: 11/24/2022] Open
Abstract
The study of gene regulation is dominated by a focus on the control of gene activation or increase in the level of expression. Just as critical is the process of gene repression or silencing. Chromatin signatures have identified enhancers, however, genome-wide identification of silencers by computational or experimental approaches are lacking. Here, we first define uncharacterized cis-regulatory elements likely containing silencers and find that 41.5% of ~7500 tested elements show silencer activity using massively parallel reporter assay (MPRA). We trained a support vector machine classifier based on MPRA data to predict candidate silencers in over 100 human and mouse cell or tissue types. The predicted candidate silencers exhibit characteristics expected of silencers. Leveraging promoter-capture HiC data, we find that over 50% of silencers are interacting with gene promoters having very low to no expression. Our results suggest a general strategy for genome-wide identification and characterization of silencer elements. Identification of silencer elements by computational or experimental approaches in a genome-wide manner is still challenging. Here authors define uncharacterized cis-regulatory elements (CREs) in human and mouse genomes likely containing silencer elements, and test them in cells using massively parallel reporter assays to identify silencer elements that showed silencer activity.
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Affiliation(s)
- Naresh Doni Jayavelu
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Ajay Jajodia
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Arpit Mishra
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - R David Hawkins
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA.
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15
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Brussa Reis L, Turchetto-Zolet AC, Fonini M, Ashton-Prolla P, Rosset C. The Role of Co-Deleted Genes in Neurofibromatosis Type 1 Microdeletions: An Evolutive Approach. Genes (Basel) 2019; 10:E839. [PMID: 31652930 PMCID: PMC6896060 DOI: 10.3390/genes10110839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 12/16/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a cancer predisposition syndrome that results from dominant loss-of-function mutations mainly in the NF1 gene. Large rearrangements are present in 5-10% of affected patients, generally encompass NF1 neighboring genes, and are correlated with a more severe NF1 phenotype. Evident genotype-phenotype correlations and the importance of the co-deleted genes are difficult to establish. In our study we employed an evolutionary approach to provide further insights into the understanding of the fundamental function of genes that are co-deleted in subjects with NF1 microdeletions. Our goal was to access the ortholog and paralog relationship of these genes in primates and verify if purifying or positive selection are acting on these genes. Fourteen genes were analyzed in twelve mammalian species. Of these, four and ten genes showed positive selection and purifying selection, respectively. The protein, RNF135, showed three sites under positive selection at the RING finger domain, which may have been selected to increase efficiency in ubiquitination routes in primates. The phylogenetic analysis suggests distinct evolutionary constraint between the analyzed genes. With these analyses, we hope to help clarify the correlation of the co-deletion of these genes and the more severe phenotype of NF1.
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Affiliation(s)
- Larissa Brussa Reis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, UFRGS, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
| | - Andreia Carina Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, UFRGS, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
| | - Maievi Fonini
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, UFRGS, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
- Serviço de Genética Médica do Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
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16
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O’Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin 2019; 12:26. [PMID: 31053162 PMCID: PMC6498470 DOI: 10.1186/s13072-019-0275-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/23/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.
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Affiliation(s)
- Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Sofie L. Bates
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Sakereh S. Carter
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Karly A. Nisson
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Julian Halmai
- Department of Neurology and Stem Cell Program, University of California, Sacramento, CA 95817 USA
| | - Kyle D. Fink
- Department of Neurology and Stem Cell Program, University of California, Sacramento, CA 95817 USA
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
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17
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Takimoto M. Multidisciplinary Roles of LRRFIP1/GCF2 in Human Biological Systems and Diseases. Cells 2019; 8:cells8020108. [PMID: 30709060 PMCID: PMC6406849 DOI: 10.3390/cells8020108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/21/2019] [Accepted: 01/27/2019] [Indexed: 01/28/2023] Open
Abstract
Leucine Rich Repeat of Flightless-1 Interacting Protein 1/GC-binding factor 2 (LRRFIP1/GCF2) cDNA was cloned for a transcriptional repressor GCF2, which bound sequence-specifically to a GC-rich element of epidermal growth factor receptor (EGFR) gene and repressed its promotor. LRRFIP1/GCF2 was also cloned as a double stranded RNA (dsRNA)-binding protein to trans-activation responsive region (TAR) RNA of Human Immunodeficiency Virus-1 (HIV-1), termed as TAR RNA interacting protein (TRIP), and as a binding protein to the Leucine Rich Repeat (LRR) of Flightless-1(Fli-1), termed as Flightless-1 LRR associated protein 1 (FLAP1) and LRR domain of Flightless-1 interacting Protein 1 (LRRFIP1). Subsequent functional studies have revealed that LRRFIP1/GCF2 played multiple roles in the regulation of diverse biological systems and processes, such as in immune response to microorganisms and auto-immunity, remodeling of cytoskeletal system, signal transduction pathways, and transcriptional regulations of genes. Dysregulations of LRRFIP1/GCF2 have been implicated in the causes of several experimental and clinico-pathological states and the responses to them, such as autoimmune diseases, excitotoxicity after stroke, thrombosis formation, inflammation and obesity, the wound healing process, and in cancers. LRRFIP1/GCF2 is a bioregulator in multidisciplinary systems of the human body and its dysregulation can cause diverse human diseases.
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Affiliation(s)
- Masato Takimoto
- Institute for Genetic Medicine, Hokkaido University, Hokkaido 060-0815, Japan.
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18
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Easwaran H, Baylin SB. Origin and Mechanisms of DNA Methylation Dynamics in Cancers. RNA TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-14792-1_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Ferreira M, Verbinnen I, Fardilha M, Van Eynde A, Bollen M. The deletion of the protein phosphatase 1 regulator NIPP1 in testis causes hyperphosphorylation and degradation of the histone methyltransferase EZH2. J Biol Chem 2018; 293:18031-18039. [PMID: 30305391 DOI: 10.1074/jbc.ac118.005577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
Germ cell proliferation is epigenetically controlled, mainly through DNA methylation and histone modifications. However, the pivotal epigenetic regulators of germ cell self-renewal and differentiation in postnatal testis are still poorly defined. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of Polycomb repressive complex 2, represses target genes through trimethylation of histone H3 at Lys-27 (H3K27me3), and interacts (in)directly with both protein phosphatase 1 (PP1) and nuclear inhibitor of PP1 (NIPP1). Here, we report that postnatal, testis-specific ablation of NIPP1 in mice results in loss of EZH2 and reduces H3K27me3 levels. Mechanistically, the NIPP1 deletion abrogated PP1-mediated EZH2 dephosphorylation at two cyclin-dependent kinase sites (Thr-345/487), thereby generating hyperphosphorylated EZH2, which is a substrate for proteolytic degradation. Accordingly, alanine mutation of these residues prolonged the half-life of EZH2 in male germ cells. Our study discloses a key role for the PP1:NIPP1 holoenzyme in stabilizing EZH2 and maintaining the H3K27me3 mark on genes that are important for germ cell development and spermatogenesis.
