1
|
Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
2
|
Abstract
Cardiac hypertrophy (CH) is generally considered adaptive responses that may occur after myocardial infarction, pressure overload, volume overload, inflammatory heart muscle disease, or idiopathic dilated cardiomyopathy, whereas long-term stimulation eventually leads to heart failure (HF). However, the current molecular mechanisms involved in CH are unclear. Recently, increasing evidences reveal that long non-coding RNAs (lncRNAs) play vital roles in CH. Different lncRNAs can promote or inhibit the pathological process of CH by different mechanisms, while the regulation of lncRNAs expression can improve CH. Thus, CH-related lncRNAs may become a novel field of research on CH.
Collapse
Affiliation(s)
- Jinghui Sun
- Cardiovascular Disease Research Center, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Haidian District, Beijing, 100091, China
| | - Chenglong Wang
- Cardiovascular Disease Research Center, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Haidian District, Beijing, 100091, China.
| |
Collapse
|
3
|
Pal D, Riester SM, Hasan B, Tufa SF, Dudakovic A, Keene DR, van Wijnen AJ, Schweitzer R. Ezh2 Is Essential for Patterning of Multiple Musculoskeletal Tissues but Dispensable for Tendon Differentiation. Stem Cells Dev 2021; 30:601-609. [PMID: 33757300 DOI: 10.1089/scd.2020.0209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An efficient musculoskeletal system depends on the precise assembly and coordinated growth and function of muscles, skeleton, and tendons. However, the mechanisms that drive integrated musculoskeletal development and coordinated growth and differentiation of each of these tissues are still being uncovered. Epigenetic modifiers have emerged as critical regulators of cell fate differentiation, but so far almost nothing is known about their roles in tendon biology. Previous studies have shown that epigenetic modifications driven by Enhancer of zeste homolog 2 (EZH2), a major histone methyltransferase, have significant roles in vertebrate development including skeletal patterning and bone formation. We now find that targeting Ezh2 through the limb mesenchyme also has significant effects on tendon and muscle patterning, likely reflecting the essential roles of early mesenchymal cues mediated by Ezh2 for coordinated patterning and development of all tissues of the musculoskeletal system. Conversely, loss of Ezh2 in the tendon cells did not disrupt overall tendon structure or collagen organization suggesting that tendon differentiation and maturation are independent of Ezh2 signaling.
Collapse
Affiliation(s)
- Deepanwita Pal
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA
| | - Scott M Riester
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Bashar Hasan
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sara F Tufa
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas R Keene
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA.,Department of Orthopedics, Oregon Health & Science University, Portland, USA
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ronen Schweitzer
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA.,Department of Orthopedics, Oregon Health & Science University, Portland, USA
| |
Collapse
|
4
|
Li M, Zhao Q, Belloli R, Duffy CR, Cai HN. Insulator foci distance correlates with cellular and nuclear morphology in early Drosophila embryos. Dev Biol 2021; 476:189-199. [PMID: 33844976 DOI: 10.1016/j.ydbio.2021.03.022] [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: 09/23/2020] [Revised: 02/16/2021] [Accepted: 03/26/2021] [Indexed: 11/25/2022]
Abstract
The three-dimensional (3D) organization of the genome is highly dynamic, changing during development and varying across different tissues and cell types. Recent studies indicate that these changes alter regulatory interactions, leading to changes in gene expression. Despite its importance, the mechanisms that influence genomic organization remain poorly understood. We have previously identified a network of chromatin boundary elements, or insulators, in the Drosophila Antennapedia homeotic complex (ANT-C). These genomic elements interact with one another to tether chromatin loops that could block or promote enhancer-promoter interactions. To understand the function of these insulators, we assessed their interactions by measuring their 3D nuclear distance in developing animal tissues. Our data suggest that the ANT-C Hox complex might be in a folded or looped configuration rather than in a random or extended form. The architecture of the ANT-C complex, as read out by the pair-wise distance between insulators, undergoes a strong compression during late embryogenesis, coinciding with the reduction of cell and nuclear diameters due to continued cell divisions in post-cleavage cells. Our results suggest that genomic architecture and gene regulation may be influenced by cellular morphology and movement during development.
Collapse
Affiliation(s)
- Mo Li
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Qing Zhao
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Ryan Belloli
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Carly R Duffy
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Haini N Cai
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA.
| |
Collapse
|
5
|
Kumari R, Jat P. Mechanisms of Cellular Senescence: Cell Cycle Arrest and Senescence Associated Secretory Phenotype. Front Cell Dev Biol 2021; 9:645593. [PMID: 33855023 PMCID: PMC8039141 DOI: 10.3389/fcell.2021.645593] [Citation(s) in RCA: 587] [Impact Index Per Article: 195.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stable cell cycle arrest that can be triggered in normal cells in response to various intrinsic and extrinsic stimuli, as well as developmental signals. Senescence is considered to be a highly dynamic, multi-step process, during which the properties of senescent cells continuously evolve and diversify in a context dependent manner. It is associated with multiple cellular and molecular changes and distinct phenotypic alterations, including a stable proliferation arrest unresponsive to mitogenic stimuli. Senescent cells remain viable, have alterations in metabolic activity and undergo dramatic changes in gene expression and develop a complex senescence-associated secretory phenotype. Cellular senescence can compromise tissue repair and regeneration, thereby contributing toward aging. Removal of senescent cells can attenuate age-related tissue dysfunction and extend health span. Senescence can also act as a potent anti-tumor mechanism, by preventing proliferation of potentially cancerous cells. It is a cellular program which acts as a double-edged sword, with both beneficial and detrimental effects on the health of the organism, and considered to be an example of evolutionary antagonistic pleiotropy. Activation of the p53/p21WAF1/CIP1 and p16INK4A/pRB tumor suppressor pathways play a central role in regulating senescence. Several other pathways have recently been implicated in mediating senescence and the senescent phenotype. Herein we review the molecular mechanisms that underlie cellular senescence and the senescence associated growth arrest with a particular focus on why cells stop dividing, the stability of the growth arrest, the hypersecretory phenotype and how the different pathways are all integrated.