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Affiliation(s)
- Mónica Ferreira
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and; Institute for Research in Biomedicine (iBiMED), Health Sciences Department, University of Aveiro, 3810 Aveiro, Portugal
| | - Iris Verbinnen
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and
| | - Margarida Fardilha
- Institute for Research in Biomedicine (iBiMED), Health Sciences Department, University of Aveiro, 3810 Aveiro, Portugal
| | - Aleyde Van Eynde
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and.
| | - Mathieu Bollen
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and.
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20
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Du J, Kirk B, Zeng J, Ma J, Wang Q. Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes. Nucleic Acids Res 2018; 46:8848-8864. [PMID: 29992232 PMCID: PMC6158500 DOI: 10.1093/nar/gky595] [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: 03/01/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are essential for maintaining epigenetic memory in both embryonic stem cells and differentiated cells. To date, how they are localized to hundreds of specific target genes within a vertebrate genome had remained elusive. Here, by focusing on short cis-acting DNA elements of single functions, we discovered three classes of response elements in human genome: Polycomb response elements (PREs), Trithorax response elements (TREs) and Polycomb/Trithorax response elements (P/TREs). In particular, the four PREs (PRE14, 29, 39 and 48) are the first set of, to our knowledge, bona fide vertebrate PREs ever discovered, while many previously reported Drosophila or vertebrate PREs are likely P/TREs. We further demonstrated that YY1 and CpG islands are specifically enriched in the four TREs (PRE30, 41, 44 and 55), but not in the PREs. The three classes of response elements as unraveled in this study should guide further global investigation and open new doors for a deeper understanding of PcG and TrxG mechanisms in vertebrates.
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Affiliation(s)
- Junqing Du
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Brian Kirk
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jia Zeng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jianpeng Ma
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Qinghua Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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21
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Unbiased shRNA screening, using a combination of FACS and high-throughput sequencing, enables identification of novel modifiers of Polycomb silencing. Sci Rep 2018; 8:12128. [PMID: 30108332 PMCID: PMC6092423 DOI: 10.1038/s41598-018-30649-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/03/2018] [Indexed: 12/19/2022] Open
Abstract
Polycomb silencing is an important and rapidly growing field that is relevant to a broad range of aspects of human health, including cancer and stem cell biology. To date, the regulatory mechanisms for the fine-tuning of Polycomb silencing remain unclear, but it is likely that there is a series of unidentified factors that functionally modify or balance the silencing. However, a practical gene screening strategy for identifying such factors has not yet been developed. The failure of screening strategies used thus far is probably due to the effect of the loss-of-function phenotypes of these factors on cell cycle progression. Here, by applying fluorescence-activated cell sorter (FACS) and high-throughput sequencing (HTS) technology in a large-scale lentivirus-mediated shRNA screening, we obtained a consecutive dataset from all shRNAs tested, which highlighted a substantial number of genes that may control Polycomb silencing. We consider that this unbiased strategy can readily be applied to a wide range of studies to uncover novel regulatory layers for expression of genes of interest.
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22
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Goren E, Liu P, Wang C, Wang C. BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates. Bioinformatics 2018; 34:2909-2917. [DOI: 10.1093/bioinformatics/bty227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/18/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Emily Goren
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Chao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Chong Wang
- Department of Statistics, Iowa State University, Ames, IA, USA
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
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23
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Ferreccio A, Mathieu J, Detraux D, Somasundaram L, Cavanaugh C, Sopher B, Fischer K, Bello T, M Hussein A, Levy S, Cook S, Sidhu SB, Artoni F, Palpant NJ, Reinecke H, Wang Y, Paddison P, Murry C, Jayadev S, Ware C, Ruohola-Baker H. Inducible CRISPR genome editing platform in naive human embryonic stem cells reveals JARID2 function in self-renewal. Cell Cycle 2018; 17:535-549. [PMID: 29466914 DOI: 10.1080/15384101.2018.1442621] [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: 12/25/2022] Open
Abstract
To easily edit the genome of naïve human embryonic stem cells (hESC), we introduced a dual cassette encoding an inducible Cas9 into the AAVS1 site of naïve hESC (iCas9). The iCas9 line retained karyotypic stability, expression of pluripotency markers, differentiation potential, and stability in 5iLA and EPS pluripotency conditions. The iCas9 line induced efficient homology-directed repair (HDR) and non-homologous end joining (NHEJ) based mutations through CRISPR-Cas9 system. We utilized the iCas9 line to study the epigenetic regulator, PRC2 in early human pluripotency. The PRC2 requirement distinguishes between early pluripotency stages, however, what regulates PRC2 activity in these stages is not understood. We show reduced H3K27me3 and pluripotency markers in JARID2 2iL-I-F hESC mutants, indicating JARID2 requirement in maintenance of hESC 2iL-I-F state. These data suggest that JARID2 regulates PRC2 in 2iL-I-F state and the lack of PRC2 function in 5iLA state may be due to lack of sufficient JARID2 protein.
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Affiliation(s)
- Amy Ferreccio
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Julie Mathieu
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,c Department of Comparative Medicine , University of Washington , Seattle , Washington 98195 , USA
| | - Damien Detraux
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Logeshwaran Somasundaram
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Christopher Cavanaugh
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,c Department of Comparative Medicine , University of Washington , Seattle , Washington 98195 , USA
| | - Bryce Sopher
- d Department of Neurobiology , University of Washington , Seattle , WA 98109 , USA
| | - Karin Fischer
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Thomas Bello
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,e Department of Molecular and Cellular Biology , University of Washington , Seattle , WA , 98109 , USA
| | - Abdiasis M Hussein
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Shiri Levy
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Savannah Cook
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,c Department of Comparative Medicine , University of Washington , Seattle , Washington 98195 , USA
| | - Sonia B Sidhu
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Filippo Artoni
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA
| | - Nathan J Palpant
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,f Department of Pathology , University of Washington , Seattle , WA 98109 , USA
| | - Hans Reinecke
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,f Department of Pathology , University of Washington , Seattle , WA 98109 , USA
| | - Yuliang Wang
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,g Paul G. Allen School of Computer Science & Engineering
| | - Patrick Paddison
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,h Human Biology Division , Fred Hutchinson Cancer Research Center , Seattle , WA 98109 , USA
| | - Charles Murry
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,f Department of Pathology , University of Washington , Seattle , WA 98109 , USA.,i Center for Cardiovascular Biology , University of Washington School of Medicine , Seattle , Washington , 98109 , USA.,j Department of Bioengineering , University of Washington , Seattle , WA 98195 , USA.,k Department of Medicine/Cardiology , University of Washington , Seattle , WA 98195 , USA
| | - Suman Jayadev
- d Department of Neurobiology , University of Washington , Seattle , WA 98109 , USA
| | - Carol Ware
- b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,c Department of Comparative Medicine , University of Washington , Seattle , Washington 98195 , USA
| | - Hannele Ruohola-Baker
- a Department of Biochemistry , University of Washington , Seattle , Washington 98195 , USA.,b Institute for Stem Cell and Regenerative Medicine , University of Washington , Seattle , Washington 98109 , USA.,e Department of Molecular and Cellular Biology , University of Washington , Seattle , WA , 98109 , USA.,j Department of Bioengineering , University of Washington , Seattle , WA 98195 , USA
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24
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Feigin ME, Garvin T, Bailey P, Waddell N, Chang DK, Kelley DR, Shuai S, Gallinger S, McPherson JD, Grimmond SM, Khurana E, Stein LD, Biankin AV, Schatz MC, Tuveson DA. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat Genet 2017; 49:825-833. [PMID: 28481342 PMCID: PMC5659388 DOI: 10.1038/ng.3861] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 04/10/2017] [Indexed: 12/15/2022]
Abstract
The contributions of coding mutations to tumorigenesis are relatively well known; however, little is known about somatic alterations in noncoding DNA. Here we describe GECCO (Genomic Enrichment Computational Clustering Operation) to analyze somatic noncoding alterations in 308 pancreatic ductal adenocarcinomas (PDAs) and identify commonly mutated regulatory regions. We find recurrent noncoding mutations to be enriched in PDA pathways, including axon guidance and cell adhesion, and newly identified processes, including transcription and homeobox genes. We identified mutations in protein binding sites correlating with differential expression of proximal genes and experimentally validated effects of mutations on expression. We developed an expression modulation score that quantifies the strength of gene regulation imposed by each class of regulatory elements, and found the strongest elements were most frequently mutated, suggesting a selective advantage. Our detailed single-cancer analysis of noncoding alterations identifies regulatory mutations as candidates for diagnostic and prognostic markers, and suggests new mechanisms for tumor evolution.
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Affiliation(s)
- Michael E Feigin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, USA
| | - Tyler Garvin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- The Kinghorn Cancer Centre, Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
- Department of Surgery, Bankstown Hospital, Bankstown, Sydney, New South Wales, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales, Australia
| | - David R Kelley
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Shimin Shuai
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of General Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - John D McPherson
- Genome Technologies Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sean M Grimmond
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ekta Khurana
- Sandra and Edward Meyer Cancer Center, Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Informatics and Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales, Australia
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, UK
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, USA
- Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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25
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Daer RM, Cutts JP, Brafman DA, Haynes KA. The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells. ACS Synth Biol 2017; 6:428-438. [PMID: 27783893 DOI: 10.1021/acssynbio.5b00299] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.
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Affiliation(s)
- René M. Daer
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Josh P. Cutts
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - David A. Brafman
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Karmella A. Haynes
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
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26
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Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hot Spots. Mol Cell Biol 2017; 37:MCB.00942-15. [PMID: 27821479 DOI: 10.1128/mcb.00942-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination initiates following the formation of DNA double-strand breaks (DSBs) by the Spo11 endonuclease early in prophase I, at discrete regions in the genome coined "hot spots." In mammals, meiotic DSB site selection is directed in part by sequence-specific binding of PRDM9, a polymorphic histone H3 (H3K4Me3) methyltransferase. However, other chromatin features needed for meiotic hot spot specification are largely unknown. Here we show that the recombinogenic cores of active hot spots in mice harbor several histone H3 and H4 acetylation and methylation marks that are typical of open, active chromatin. Further, deposition of these open chromatin-associated histone marks is dynamic and is manifest at spermatogonia and/or pre-leptotene-stage cells, which facilitates PRDM9 binding and access for Spo11 to direct the formation of DSBs, which are initiated at the leptotene stage. Importantly, manipulating histone acetylase and deacetylase activities established that histone acetylation marks are necessary for both hot spot activity and crossover resolution. We conclude that there are functional roles for histone acetylation marks at mammalian meiotic recombination hot spots.
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27
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TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation. Oncogene 2017; 36:2991-3001. [PMID: 28068325 DOI: 10.1038/onc.2016.453] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 08/11/2016] [Accepted: 10/03/2016] [Indexed: 02/07/2023]
Abstract
Histone methyl transferase EZH2 (Enhancer of Zeste Homolog 2) is generally associated with H3K27 methylation and gene silencing, as a member of the polycomb repressor 2 (PRC2) complex. Immunoprecipitation and mass spectrometry of the EZH2-protein interactome in estrogen receptor positive, breast cancer-derived MCF7 cells revealed EZH2 interactions with subunits of chromatin remodeler SWI/SNF complex and TRIM28, which formed a complex with EZH2 distinct from PRC2. Unexpectedly, transcriptome profiling showed that EZH2 primarily activates, rather than represses, transcription in MCF7 cells and with TRIM28 co-regulates a set of genes associated with stem cell maintenance and poor survival of breast cancer patients. TRIM28 depletion repressed EZH2 recruitment to chromatin and expression of this gene set, in parallel with decreased CD44hi/CD24lo mammosphere formation. Mammosphere formation, inhibited by EZH2 depletion, was rescued by ectopic expression of EZH2 but not by TRIM28 expression or by EZH2 mutated at the region (pre-SET domain) of TRIM28 interaction. These results support PRC2-independent functions of EZH2 and TRIM28 in activation of gene expression that promotes mammary stem cell enrichment and maintenance.