Collapse
Affiliation(s)
- Ruchi Kumari
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, United Kingdom
| | - Parmjit Jat
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, United Kingdom
| |
Collapse
|
6
|
Ghasemi R, Struthers H, Wilson ER, Spencer DH. Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells. Leukemia 2020; 35:404-416. [PMID: 32398790 PMCID: PMC7657955 DOI: 10.1038/s41375-020-0856-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 11/09/2022]
Abstract
Transcriptional regulation of the HOXA genes is thought to involve CTCF-mediated chromatin loops and the opposing actions of the COMPASS and Polycomb epigenetic complexes. We investigated the role of these mechanisms at the HOXA cluster in AML cells with the common NPM1c mutation, which express both HOXA and HOXB genes. CTCF binding at the HOXA locus is conserved across primary AML samples, regardless of HOXA gene expression, and defines a continuous chromatin domain marked by COMPASS-associated histone H3 trimethylation in NPM1-mutant primary AML samples. Profiling of the three-dimensional chromatin architecture in primary AML samples with the NPM1c mutation identified chromatin loops between the HOXA cluster and loci in the SNX10 and SKAP2 genes, and an intergenic region located 1.4 Mbp upstream of the HOXA locus. Deletion of CTCF binding sites in the NPM1-mutant OCI-AML3 AML cell line reduced multiple long-range interactions, but resulted in CTCF-independent loops with sequences in SKAP2 that were marked by enhancer-associated histone modifications in primary AML samples. HOXA gene expression was maintained in CTCF binding site mutants, indicating that transcriptional activity at the HOXA locus in NPM1-mutant AML cells may be sustained through persistent interactions with SKAP2 enhancers, or by intrinsic factors within the HOXA gene cluster.
Collapse
Affiliation(s)
- Reza Ghasemi
- Division of Oncology, Department of Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Heidi Struthers
- Division of Oncology, Department of Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Elisabeth R Wilson
- Division of Oncology, Department of Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - David H Spencer
- Division of Oncology, Department of Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO, USA. .,McDonnell Genome Institute, Washington University, St. Louis, MO, USA.
| |
Collapse
|
7
|
From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
8
|
Kalha S, Shrestha B, Sanz Navarro M, Jones KB, Klein OD, Michon F. Bmi1+ Progenitor Cell Dynamics in Murine Cornea During Homeostasis and Wound Healing. Stem Cells 2018; 36:562-573. [PMID: 29282831 DOI: 10.1002/stem.2767] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/27/2017] [Accepted: 12/09/2017] [Indexed: 01/06/2023]
Abstract
The outermost layer of the eye, the cornea, is renewed continuously throughout life. Stem cells of the corneal epithelium reside in the limbus at the corneal periphery and ensure homeostasis of the central epithelium. However, in young mice, homeostasis relies on cells located in the basal layer of the central corneal epithelium. Here, we first studied corneal growth during the transition from newborn to adult and assessed Keratin 19 (Krt19) expression as a hallmark of corneal maturation. Next, we set out to identify a novel marker of murine corneal epithelial progenitor cells before, during and after maturation, and we found that Bmi1 is expressed in the basal epithelium of the central cornea and limbus. Furthermore, we demonstrated that Bmi1+ cells participated in tissue replenishment in the central cornea. These Bmi1+ cells did not maintain homeostasis of the cornea for more than 3 months, reflecting their status as progenitor rather than stem cells. Finally, after injury, Bmi1+ cells fueled homeostatic maintenance, whereas wound closure occurred via epithelial reorganization. Stem Cells 2018;36:562-573.
Collapse
Affiliation(s)
- Solja Kalha
- Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Bideep Shrestha
- Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maria Sanz Navarro
- Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kyle B Jones
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, USA.,Department of Pediatrics and Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Frederic Michon
- Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Keele Medical School and Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire, England, United Kingdom
| |
Collapse
|
9
|
Yuan G, Chen X, Lu J, Feng Z, Chen S, Chen R, Wei W, Zhou F, Xie D. Chromobox homolog 8 is a predictor of muscle invasive bladder cancer and promotes cell proliferation by repressing the p53 pathway. Cancer Sci 2017; 108:2166-2175. [PMID: 28837252 PMCID: PMC5665758 DOI: 10.1111/cas.13383] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/08/2017] [Accepted: 08/16/2017] [Indexed: 12/16/2022] Open
Abstract
Chromobox homolog 8 (CBX8), also known as human polycomb 8, is a repressor that maintains the transcriptionally repressive state in various cellular genes, and has been reported to promote tumorigenesis. In the present study, we examined CBX8 expression in eight pairs of muscle invasive bladder cancer tissues and adjacent non-tumor tissues, and found that CBX8 was frequently upregulated in muscle invasive bladder cancer tissues when compared to adjacent non-tumor tissues. Analysis showed that high expression of CBX8 in 152 muscle invasive bladder cancer specimens was associated with progression of the T, N, and M stages (P = 0.004, 0.005, <0.001, respectively). Furthermore, Kaplan-Meier survival analysis and log-rank test showed that muscle invasive bladder cancer patients with high CBX8 expression had a poor rate of overall survival (P < 0.001) and 5-year recurrence-free survival (P < 0.001) compared to patients with low CBX8 expression. High CBX8 expression predicted poor overall survival and 5-year recurrence-free survival in T and N stages of muscle invasive bladder cancer patients. Moreover, knockdown of CBX8 inhibited cell proliferation of urothelial carcinoma of the bladder both in vitro and in vivo. In addition, CBX8 depletion resulted in cell cycle delay of urothelial carcinoma cells of the bladder at the G2/M phase by the p53 pathway. The data suggest that high expression of CBX8 plays a critical oncogenic role in aggressiveness of urothelial carcinoma cells of the bladder through promoting cancer cell proliferation by repressing the p53 pathway, and CBX8 could be used as a novel predictor for muscle invasive bladder cancer patients.