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28
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Comet I, Riising EM, Leblanc B, Helin K. Maintaining cell identity: PRC2-mediated regulation of transcription and cancer. Nat Rev Cancer 2016; 16:803-810. [PMID: 27658528 DOI: 10.1038/nrc.2016.83] [Citation(s) in RCA: 316] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of Polycomb repressive complex 2 (PRC2), has attracted broad research attention in the past few years because of its involvement in the development and maintenance of many types of cancer and the use of specific EZH2 inhibitors in clinical trials. Several observations show that PRC2 can have both oncogenic and tumour-suppressive functions. We propose that these apparently opposing roles of PRC2 in cancer are a consequence of the molecular function of the complex in maintaining, rather than specifying, the transcriptional repression state of its several thousand target genes.
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Affiliation(s)
- Itys Comet
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Eva M Riising
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin Leblanc
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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29
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Dysregulation of histone methyltransferases in breast cancer - Opportunities for new targeted therapies? Mol Oncol 2016; 10:1497-1515. [PMID: 27717710 DOI: 10.1016/j.molonc.2016.09.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 01/24/2023] Open
Abstract
Histone methyltransferases (HMTs) catalyze the methylation of lysine and arginine residues on histone tails and non-histone targets. These important post-translational modifications are exquisitely regulated and affect chromatin compaction and transcriptional programs leading to diverse biological outcomes. There is accumulating evidence that genetic alterations of several HMTs impinge on oncogenic or tumor-suppressor functions and influence both cancer initiation and progression. HMTs therefore represent an opportunity for therapeutic targeting in those patients with tumors in which HMTs are dysregulated, to reverse the histone marks and transcriptional programs associated with aggressive tumor behavior. In this review, we describe the known histone methyltransferases and their emerging roles in breast cancer tumorigenesis.
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30
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Ray MK, Wiskow O, King MJ, Ismail N, Ergun A, Wang Y, Plys AJ, Davis CP, Kathrein K, Sadreyev R, Borowsky ML, Eggan K, Zon L, Galloway JL, Kingston RE. CAT7 and cat7l Long Non-coding RNAs Tune Polycomb Repressive Complex 1 Function during Human and Zebrafish Development. J Biol Chem 2016; 291:19558-72. [PMID: 27405765 DOI: 10.1074/jbc.m116.730853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Indexed: 11/06/2022] Open
Abstract
The essential functions of polycomb repressive complex 1 (PRC1) in development and gene silencing are thought to involve long non-coding RNAs (lncRNAs), but few specific lncRNAs that guide PRC1 activity are known. We screened for lncRNAs, which co-precipitate with PRC1 from chromatin and found candidates that impact polycomb group protein (PcG)-regulated gene expression in vivo A novel lncRNA from this screen, CAT7, regulates expression and polycomb group binding at the MNX1 locus during early neuronal differentiation. CAT7 contains a unique tandem repeat domain that shares high sequence similarity to a non-syntenic zebrafish analog, cat7l Defects caused by interference of cat7l RNA during zebrafish embryogenesis were rescued by human CAT7 RNA, enhanced by interference of a PRC1 component, and suppressed by interference of a known PRC1 target gene, demonstrating cat7l genetically interacts with a PRC1. We propose a model whereby PRC1 acts in concert with specific lncRNAs and that CAT7/cat7l represents convergent lncRNAs that independently evolved to tune PRC1 repression at individual loci.
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Affiliation(s)
- Mridula K Ray
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Ole Wiskow
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138
| | - Matthew J King
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114
| | - Nidha Ismail
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114
| | - Ayla Ergun
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02114
| | - Yanqun Wang
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Aaron J Plys
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Christopher P Davis
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Katie Kathrein
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Boston, Massachusetts, 02115, and
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02114
| | - Mark L Borowsky
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, The Howard Hughes Medical Institute, Cambridge, MA 02138
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Boston, Massachusetts, 02115, and
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114,
| | - Robert E Kingston
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114,
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31
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Du M, Jiao S, Bien SA, Gala M, Abecasis G, Bezieau S, Brenner H, Butterbach K, Caan BJ, Carlson CS, Casey G, Chang-Claude J, Conti DV, Curtis KR, Duggan D, Gallinger S, Haile RW, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hudson TJ, Jenkins MA, Küry S, Le Marchand L, Leal SM, Newcomb PA, Nickerson DA, Potter JD, Schoen RE, Schumacher FR, Seminara D, Slattery ML, Hsu L, Chan AT, White E, Berndt SI, Peters U. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PLoS One 2016; 11:e0157521. [PMID: 27379672 PMCID: PMC4933364 DOI: 10.1371/journal.pone.0157521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 06/01/2016] [Indexed: 01/27/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).
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Affiliation(s)
- Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Stephanie A. Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States of America
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J. Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, United States of America
| | - Christopher S. Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Graham Casey
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David V. Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Keith R. Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Steven Gallinger
- Department of Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - Robert W. Haile
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, United States of America
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L. Hopper
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark A. Jenkins
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States of America
| | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Deborah A. Nickerson
- Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Fredrick R. Schumacher
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, United States of America
| | - Martha L. Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, United States of America
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
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Houseman EA, Kile ML, Christiani DC, Ince TA, Kelsey KT, Marsit CJ. Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. BMC Bioinformatics 2016; 17:259. [PMID: 27358049 PMCID: PMC4928286 DOI: 10.1186/s12859-016-1140-4] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/19/2016] [Indexed: 12/28/2022] Open
Abstract
Background Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types. Results We propose a simple method for reference-free deconvolution that provides both proportions of putative cell types defined by their underlying methylomes, the number of these constituent cell types, as well as a method for evaluating the extent to which the underlying methylomes reflect specific types of cells. We demonstrate these methods in an analysis of 23 Infinium data sets from 13 distinct data collection efforts; these empirical evaluations show that our algorithm can reasonably estimate the number of constituent types, return cell proportion estimates that demonstrate anticipated associations with underlying phenotypic data; and methylomes that reflect the underlying biology of constituent cell types. Conclusions Our methodology permits an explicit quantitation of the mediation of phenotypic associations with DNA methylation by cell composition effects. Although more work is needed to investigate functional information related to estimated methylomes, our proposed method provides a novel and useful foundation for conducting DNA methylation studies on heterogeneous tissues lacking reference data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1140-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Andres Houseman
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA.
| | - Molly L Kile
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tan A Ince
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University, Providence, USA
| | - Carmen J Marsit
- Department of Community and Family Medicine, Dartmouth Medical School, Hanover, NH, USA
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Song Y, Wu F, Wu J. Targeting histone methylation for cancer therapy: enzymes, inhibitors, biological activity and perspectives. J Hematol Oncol 2016; 9:49. [PMID: 27316347 PMCID: PMC4912745 DOI: 10.1186/s13045-016-0279-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
Post-translational methylation of histone lysine or arginine residues plays important roles in gene regulation and other physiological processes. Aberrant histone methylation caused by a gene mutation, translocation, or overexpression can often lead to initiation of a disease such as cancer. Small molecule inhibitors of such histone modifying enzymes that correct the abnormal methylation could be used as novel therapeutics for these diseases, or as chemical probes for investigation of epigenetics. Discovery and development of histone methylation modulators are in an early stage and undergo a rapid expansion in the past few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Several compounds have been in clinical trials for safety, pharmacokinetics, and efficacy, targeting several types of cancer. This review summarizes the biochemistry, structures, and biology of cancer-relevant histone methylation modifying enzymes, small molecule inhibitors and their preclinical and clinical antitumor activities. Perspectives for targeting histone methylation for cancer therapy are also discussed.