Collapse
Affiliation(s)
- Gang‐jun Yuan
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina,Department of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Xin Chen
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina,Department of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Jun Lu
- Department of UrologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Zi‐hao Feng
- Department of UrologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Si‐liang Chen
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Ri‐xin Chen
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Wen‐su Wei
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Fang‐jian Zhou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina,Department of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Dan Xie
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| |
Collapse
|
10
|
Epigenetic Alterations in Human Papillomavirus-Associated Cancers. Viruses 2017; 9:v9090248. [PMID: 28862667 PMCID: PMC5618014 DOI: 10.3390/v9090248] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/25/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
Approximately 15–20% of human cancers are caused by viruses, including human papillomaviruses (HPVs). Viruses are obligatory intracellular parasites and encode proteins that reprogram the regulatory networks governing host cellular signaling pathways that control recognition by the immune system, proliferation, differentiation, genomic integrity, and cell death. Given that key proteins in these regulatory networks are also subject to mutation in non-virally associated diseases and cancers, the study of oncogenic viruses has also been instrumental to the discovery and analysis of many fundamental cellular processes, including messenger RNA (mRNA) splicing, transcriptional enhancers, oncogenes and tumor suppressors, signal transduction, immune regulation, and cell cycle control. More recently, tumor viruses, in particular HPV, have proven themselves invaluable in the study of the cancer epigenome. Epigenetic silencing or de-silencing of genes can have cellular consequences that are akin to genetic mutations, i.e., the loss and gain of expression of genes that are not usually expressed in a certain cell type and/or genes that have tumor suppressive or oncogenic activities, respectively. Unlike genetic mutations, the reversible nature of epigenetic modifications affords an opportunity of epigenetic therapy for cancer. This review summarizes the current knowledge on epigenetic regulation in HPV-infected cells with a focus on those elements with relevance to carcinogenesis.
Collapse
|
11
|
Hu Q, Wu W, Zeng A, Yu T, Shen F, Nie E, Wang Y, Liu N, Zhang J, You Y. Polycomb group expression signatures in the malignant progression of gliomas. Oncol Lett 2017; 13:2583-2590. [PMID: 28454437 PMCID: PMC5403712 DOI: 10.3892/ol.2017.5753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 12/16/2016] [Indexed: 12/03/2022] Open
Abstract
Polycomb group (PcG) proteins form at least two key complexes, namely polycomb repressive complex 1 and polycomb repressive complex 2. These complexes are involved in the progression of various cancers. Systematic research has not been conducted on the aberrant expression of PcG members in gliomas. Using the Chinese Glioma Genome Atlas data set, PcG expression patterns between normal brain tissues and glioma samples were analyzed, and a PcG-based classifier was then developed using BRB Cox regression and risk-score model. These results were validated in an independent GSE16011 set. A total of six PcGs [chromobox protein homolog (CBX) 6, CBX7, PHD finger protein 1, enhancer of zeste homolog 2 (EZH2), DNA (cytosine-5-)-methyltransferase 3β (DNMT3B) and polyhomeotic-like protein 2] were identified to be associated with glioma grade. Survival analysis then revealed a five-PcG gene signature one protective gene (enhancer of zeste homolog 1) and four risky genes (EZH2, PHD finger protein 19, DNMT3A and DNMT3B), which may identify patients with high risk of poor prognosis of glioma. Multivariate Cox analysis indicated that the five-PcG signature was an independent prognostic biomarker. These findings indicated that a novel prognostic classifier, five-PcG signature, served as an independent prognostic marker for patients with glioma.
Collapse
Affiliation(s)
- Qi Hu
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Weining Wu
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Ailiang Zeng
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Tianfu Yu
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Feng Shen
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Er Nie
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yingyi Wang
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Ning Liu
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Junxia Zhang
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yongping You
- Department of Neurosurgery, First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| |
Collapse
|
12
|
Roles of pRB in the Regulation of Nucleosome and Chromatin Structures. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5959721. [PMID: 28101510 PMCID: PMC5215604 DOI: 10.1155/2016/5959721] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/08/2016] [Indexed: 01/31/2023]
Abstract
Retinoblastoma protein (pRB) interacts with E2F and other protein factors to play a pivotal role in regulating the expression of target genes that induce cell cycle arrest, apoptosis, and differentiation. pRB controls the local promoter activity and has the ability to change the structure of nucleosomes and/or chromosomes via histone modification, epigenetic changes, chromatin remodeling, and chromosome organization. Functional inactivation of pRB perturbs these cellular events and causes dysregulated cell growth and chromosome instability, which are hallmarks of cancer cells. The role of pRB in regulation of nucleosome/chromatin structures has been shown to link to tumor suppression. This review focuses on the ability of pRB to control nucleosome/chromatin structures via physical interactions with histone modifiers and chromatin factors and describes cancer therapies based on targeting these protein factors.
Collapse
|
13
|
Wang Z, Zhang XJ, Ji YX, Zhang P, Deng KQ, Gong J, Ren S, Wang X, Chen I, Wang H, Gao C, Yokota T, Ang YS, Li S, Cass A, Vondriska TM, Li G, Deb A, Srivastava D, Yang HT, Xiao X, Li H, Wang Y. The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy. Nat Med 2016; 22:1131-1139. [PMID: 27618650 PMCID: PMC5053883 DOI: 10.1038/nm.4179] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/05/2016] [Indexed: 12/13/2022]
Abstract
Epigenetic reprogramming is a critical process of pathological gene induction during cardiac hypertrophy and remodeling, but the underlying regulatory mechanisms remain to be elucidated. Here we identified a heart-enriched long noncoding (lnc)RNA, named cardiac-hypertrophy-associated epigenetic regulator (Chaer), which is necessary for the development of cardiac hypertrophy. Mechanistically, Chaer directly interacts with the catalytic subunit of polycomb repressor complex 2 (PRC2). This interaction, which is mediated by a 66-mer motif in Chaer, interferes with PRC2 targeting to genomic loci, thereby inhibiting histone H3 lysine 27 methylation at the promoter regions of genes involved in cardiac hypertrophy. The interaction between Chaer and PRC2 is transiently induced after hormone or stress stimulation in a process involving mammalian target of rapamycin complex 1, and this interaction is a prerequisite for epigenetic reprogramming and induction of genes involved in hypertrophy. Inhibition of Chaer expression in the heart before, but not after, the onset of pressure overload substantially attenuates cardiac hypertrophy and dysfunction. Our study reveals that stress-induced pathological gene activation in the heart requires a previously uncharacterized lncRNA-dependent epigenetic checkpoint.
Collapse
Affiliation(s)
- Zhihua Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Xiao-Jing Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Yan-Xiao Ji
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Peng Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Ke-Qiong Deng
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Jun Gong
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Shuxun Ren
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Xinghua Wang
- Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Iris Chen
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - He Wang
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Chen Gao
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Tomohiro Yokota
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Yen Sin Ang
- Gladstone Institute of Cardiovascular Diseases, San Francisco, California, USA
- University of California San Francisco, School of Medicine, San Francisco, California, USA
| | - Shen Li
- Department of Medicine, Cardiology Division, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Ashley Cass
- Department of Integrative Biology and Physiology, College of Life Sciences, Molecular Biology Institute, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Bioinformatics Interdepartmental Program, University of California at Los Angeles, Los Angeles, California, USA
| | - Thomas M. Vondriska
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Guangping Li
- Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Arjun Deb
- Department of Medicine, Cardiology Division, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Diseases, San Francisco, California, USA
- University of California San Francisco, School of Medicine, San Francisco, California, USA
| | - Huang-Tian Yang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Laboratory of Molecular Cardiology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, College of Life Sciences, Molecular Biology Institute, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Bioinformatics Interdepartmental Program, University of California at Los Angeles, Los Angeles, California, USA
| | - Hongliang Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Animal Experiment Center–Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Yibin Wang
- Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
- Department of Medicine, Cardiology Division, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
- Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| |
Collapse
|
14
|
Brinkmeier ML, Geister KA, Jones M, Waqas M, Maillard I, Camper SA. The Histone Methyltransferase Gene Absent, Small, or Homeotic Discs-1 Like Is Required for Normal Hox Gene Expression and Fertility in Mice. Biol Reprod 2015; 93:121. [PMID: 26333994 DOI: 10.1095/biolreprod.115.131516] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/01/2015] [Indexed: 01/27/2023] Open
Abstract
Chromatin remodeling influences gene expression in developing and adult organisms. Active and repressive marks of histone methylation dictate the embryonic expression boundaries of developmentally regulated genes, including the Hox gene cluster. Drosophila ash1 (absent, small or homeotic discs 1) gene encodes a histone methyltransferase essential for regulation of Hox gene expression that interacts genetically with other members of the trithorax group (TrxG). While mammalian members of the mixed lineage leukemia (Mll) family of TrxG genes have roles in regulation of Hox gene expression, little is known about the expression and function of the mammalian ortholog of the Drosophila ash1 gene, Ash1-like (Ash1l). Here we report the expression of mouse Ash1l gene in specific structures within various organs and provide evidence that reduced Ash1l expression has tissue-specific effects on mammalian development and adult homeostasis. Mutants exhibit partially penetrant postnatal lethality and failure to thrive. Surviving mutants have growth insufficiency, skeletal transformations, and infertility associated with developmental defects in both male and female reproductive organs. Specifically, expression of Hoxa11 and Hoxd10 are altered in the epididymis of Ash1l mutant males and Hoxa10 is reduced in the uterus of Ash1l mutant females. In summary, we show that the histone methyltransferase Ash1l is important for the development and function of several tissues and for proper expression of homeotic genes in mammals.
Collapse
Affiliation(s)
| | - Krista A Geister
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan
| | - Morgan Jones
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan
| | - Meriam Waqas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Ivan Maillard
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
15
|
Srivastava S, Dhawan J, Mishra RK. Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters. Mech Dev 2015; 138 Pt 2:160-169. [PMID: 26254900 DOI: 10.1016/j.mod.2015.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 01/07/2023]
Abstract
Hox gene expression imparts segment identity to body structures along the anterior-posterior axis and is tightly governed by higher order chromatin mechanisms. Chromatin regulatory features of the homeotic complex are best defined in Drosophila melanogaster, where multiple cis-regulatory elements have been identified that ensure collinear Hox gene expression patterns in accordance with their genomic organization. Recent studies focused on delineating the epigenetic features of the vertebrate Hox clusters have helped reveal their dynamic chromatin organization and its impact on gene expression. Enrichment for the 'activating' H3K4me3 and 'repressive' H3K27me3 histone modifications is a particularly strong read-out for transcriptional status and correlates well with the evidence for chromatin loop domain structures and stage specific topological changes at these loci. However, it is not clear how such distinct domains are imposed and regulated independent of each other. Comparative analysis of the chromatin structure and organization of the homeotic gene clusters in fly and mammals is increasingly revealing the functional conservation of chromatin mediated mechanisms. Here we discuss the case for interspersed boundary elements existing within mammalian Hox clusters along with their possible roles and mechanisms of action. Recent studies suggest a role for factors other than the well characterized vertebrate boundary factor CTCF, such as the GAGA binding factor (GAF), in maintaining chromatin domains at the Hox loci. We also present data demonstrating how such regulatory elements may be involved in organizing higher order structure and demarcating active domains of gene expression at the mammalian Hox clusters.
Collapse
Affiliation(s)
- Surabhi Srivastava
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| |
Collapse
|
16
|
Li G, Warden C, Zou Z, Neman J, Krueger JS, Jain A, Jandial R, Chen M. Altered expression of polycomb group genes in glioblastoma multiforme. PLoS One 2013; 8:e80970. [PMID: 24260522 PMCID: PMC3829908 DOI: 10.1371/journal.pone.0080970] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/08/2013] [Indexed: 01/04/2023] Open
Abstract
The Polycomb group (PcG) proteins play a critical role in histone mediated epigenetics which has been implicated in the malignant evolution of glioblastoma multiforme (GBM). By systematically interrogating The Cancer Genome Atlas (TCGA), we discovered widespread aberrant expression of the PcG members in GBM samples compared to normal brain. The most striking differences were upregulation of EZH2, PHF19, CBX8 and PHC2 and downregulation of CBX7, CBX6, EZH1 and RYBP. Interestingly, changes in EZH2, PHF19, CBX7, CBX6 and EZH1 occurred progressively as astrocytoma grade increased. We validated the aberrant expression of CBX6, CBX7, CBX8 and EZH2 in GBM cell lines by Western blotting and qRT-PCR, and further the aberrant expression of CBX6 in GBM tissue samples by immunohistochemical staining. To determine if there was functional significance to the diminished CBX6 levels in GBM, CBX6 was overexpressed in GBM cells resulting in decreased proliferative capacity. In conclusion, aberrant expression of PcG proteins in GBMs may play a role in the development or maintenance of the malignancy.