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Affiliation(s)
- Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Fangrui Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Jingyu Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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Marchesi I, Bagella L. Targeting Enhancer of Zeste Homolog 2 as a promising strategy for cancer treatment. World J Clin Oncol 2016; 7:135-148. [PMID: 27081636 PMCID: PMC4826959 DOI: 10.5306/wjco.v7.i2.135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 11/20/2015] [Accepted: 02/16/2016] [Indexed: 02/06/2023] Open
Abstract
Polycomb group proteins represent a global silencing system involved in development regulation. In specific, they regulate the transition from proliferation to differentiation, contributing to stem-cell maintenance and inhibiting an inappropriate activation of differentiation programs. Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb repressive complex 2, which induces transcriptional inhibition through the tri-methylation of histone H3, an epigenetic change associated with gene silencing. EZH2 expression is high in precursor cells while its level decreases in differentiated cells. EZH2 is upregulated in various cancers with high levels associated with metastatic cancer and poor prognosis. Indeed, aberrant expression of EZH2 causes the inhibition of several tumor suppressors and differentiation genes, resulting in an uncontrolled proliferation and tumor formation. This editorial explores the role of Polycomb repressive complex 2 in cancer, focusing in particular on EZH2. The canonical function of EZH2 in gene silencing, the non-canonical activities as the methylation of other proteins and the role in gene transcriptional activation, were summarized. Moreover, mutations of EZH2, responsible for an increased methyltransferase activity in cancer, were recapitulated. Finally, various drugs able to inhibit EZH2 with different mechanism were described, specifically underscoring the effects in several cancers, in order to clarify the role of EZH2 and understand if EZH2 blockade could be a new strategy for developing specific therapies or a way to increase sensitivity of cancer cells to standard therapies.
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Tastanova A, Schulz A, Folcher M, Tolstrup A, Puklowski A, Kaufmann H, Fussenegger M. Overexpression of YY1 increases the protein production in mammalian cells. J Biotechnol 2016; 219:72-85. [DOI: 10.1016/j.jbiotec.2015.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 01/07/2023]
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Jamieson K, Wiles ET, McNaught KJ, Sidoli S, Leggett N, Shao Y, Garcia BA, Selker EU. Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Genome Res 2015; 26:97-107. [PMID: 26537359 PMCID: PMC4691754 DOI: 10.1101/gr.194555.115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 11/04/2015] [Indexed: 12/25/2022]
Abstract
Methylated lysine 27 on histone H3 (H3K27me) marks repressed “facultative heterochromatin,” including developmentally regulated genes in plants and animals. The mechanisms responsible for localization of H3K27me are largely unknown, perhaps in part because of the complexity of epigenetic regulatory networks. We used a relatively simple model organism bearing both facultative and constitutive heterochromatin, Neurospora crassa, to explore possible interactions between elements of heterochromatin. In higher eukaryotes, reductions of H3K9me3 and DNA methylation in constitutive heterochromatin have been variously reported to cause redistribution of H3K27me3. In Neurospora, we found that elimination of any member of the DCDC H3K9 methylation complex caused massive changes in the distribution of H3K27me; regions of facultative heterochromatin lost H3K27me3, while regions that are normally marked by H3K9me3 became methylated at H3K27. Elimination of DNA methylation had no obvious effect on the distribution of H3K27me. Elimination of HP1, which “reads” H3K9me3, also caused major changes in the distribution of H3K27me, indicating that HP1 is important for normal localization of facultative heterochromatin. Because loss of HP1 caused redistribution of H3K27me2/3, but not H3K9me3, these normally nonoverlapping marks became superimposed. Indeed, mass spectrometry revealed substantial cohabitation of H3K9me3 and H3K27me2 on H3 molecules from an hpo strain. Loss of H3K27me machinery (e.g., the methyltransferase SET-7) did not impact constitutive heterochromatin but partially rescued the slow growth of the DCDC mutants, suggesting that the poor growth of these mutants is partly attributable to ectopic H3K27me. Altogether, our findings with Neurospora clarify interactions of facultative and constitutive heterochromatin in eukaryotes.
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Affiliation(s)
- Kirsty Jamieson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Elizabeth T Wiles
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics and the Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA
| | - Neena Leggett
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Yanchun Shao
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics and the Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
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The quest for mammalian Polycomb response elements: are we there yet? Chromosoma 2015; 125:471-96. [PMID: 26453572 PMCID: PMC4901126 DOI: 10.1007/s00412-015-0539-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
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Kok K, Ay A, Li LM, Arnosti DN. Genome-wide errant targeting by Hairy. eLife 2015; 4. [PMID: 26305409 PMCID: PMC4547095 DOI: 10.7554/elife.06394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/24/2015] [Indexed: 01/08/2023] Open
Abstract
Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.