Collapse
Affiliation(s)
- Gang Li
- Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, California, United States of America
| | - Charles Warden
- Bioinformatics Core, Department of Molecular Medicine, City of Hope National Medical Center, Duarte, California, United States of America
| | - Zhaoxia Zou
- Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, California, United States of America
| | - Josh Neman
- Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, California, United States of America
| | | | - Alisha Jain
- Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, California, United States of America
| | - Rahul Jandial
- Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, California, United States of America
| | - Mike Chen
- Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail:
| |
Collapse
|
17
|
Lai HL, Wang QT. Additional sex combs-like 2 is required for polycomb repressive complex 2 binding at select targets. PLoS One 2013; 8:e73983. [PMID: 24040135 PMCID: PMC3767597 DOI: 10.1371/journal.pone.0073983] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/25/2013] [Indexed: 12/23/2022] Open
Abstract
Polycomb Group (PcG) proteins are epigenetic repressors of gene expression. The Drosophila Additional sex combs (Asx) gene and its mammalian homologs exhibit PcG function in genetic assays; however, the mechanism by which Asx family proteins mediate gene repression is not well understood. ASXL2, one of three mammalian homologs for Asx, is highly expressed in the mammalian heart and is required for the maintenance of cardiac function. We have previously shown that Asxl2 deficiency results in a reduction in the bulk level of histone H3 lysine 27 trimethylation (H3K27me3), a repressive mark generated by the Polycomb Repressive Complex 2 (PRC2). Here we identify several ASXL2 target genes in the heart and investigate the mechanism by which ASXL2 facilitates their repression. We show that the Asxl2-deficient heart is defective in converting H3K27me2 to H3K27me3 and in removing ubiquitin from mono-ubiquitinated histone H2A. ASXL2 and PRC2 interact in the adult heart and co-localize to target promoters. ASXL2 is required for the binding of PRC2 and for the enrichment of H3K27me3 at target promoters. These results add a new perspective to our understanding of the mechanisms that regulate PcG activity and gene repression.
Collapse
Affiliation(s)
- Hsiao-Lei Lai
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Q. Tian Wang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
| |
Collapse
|
18
|
Abstract
The molecular mechanisms underlying oncogenesis in leukemias associated with rearrangement of the Mixed Lineage Leukemia (MLL) gene have received a considerable amount of attention over the last two decades. In this review we will focus on recent studies, published over the past year, that reveal new insights into the multi-protein complexes formed by MLL and MLL fusion proteins, the role of epigenetic deregulation in MLL fusion function, downstream transcriptional target genes, the importance of the leukemia cell of origin, the role played by microRNAs, cooperating mutations and the implications that recent research has for the therapy of MLL-rearranged leukemia.
Collapse
|
19
|
Wang QT. Epigenetic regulation of cardiac development and function by polycomb group and trithorax group proteins. Dev Dyn 2012; 241:1021-33. [PMID: 22514007 DOI: 10.1002/dvdy.23796] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2012] [Indexed: 12/29/2022] Open
Abstract
Heart disease is a leading cause of death and disability in developed countries. Heart disease includes a broad range of diseases that affect the development and/or function of the cardiovascular system. Some of these diseases, such as congenital heart defects, are present at birth. Others develop over time and may be influenced by both genetic and environmental factors. Many of the known heart diseases are associated with abnormal expression of genes. Understanding the factors and mechanisms that regulate gene expression in the heart is essential for the detection, treatment, and prevention of heart diseases. Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are special families of chromatin factors that regulate developmental gene expression in many tissues and organs. Accumulating evidence suggests that these proteins are important regulators of development and function of the heart as well. A better understanding of their roles and functional mechanisms will translate into new opportunities for combating heart disease.
Collapse
Affiliation(s)
- Q Tian Wang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
| |
Collapse
|
20
|
Mohamed Ariff I, Mitra A, Basu A. Epigenetic regulation of self-renewal and fate determination in neural stem cells. J Neurosci Res 2011; 90:529-39. [DOI: 10.1002/jnr.22804] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/18/2011] [Accepted: 09/02/2011] [Indexed: 01/30/2023]
|
21
|
Harnessing of the nucleosome-remodeling-deacetylase complex controls lymphocyte development and prevents leukemogenesis. Nat Immunol 2011; 13:86-94. [PMID: 22080921 PMCID: PMC3868219 DOI: 10.1038/ni.2150] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 09/24/2011] [Indexed: 12/11/2022]
Abstract
Cell fate decisions depend on the interplay between chromatin regulators and transcription factors. Here we show that activity of the Mi-2β nucleosome remodeling and deacetylase (NuRD) complex was controlled by the Ikaros family of lymphoid-lineage determining proteins. Ikaros, an integral component of the NuRD complex in lymphocytes, tethered this complex to active lymphoid differentiation genes. Loss in Ikaros DNA binding activity caused a local increase in Mi-2β chromatin remodeling and histone deacetylation and suppression of lymphoid gene expression. The NuRD complex also redistributed to transcriptionally poised non-Ikaros gene targets, involved in proliferation and metabolism, inducing their reactivation. Thus, release of NuRD from Ikaros regulation blocks lymphocyte maturation and mediates progression to a leukemic state by engaging functionally opposing epigenetic and genetic networks.
Collapse
|
22
|
Takawa M, Masuda K, Kunizaki M, Daigo Y, Takagi K, Iwai Y, Cho HS, Toyokawa G, Yamane Y, Maejima K, Field HI, Kobayashi T, Akasu T, Sugiyama M, Tsuchiya E, Atomi Y, Ponder BAJ, Nakamura Y, Hamamoto R. Validation of the histone methyltransferase EZH2 as a therapeutic target for various types of human cancer and as a prognostic marker. Cancer Sci 2011; 102:1298-305. [PMID: 21539681 PMCID: PMC11159278 DOI: 10.1111/j.1349-7006.2011.01958.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The emphasis in anticancer drug discovery has always been on finding a drug with great antitumor potential but few side-effects. This can be achieved if the drug is specific for a molecular site found only in tumor cells. Here, we find the enhancer of zeste homolog 2 (EZH2) to be highly overexpressed in lung and other cancers, and show that EZH2 is integral to proliferation in cancer cells. Quantitative real-time PCR analysis revealed higher expression of EZH2 in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P < 0.0001), and we confirmed that a wide range of cancers also overexpress EZH2, using cDNA microarray analysis. Immunohistochemical analysis showed positive staining for EZH2 in 14 of 29 cases of bladder cancer, 135 of 292 cases of non-small-cell lung cancer (NSCLC), and 214 of 245 cases of colorectal cancer, whereas no significant staining was observed in various normal tissues. We found elevated expression of EZH2 to be associated with poor prognosis for patients with NSCLC (P = 0.0239). In lung and bladder cancer cells overexpressing EZH2, suppression of EZH2 using specific siRNAs inhibited incorporation of BrdU and resulted in significant suppression of cell growth, even though no significant effect was observed in the normal cell strain CCD-18Co, which has undetectable EZH2. Because EZH2 expression was scarcely detectable in all normal tissues we examined, EZH2 shows promise as a tumor-specific therapeutic target. Furthermore, as elevated levels of EZH2 are associated with poor prognosis of patients with NSCLC, its overexpression in resected specimens could prove a useful molecular marker, indicating the necessity for a more extensive follow-up in some lung cancer patients after surgical treatment.
Collapse
Affiliation(s)
- Masashi Takawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
An S, Yeo KJ, Jeon YH, Song JJ. Crystal structure of the human histone methyltransferase ASH1L catalytic domain and its implications for the regulatory mechanism. J Biol Chem 2011; 286:8369-8374. [PMID: 21239497 PMCID: PMC3048721 DOI: 10.1074/jbc.m110.203380] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/03/2011] [Indexed: 12/25/2022] Open
Abstract
Absent, small, or homeotic disc1 (Ash1) is a trithorax group histone methyltransferase that is involved in gene activation. Although there are many known histone methyltransferases, their regulatory mechanisms are poorly understood. Here, we present the crystal structure of the human ASH1L catalytic domain, showing its substrate binding pocket blocked by a loop from the post-SET domain. In this configuration, the loop limits substrate access to the active site. Mutagenesis of the loop stimulates ASH1L histone methyltransferase activity, suggesting that ASH1L activity may be regulated through the loop from the post-SET domain. In addition, we show that human ASH1L specifically methylates histone H3 Lys-36. Our data implicate that there may be a regulatory mechanism of ASH1L histone methyltransferases.
Collapse
Affiliation(s)
- Sojin An
- From the Structural Biology Laboratory of Epigenetics, Department of Biological Sciences, Graduate school of Nanoscience and Technology (World Class University), KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 335 Gwahangno, Yuseong-gu, Daejeon 305-701 and
| | - Kwon Joo Yeo
- the Division of Magnetic Resonance, Korea Basic Science Institute (KBSI) and University of Science and Technology, 804-1, Yangcheong-Ri, Ochang, Chungbuk 363-883, Korea
| | - Young Ho Jeon
- the Division of Magnetic Resonance, Korea Basic Science Institute (KBSI) and University of Science and Technology, 804-1, Yangcheong-Ri, Ochang, Chungbuk 363-883, Korea
| | - Ji-Joon Song
- From the Structural Biology Laboratory of Epigenetics, Department of Biological Sciences, Graduate school of Nanoscience and Technology (World Class University), KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 335 Gwahangno, Yuseong-gu, Daejeon 305-701 and.
| |
Collapse
|
24
|
Human papillomavirus E7 oncoprotein induces KDM6A and KDM6B histone demethylase expression and causes epigenetic reprogramming. Proc Natl Acad Sci U S A 2011; 108:2130-5. [PMID: 21245294 DOI: 10.1073/pnas.1009933108] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Despite the availability of vaccines, human papillomavirus (HPV) infections remain a cause of significant cancer morbidity and mortality. We have previously shown that HPV16 E7 associates with and diminishes E2F6-containing polycomb repressive complexes. Here, we show that repressive trimethyl marks on lysine 27 of histone 3, which are necessary for binding of polycomb repressive complexes, are decreased in HPV16 E7-expressing cells and HPV16-positive cervical lesions. This is caused by transcriptional induction of the KDM6A and KDM6B histone 3 lysine 27-specific demethylases. HPV16 E7-mediated KDM6B induction accounts for expression of the cervical cancer biomarker, p16(INK4A). Moreover, KDM6A- and KDM6B-responsive Homeobox genes are expressed at significantly higher levels, suggesting that HPV16 E7 results in reprogramming of host epithelial cells. These effects are independent of the ability of E7 to inhibit the retinoblastoma tumor suppressor protein. Most importantly, these effects are reversed when E7 expression is silenced, indicating that this pathway may have prognostic and/or therapeutic significance.
Collapse
|
25
|
Hsieh J, Eisch AJ. Epigenetics, hippocampal neurogenesis, and neuropsychiatric disorders: unraveling the genome to understand the mind. Neurobiol Dis 2010; 39:73-84. [PMID: 20114075 DOI: 10.1016/j.nbd.2010.01.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 01/07/2010] [Accepted: 01/11/2010] [Indexed: 01/16/2023] Open
Abstract
In mature, differentiated neurons in the central nervous system (CNS), epigenetic mechanisms--including DNA methylation, histone modification, and regulatory noncoding RNAs--play critical roles in encoding experience and environmental stimuli into stable, behaviorally meaningful changes in gene expression. For example, epigenetic changes in mature hippocampal neurons have been implicated in learning and memory and in a variety of neuropsychiatric disorders, including depression. With all the recent (and warranted) attention given to epigenetic modifications in mature neurons, it is easy to forget that epigenetic mechanisms were initially described for their ability to promote differentiation and drive cell fate in embryonic and early postnatal development, including neurogenesis. Given the discovery of ongoing neurogenesis in the adult brain and the intriguing links among adult hippocampal neurogenesis, hippocampal function, and neuropsychiatric disorders, it is timely to complement the ongoing discussions on the role of epigenetics in mature neurons with a review on what is currently known about the role of epigenetics in adult hippocampal neurogenesis. The process of adult hippocampal neurogenesis is complex, with neural stem cells (NSCs) giving rise to fate-restricted progenitors and eventually mature dentate gyrus granule cells. Notably, neurogenesis occurs within an increasingly well-defined "neurogenic niche", where mature cellular elements like vasculature, astrocytes, and neurons release signals that can dynamically regulate neurogenesis. Here we review the evidence that key stages and aspects of adult neurogenesis are driven by epigenetic mechanisms. We discuss the intrinsic changes occurring within NSCs and their progeny that are critical for neurogenesis. We also discuss how extrinsic changes occurring in cellular components in the niche can result in altered neurogenesis. Finally we describe the potential relevance of epigenetics for understanding the relationship between hippocampal neurogenesis in neuropsychiatric disorders. We propose that a more thorough understanding of the molecular and genetic mechanisms that control the complex process of neurogenesis, including the proliferation and differentiation of NSCs, will lead to novel therapeutics for the treatment of neuropsychiatric disorders.