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Affiliation(s)
- Kurtulus Kok
- Genetics Program, Michigan State University, East Lansing, United States
| | - Ahmet Ay
- Departments of Biology and Mathematics, Colgate University, Hamilton, United States
| | - Li M Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - David N Arnosti
- Genetics Program, Michigan State University, East Lansing, United States
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Johnson KC, Koestler DC, Fleischer T, Chen P, Jenson EG, Marotti JD, Onega T, Kristensen VN, Christensen BC. DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer. Clin Epigenetics 2015. [PMID: 26213588 PMCID: PMC4514996 DOI: 10.1186/s13148-015-0094-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Ductal carcinoma in situ (DCIS) is a heterogeneous, pre-invasive lesion associated with an increased risk for future invasive ductal carcinoma. However, accurate risk stratification for development of invasive disease and appropriate treatment decisions remain clinical challenges. DNA methylation alterations are early events in the progression of cancer and represent emerging molecular markers that may predict invasive recurrence more accurately than traditional measures of DCIS prognosis. Results We measured DNA methylation using the Illumina HumanMethylation450K array of estrogen-receptor positive DCIS (n = 40) and adjacent-normal (n = 15) tissues from subjects in the New Hampshire Mammography Network longitudinal breast imaging registry. We identified locus-specific methylation differences between DCIS and matched adjacent-normal tissue (95,609 CpGs, Q < 0.05). Among 40 DCIS cases, 13 later developed invasive disease and we identified 641 CpG sites that exhibited differential DNA methylation (P < 0.01 and median |∆β| > 0.1) in these cases compared with age-matched subjects without invasive disease. The set of differentially methylated CpG loci associated with disease progression was enriched in homeobox-containing genes (P = 1.3E-09) and genes involved with limb morphogenesis (P = 1.0E-05). In an independent cohort, a subset of genes with progression-related differential methylation between DCIS and invasive breast cancer were confirmed. Further, the functional relevance of these genes’ regulation by methylation was demonstrated in early stage breast cancers from The Cancer Genome Atlas database. Conclusions This work contributes to the understanding of epigenetic alterations that occur in DCIS and illustrates the potential of DNA methylation as markers of DCIS progression. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0094-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin C Johnson
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway ; The K.G. Jebsen Center for Breast Cancer, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Panpan Chen
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA
| | - Erik G Jenson
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Jonathan D Marotti
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Tracy Onega
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA ; The Dartmouth Institute, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766 USA
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway ; The K.G. Jebsen Center for Breast Cancer, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway ; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus Hospital, Lørenskog, Norway
| | - Brock C Christensen
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
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Abou El Hassan M, Huang K, Eswara MBK, Zhao M, Song L, Yu T, Liu Y, Liu JC, McCurdy S, Ma A, Wither J, Jin J, Zacksenhaus E, Wrana JL, Bremner R. Cancer Cells Hijack PRC2 to Modify Multiple Cytokine Pathways. PLoS One 2015; 10:e0126466. [PMID: 26030458 PMCID: PMC4450877 DOI: 10.1371/journal.pone.0126466] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/03/2015] [Indexed: 01/21/2023] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator induced in many cancers. It is thought to drive tumorigenesis by repressing division, stemness, and/or developmental regulators. Cancers evade immune detection, and diverse immune regulators are perturbed in different tumors. It is unclear how such cell-specific effects are coordinated. Here, we show a profound and cancer-selective role for PRC2 in repressing multiple cytokine pathways. We find that PRC2 represses hundreds of IFNγ stimulated genes (ISGs), cytokines and cytokine receptors. This target repertoire is significantly broadened in cancer vs non-cancer cells, and is distinct in different cancer types. PRC2 is therefore a higher order regulator of the immune program in cancer cells. Inhibiting PRC2 with either RNAi or EZH2 inhibitors activates cytokine/cytokine receptor promoters marked with bivalent H3K27me3/H3K4me3 chromatin, and augments responsiveness to diverse immune signals. PRC2 inhibition rescues immune gene induction even in the absence of SWI/SNF, a tumor suppressor defective in ~20% of human cancers. This novel PRC2 function in tumor cells could profoundly impact the mechanism of action and efficacy of EZH2 inhibitors in cancer treatment.
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Affiliation(s)
| | - Katherine Huang
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Manoja B. K. Eswara
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Michael Zhao
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Lan Song
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Yu Liu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Jeffrey C. Liu
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sean McCurdy
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anqi Ma
- Department of Structural and Chemical Biology, Icahn School of Medicine, Mt Sinai Hospital, New York, New York, United States of America
| | - Joan Wither
- Toronto Western Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jian Jin
- Department of Structural and Chemical Biology, Icahn School of Medicine, Mt Sinai Hospital, New York, New York, United States of America
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey L. Wrana
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Bajusz I, Sipos L, Pirity MK. Nucleotide substitutions revealing specific functions of Polycomb group genes. Mol Genet Metab 2015; 114:547-56. [PMID: 25669595 DOI: 10.1016/j.ymgme.2015.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023]
Abstract
POLYCOMB group (PCG) proteins belong to the family of epigenetic regulators of genes playing important roles in differentiation and development. Mutants of PcG genes were isolated first in the fruit fly, Drosophila melanogaster, resulting in spectacular segmental transformations due to the ectopic expression of homeotic genes. Homologs of Drosophila PcG genes were also identified in plants and in vertebrates and subsequent experiments revealed the general role of PCG proteins in the maintenance of the repressed state of chromatin through cell divisions. The past decades of gene targeting experiments have allowed us to make significant strides towards understanding how the network of PCG proteins influences multiple aspects of cellular fate determination during development. Being involved in the transmission of specific expression profiles of different cell lineages, PCG proteins were found to control wide spectra of unrelated epigenetic processes in vertebrates, such as stem cell plasticity and renewal, genomic imprinting and inactivation of X-chromosome. PCG proteins also affect regulation of metabolic genes being important for switching programs between pluripotency and differentiation. Insight into the precise roles of PCG proteins in normal physiological processes has emerged from studies employing cell culture-based systems and genetically modified animals. Here we summarize the findings obtained from PcG mutant fruit flies and mice generated to date with a focus on PRC1 and PRC2 members altered by nucleotide substitutions resulting in specific alleles. We also include a compilation of lessons learned from these models about the in vivo functions of this complex protein family. With multiple knockout lines, sophisticated approaches to study the consequences of peculiar missense point mutations, and insights from complementary gain-of-function systems in hand, we are now in a unique position to significantly advance our understanding of the molecular basis of in vivo functions of PcG proteins.