Collapse
Affiliation(s)
- Jenny Hsieh
- Department of Molecular Biology, University of Texas Southwestern Medical Center, TX 75390, USA.
| | | |
Collapse
|
26
|
Role of chromatin states in transcriptional memory. Biochim Biophys Acta Gen Subj 2009; 1790:445-55. [PMID: 19236904 DOI: 10.1016/j.bbagen.2009.02.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 12/16/2022]
Abstract
Establishment of cellular memory and its faithful propagation is critical for successful development of multicellular organisms. As pluripotent cells differentiate, choices in cell fate are inherited and maintained by their progeny throughout the lifetime of the organism. A major factor in this process is the epigenetic inheritance of specific transcriptional states or transcriptional memory. In this review, we discuss chromatin transitions and mechanisms by which they are inherited by subsequent generations. We also discuss illuminating cases of cellular memory in budding yeast and evaluate whether transcriptional memory in yeast is nuclear or cytoplasmically inherited.
Collapse
|
27
|
Wu HH, Su B. Adaptive evolution of SCML1 in primates, a gene involved in male reproduction. BMC Evol Biol 2008; 8:192. [PMID: 18601738 PMCID: PMC2459175 DOI: 10.1186/1471-2148-8-192] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 07/05/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genes involved in male reproduction are often the targets of natural and/or sexual selection. SCML1 is a recently identified X-linked gene with preferential expression in testis. To test whether SCML1 is the target of selection in primates, we sequenced and compared the coding region of SCML1 in major primate lineages, and we observed the signature of positive selection in primates. RESULTS We analyzed the molecular evolutionary pattern of SCML1 in diverse primate species, and we observed a strong signature of adaptive evolution which is caused by Darwinian positive selection. When compared with the paralogous genes (SCML2 and SCMH1) of the same family, SCML1 evolved rapidly in primates, which is consistent with the proposed adaptive evolution, suggesting functional modification after gene duplication. Gene expression analysis in rhesus macaques shows that during male sexual maturation, there is a significant expression change in testis, implying that SCML1 likely plays a role in testis development and spermatogenesis. The immunohistochemical data indicates that SCML1 is preferentially expressed in germ stem cells of testis, therefore likely involved in spermatogenesis. CONCLUSION The adaptive evolution of SCML1 in primates provides a new case in understanding the evolutionary process of genes involved in primate male reproduction.
Collapse
Affiliation(s)
- Hai-hui Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, PR China.
| | | |
Collapse
|
28
|
Vasanthi D, Mishra RK. Epigenetic regulation of genes during development: A conserved theme from flies to mammals. J Genet Genomics 2008; 35:413-29. [DOI: 10.1016/s1673-8527(08)60059-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/04/2008] [Accepted: 06/05/2008] [Indexed: 01/16/2023]
|
29
|
Abstract
The papillomavirus life cycle is intimately coupled to the differentiation state of the infected epithelium. Since papillomaviruses lack most of the rate-limiting enzymes required for genome synthesis, they need to uncouple keratinocyte differentiation from cell cycle arrest and maintain or reestablish a replication-competent state within terminally differentiated keratinocytes. The human papillomavirus (HPV) E7 protein appears to be a major determinant for this activity and induces aberrant S-phase entry through the inactivation of the retinoblastoma tumor suppressor and related pocket proteins. In addition, E7 can abrogate p21 and p27. Together, this leads to the activation of E2F1 to E2F5, enhanced expression of E2F-responsive genes, and increased cdk2 activity. E2F6 is a pRB-independent, noncanonical member of the E2F transcription factor family that acts as a transcriptional repressor. E2F6 expression is activated in S phase through an E2F-dependent mechanism and thus may provide a negative-feedback mechanism that slows down S-phase progression and/or exit in response to the activation of the other E2F transcription factors. Here, we show that low- and high-risk HPV E7 proteins, as well as simian virus 40 T antigen and adenovirus E1A, can associate with and inactivate the transcriptional repression activity of E2F6, thereby subverting a critical cellular defense mechanism. This may result in the extended S-phase competence of HPV-infected cells. E2F6 is a component of polycomb group complexes, which bind to silenced chromatin and are critical for the maintenance of cell fate. We show that E7-expressing cells show decreased staining for E2F6/polycomb complexes and that this is at least in part dependent on the association with E2F6.
Collapse
|
30
|
Chopra VS, Srinivasan A, Kumar RP, Mishra K, Basquin D, Docquier M, Seum C, Pauli D, Mishra RK. Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3. Dev Biol 2008; 317:660-70. [PMID: 18367161 DOI: 10.1016/j.ydbio.2008.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 01/27/2008] [Accepted: 02/02/2008] [Indexed: 01/02/2023]
Abstract
The GAGA factor (GAF), encoded by the Trithorax like gene (Trl) is a multifunctional protein involved in gene activation, Polycomb-dependent repression, chromatin remodeling and is a component of chromatin domain boundaries. Although first isolated as transcriptional activator of the Drosophila homeotic gene Ultrabithorax (Ubx), the molecular basis of this GAF activity is unknown. Here we show that dmTAF3 (also known as BIP2 and dTAF(II)155), a component of TFIID, interacts directly with GAF. We generated mutations in dmTAF3 and show that, in Trl mutant background, they affect transcription of Ubx leading to enhancement of Ubx phenotype. These results reveal that the gene activation pathway involving GAF is through its direct interaction with dmTAF3.
Collapse
|
31
|
Mishra RK, Yamagishi T, Vasanthi D, Ohtsuka C, Kondo T. Involvement of polycomb-group genes in establishing HoxD temporal colinearity. Genesis 2007; 45:570-6. [PMID: 17868118 DOI: 10.1002/dvg.20326] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Temporal colinearity in mouse HoxD is dependent on repressive activity of sequences within the 5' end of the complex. We show that a 5-kb DNA fragment from this region represses transgenes when combined in mouse as well as in Drosophila melanogaster. Moreover, repressive activity in Drosophila depends on some members of the Polycomb-group (PcG) genes, for example, extra sex combs. We also showed direct association of these factors with the repressive fragment, both in transgenic flies and in the context of the native mouse HoxD complex. These results suggest that the global repressive region of the HoxD complex functions in two very different species and that some PcG genes are involved in establishing the early repressive state of the HoxD complex, thus contributing to temporal colinearity.