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Affiliation(s)
- Izabella Bajusz
- Biological Research Centre, Hungarian Academy of Sciences, Institute of Genetics, H-6701 Szeged, Hungary.
| | - László Sipos
- Biological Research Centre, Hungarian Academy of Sciences, Institute of Genetics, H-6701 Szeged, Hungary
| | - Melinda K Pirity
- Biological Research Centre, Hungarian Academy of Sciences, Institute of Genetics, H-6701 Szeged, Hungary
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Di Giacomo D, La Starza R, Barba G, Pierini V, Baldazzi C, Storlazzi CT, Daniele G, Forghieri F, Borlenghi E, Testoni N, Mecucci C. 4q12 translocations with GSX2 expression identify a CD7(+) acute myeloid leukaemia subset. Br J Haematol 2015; 171:141-5. [PMID: 25816740 DOI: 10.1111/bjh.13368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Danika Di Giacomo
- Department of Medicine, Section of Haematology, University of Perugia, Perugia, Italy
| | - Roberta La Starza
- Department of Medicine, Section of Haematology, University of Perugia, Perugia, Italy
| | - Gianluca Barba
- Department of Medicine, Section of Haematology, University of Perugia, Perugia, Italy
| | - Valentina Pierini
- Department of Medicine, Section of Haematology, University of Perugia, Perugia, Italy
| | - Carmen Baldazzi
- Institute of Haematology and Medical Oncology 'Seràgnoli', University of Bologna, Bologna, Italy
| | | | | | - Fabio Forghieri
- Department of Medical and Surgical Sciences, Section of Haematology, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Nicoletta Testoni
- Institute of Haematology and Medical Oncology 'Seràgnoli', University of Bologna, Bologna, Italy
| | - Cristina Mecucci
- Department of Medicine, Section of Haematology, University of Perugia, Perugia, Italy.
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43
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Liu L, Jin G, Zhou X. Modeling the relationship of epigenetic modifications to transcription factor binding. Nucleic Acids Res 2015; 43:3873-85. [PMID: 25820421 PMCID: PMC4417166 DOI: 10.1093/nar/gkv255] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 12/19/2022] Open
Abstract
Transcription factors (TFs) and epigenetic modifications play crucial roles in the regulation of gene expression, and correlations between the two types of factors have been discovered. However, methods for quantitatively studying the correlations remain limited. Here, we present a computational approach to systematically investigating how epigenetic changes in chromatin architectures or DNA sequences relate to TF binding. We implemented statistical analyses to illustrate that epigenetic modifications are predictive of TF binding affinities, without the need of sequence information. Intriguingly, by considering genome locations relative to transcription start sites (TSSs) or enhancer midpoints, our analyses show that different locations display various relationship patterns. For instance, H3K4me3, H3k9ac and H3k27ac contribute more in the regions near TSSs, whereas H3K4me1 and H3k79me2 dominate in the regions far from TSSs. DNA methylation plays relatively important roles when close to TSSs than in other regions. In addition, the results show that epigenetic modification models for the predictions of TF binding affinities are cell line-specific. Taken together, our study elucidates highly coordinated, but location- and cell type-specific relationships between epigenetic modifications and binding affinities of TFs.
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Affiliation(s)
- Liang Liu
- Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Guangxu Jin
- Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Xiaobo Zhou
- Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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Houseman EA, Kelsey KT, Wiencke JK, Marsit CJ. Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective. BMC Bioinformatics 2015; 16:95. [PMID: 25887114 PMCID: PMC4392865 DOI: 10.1186/s12859-015-0527-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background The impact of cell-composition effects in analysis of DNA methylation data is now widely appreciated. With the availability of a reference data set consisting of DNA methylation measurements on isolated cell types, it is possible to impute cell proportions and adjust for them, but there is increasing interest in methods that adjust for cell composition effects when reference sets are incomplete or unavailable. Results In this article we present a theoretical basis for one such method, showing that the total effect of a phenotype on DNA methylation can be decomposed into orthogonal components, one representing the effect of phenotype on proportions of major cell types, the other representing either subtle effects in composition or global effects at focused loci, and that it is possible to separate these two types of effects in a finite data set. We demonstrate this principle empirically on nine DNA methylation data sets, showing that the first few principal components generally contain a majority of the information on cell-type present in the data, but that later principal components nevertheless contain information about a small number of loci that may represent more focused associations. We also present a new method for determining the number of linear terms to interpret as cell-mixture effects and demonstrate robustness to the choice of this parameter. Conclusions Taken together, our work demonstrates that reference-free algorithms for cell-mixture adjustment can produce biologically valid results, separating cell-mediated epigenetic effects (i.e. apparent effects arising from differences in cell composition) from those that are not cell mediated, and that in general the interpretation of associations evident from DNA methylation should be carefully considered. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0527-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Andres Houseman
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA.
| | - John K Wiencke
- Departments of Neurological Surgery, and Division of Epidemiology, University of California San Francisco, San Francisco, CA, USA.
| | - Carmen J Marsit
- Department of Community and Family Medicine, Dartmouth Medical School, Hanover, NH, USA.
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McGrath J, Trojer P. Targeting histone lysine methylation in cancer. Pharmacol Ther 2015; 150:1-22. [PMID: 25578037 DOI: 10.1016/j.pharmthera.2015.01.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 02/06/2023]
Abstract
Within the vast landscape of histone modifications lysine methylation has gained increasing attention because of its profound regulatory potential. The methylation of lysine residues on histone proteins modulates chromatin structure and thereby contributes to the regulation of DNA-based nuclear processes such as transcription, replication and repair. Protein families with opposing catalytic activities, lysine methyltransferases (KMTs) and demethylases (KDMs), dynamically control levels of histone lysine methylation and individual enzymes within these families have become candidate oncology targets in recent years. A number of high quality small molecule inhibitors of these enzymes have been identified. Several of these compounds elicit selective cancer cell killing in vitro and robust efficacy in vivo, suggesting that targeting 'histone lysine methylation pathways' may be a relevant, emerging cancer therapeutic strategy. Here, we discuss individual histone lysine methylation pathway targets, the properties of currently available small molecule inhibitors and their application in the context of cancer.
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Affiliation(s)
- John McGrath
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals, 215 1st Street Suite 200, Cambridge, MA, 02142, USA.
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46
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Pillai S, Chellappan SP. ChIP on chip and ChIP-Seq assays: genome-wide analysis of transcription factor binding and histone modifications. Methods Mol Biol 2015; 1288:447-72. [PMID: 25827896 DOI: 10.1007/978-1-4939-2474-5_26] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deregulation of transcriptional activity of many genes has been causatively linked to human diseases including cancer. Altered patterns of gene expression in normal and cancer cells are the result of inappropriate expression of transcription factors and chromatin modifying proteins. Chromatin immunoprecipitation assay is a well-established tool for investigating the interactions between regulatory proteins and DNA at distinct stages of gene activation. ChIP coupled with DNA microarrays, known as ChIP on chip, or sequencing of DNA associated with the factors (ChIP-Seq) allow us to determine the entire spectrum of in vivo DNA binding sites for a given protein. This has been of immense value because ChIP on chip assays and ChIP-Seq experiments can provide a snapshot of the transcriptional regulatory mechanisms on a genome-wide scale. This chapter outlines the general strategies used to carry out ChIP-chip assays to study the differential recruitment of regulatory molecules based on the studies conducted in our lab as well as other published protocols; these can be easily modified to a ChIP-Seq analysis.
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Affiliation(s)
- Smitha Pillai
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
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Kim H, Ekram MB, Bakshi A, Kim J. AEBP2 as a transcriptional activator and its role in cell migration. Genomics 2014; 105:108-15. [PMID: 25451679 DOI: 10.1016/j.ygeno.2014.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/31/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Aebp2 encodes an evolutionarily conserved zinc finger protein that has not been well studied so far, yet recent studies indicated that this gene is closely associated with the Polycomb Repressive Complex 2 (PRC2). Thus, the current study characterized the basic aspects of this gene, including alternative promoters and protein isoforms. According to the results, Aebp2 is controlled through three alternative promoters, deriving three different transcripts encoding the embryonic (32 kDa) and somatic (52 kDa) forms. Chromatin Immuno-Precipitation (ChIP) experiments revealed that AEBP2 binds to its own promoter as well as the promoters of Jarid2 and Snai2. While the embryonic form acts as a transcriptional repressor for Snai2, the somatic form functions as a transcriptional activator for Jarid2, Aebp2 and Snai2. Cell migration assays also demonstrated that the Aebp2 somatic form has an enhancing activity in cell migration. This is consistent with the functional association of Aebp2 with migratory neural crest cells. These results suggest that the two protein isoforms of AEBP2 may have opposite functions for the PcG target genes, and may play significant roles in cell migration during development.
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Affiliation(s)
- Hana Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Muhammad B Ekram
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Arundhati Bakshi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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48
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Grossniklaus U, Paro R. Transcriptional silencing by polycomb-group proteins. Cold Spring Harb Perspect Biol 2014; 6:a019331. [PMID: 25367972 DOI: 10.1101/cshperspect.a019331] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Polycomb-group (PcG) genes encode chromatin proteins involved in stable and heritable transcriptional silencing. PcG proteins participate in distinct multimeric complexes that deposit, or bind to, specific histone modifications (e.g., H3K27me3 and H2AK119ub1) to prevent gene activation and maintain repressed chromatin domains. PcG proteins are evolutionary conserved and play a role in processes ranging from vernalization and seed development in plants, over X-chromosome inactivation in mammals, to the maintenance of stem cell identity. PcG silencing is medically relevant as it is often observed in human disorders, including cancer, and tissue regeneration, which involve the reprogramming of PcG-controlled target genes.
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Affiliation(s)
- Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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49
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Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 2014; 159:374-387. [PMID: 25303531 PMCID: PMC4197132 DOI: 10.1016/j.cell.2014.09.030] [Citation(s) in RCA: 640] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/18/2014] [Accepted: 09/15/2014] [Indexed: 12/31/2022]
Abstract
The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of genes that control cell identity and repression of genes encoding lineage-specifying developmental regulators. Here, we use ESC cohesin ChIA-PET data to identify the local chromosomal structures at both active and repressed genes across the genome. The results produce a map of enhancer-promoter interactions and reveal that super-enhancer-driven genes generally occur within chromosome structures that are formed by the looping of two interacting CTCF sites co-occupied by cohesin. These looped structures form insulated neighborhoods whose integrity is important for proper expression of local genes. We also find that repressed genes encoding lineage-specifying developmental regulators occur within insulated neighborhoods. These results provide insights into the relationship between transcriptional control of cell identity genes and control of local chromosome structure.
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Affiliation(s)
- Jill M Dowen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Computational and Systems Biology Program
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Gang Ren
- Systems Biology Center, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
- College of Animal Science and Technology, Northwest A&F University, Xi'An, P. R. China
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Lyndon N Zhang
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Jurian Schujiers
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Keji Zhao
- Systems Biology Center, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
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50
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Yang X, Hegde VL, Rao R, Zhang J, Nagarkatti PS, Nagarkatti M. Histone modifications are associated with Δ9-tetrahydrocannabinol-mediated alterations in antigen-specific T cell responses. J Biol Chem 2014; 289:18707-18. [PMID: 24841204 DOI: 10.1074/jbc.m113.545210] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Marijuana is one of the most abused drugs due to its psychotropic effects. Interestingly, it is also used for medicinal purposes. The main psychotropic component in marijuana, Δ(9)-tetrahydrocannabinol (THC), has also been shown to mediate potent anti-inflammatory properties. Whether the immunomodulatory activity of THC is mediated by epigenetic regulation has not been investigated previously. In this study, we employed ChIP-Seq technology to examine the in vivo effect of THC on global histone methylation in lymph node cells of mice immunized with a superantigen, staphylococcal enterotoxin B. We compared genome-wide histone H3 Lys-4, Lys-27, Lys-9, and Lys-36 trimethylation and histone H3 Lys-9 acetylation patterns in such cells exposed to THC or vehicle. Our results showed that THC treatment leads to the association of active histone modification signals to Th2 cytokine genes and suppressive modification signals to Th1 cytokine genes, indicating that such a mechanism may play a critical role in the THC-mediated switch from Th1 to Th2. At the global level, a significant portion of histone methylation and acetylation regions were altered by THC. However, the overall distribution of these histone methylation signals among the genomic features was not altered significantly by THC, suggesting that THC activates the expression of a subset of genes while suppressing the expression of another subset of genes through histone modification. Functional classification of these histone marker-associated genes showed that these differentially associated genes were involved in various cellular functions, from cell cycle regulation to metabolism, suggesting that THC had a pleiotropic effect on gene expression in immune cells. Altogether, the current study demonstrates for the first time that THC may modulate immune response through epigenetic regulation involving histone modifications.
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Affiliation(s)
- Xiaoming Yang
- From the Department of Pathology, Microbiology, and Immunology, School of Medicine, and
| | - Venkatesh L Hegde
- From the Department of Pathology, Microbiology, and Immunology, School of Medicine, and
| | - Roshni Rao
- From the Department of Pathology, Microbiology, and Immunology, School of Medicine, and
| | - Jiajia Zhang
- the School of Public Health, University of South Carolina, Columbia, South Carolina 29209
| | - Prakash S Nagarkatti
- From the Department of Pathology, Microbiology, and Immunology, School of Medicine, and
| | - Mitzi Nagarkatti
- From the Department of Pathology, Microbiology, and Immunology, School of Medicine, and
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