Collapse
Affiliation(s)
- Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | | | | | | |
Collapse
|
32
|
Gierman HJ, Indemans MH, Koster J, Goetze S, Seppen J, Geerts D, van Driel R, Versteeg R. Domain-wide regulation of gene expression in the human genome. Genome Res 2007; 17:1286-95. [PMID: 17693573 PMCID: PMC1950897 DOI: 10.1101/gr.6276007] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transcription factor complexes bind to regulatory sequences of genes, providing a system of individual expression regulation. Targets of distinct transcription factors usually map throughout the genome, without clustering. Nevertheless, highly and weakly expressed genes do cluster in separate chromosomal domains with an average size of 80-90 genes. We therefore asked whether, besides transcription factors, an additional level of gene expression regulation exists that acts on chromosomal domains. Here we show that identical green fluorescent protein (GFP) reporter constructs integrated at 90 different chromosomal positions obtain expression levels that correspond to the activity of the domains of integration. These domains are up to 80 genes long and can exert an eightfold effect on the expression levels of integrated genes. 3D-FISH shows that active domains of integration have a more open chromatin structure than integration domains with weak activity. These results reveal a novel domain-wide regulatory mechanism that, together with transcription factors, exerts a dual control over gene transcription.
Collapse
Affiliation(s)
- Hinco J. Gierman
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Mireille H.G. Indemans
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Jan Koster
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Sandra Goetze
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Jurgen Seppen
- AMC Liver Centre, 1105 BK Amsterdam, The Netherlands
| | - Dirk Geerts
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Roel van Driel
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
| | - Rogier Versteeg
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
- Corresponding author.E-mail ; fax 31-20-6918626
| |
Collapse
|
33
|
Gebelein B, Mann RS. Compartmental modulation of abdominal Hox expression by engrailed and sloppy-paired patterns the fly ectoderm. Dev Biol 2007; 308:593-605. [PMID: 17573068 PMCID: PMC2856935 DOI: 10.1016/j.ydbio.2007.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 04/23/2007] [Accepted: 05/17/2007] [Indexed: 11/19/2022]
Abstract
In Drosophila, segmentation genes partition the early embryo into reiterative segments along the anterior-posterior axis, while Hox genes assign segments their identities. Each segment is also subdivided into distinct anterior (A) and posterior (P) compartments based on the expression of the engrailed (en) segmentation gene. Differences in Hox expression often correlate with compartmental boundaries, but the genetic basis for these differences is not well understood. In this study, we extend previous results to describe a genetic circuit that controls the differential expression of two Hox genes, Ultrabithorax (Ubx) and abdominal-A (abd-A), within the A and P compartments of the abdominal ectoderm. Consistent with earlier findings, we show that en is essential for high Abd-A levels and low Ubx levels in the P compartment, whereas sloppy-paired (slp) is required for high Ubx levels in the A compartment. Overall, these results demonstrate that the compartmental expression of Ubx and abd-A is established through a repressive regulatory network between en, slp, Ubx and abd-A. We also show that abd-A expression in the P compartment is important for the formation of abdominal-specific cell types, suggesting that en and slp modulation of Hox expression within the A and P compartments is essential for embryonic patterning.
Collapse
Affiliation(s)
- Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA.
| | | |
Collapse
|
34
|
Bello B, Holbro N, Reichert H. Polycomb group genes are required for neural stem cell survival in postembryonic neurogenesis ofDrosophila. Development 2007; 134:1091-9. [PMID: 17287254 DOI: 10.1242/dev.02793] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genes of the Polycomb group (PcG) are part of a cellular memory system that maintains appropriate inactive states of Hox gene expression in Drosophila. Here, we investigate the role of PcG genes in postembryonic development of the Drosophila CNS. We use mosaic-based MARCM techniques to analyze the role of these genes in the persistent larval neuroblasts and progeny of the central brain and thoracic ganglia. We find that proliferation in postembryonic neuroblast clones is dramatically reduced in the absence of Polycomb, Sex combs extra, Sex combs on midleg, Enhancer of zeste or Suppressor of zeste 12. The proliferation defects in these PcG mutants are due to the loss of neuroblasts by apoptosis in the mutant clones. Mutation of PcG genes in postembryonic lineages results in the ectopic expression of posterior Hox genes, and experimentally induced misexpression of posterior Hox genes, which in the wild type causes neuroblast death, mimics the PcG loss-of-function phenotype. Significantly, full restoration of wild-type-like properties in the PcG mutant lineages is achieved by blocking apoptosis in the neuroblast clones. These findings indicate that loss of PcG genes leads to aberrant derepression of posterior Hox gene expression in postembryonic neuroblasts, which causes neuroblast death and termination of proliferation in the mutant clones. Our findings demonstrate that PcG genes are essential for normal neuroblast survival in the postembryonic CNS of Drosophila. Moreover, together with data on mammalian PcG genes, they imply that repression of aberrant reactivation of Hox genes may be a general and evolutionarily conserved role for PcG genes in CNS development.
Collapse
Affiliation(s)
- Bruno Bello
- Biozentrum, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland.
| | | | | |
Collapse
|
35
|
Andreu-Vieyra C, Matzuk MM. Epigenetic modifications by Trithorax group proteins during early embryogenesis: do members of Trx-G function as maternal effect genes? Reprod Biomed Online 2007; 14:201-7. [PMID: 17298723 DOI: 10.1016/s1472-6483(10)60788-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Maternal effect genes encode transcripts that are expressed during oogenesis. These gene products are stored in the oocyte and become functional during resumption of meiosis and zygote genome activation, and in embryonic stem cells. To date, a few maternal effect genes have been identified in mammals. Epigenetic modifications have been shown to be important during early embryonic development and involve DNA methylation and post-translational modification of core histones. During development, two families of proteins have been shown to be involved in epigenetic changes: Trithorax group (Trx-G) and Polycomb group (Pc-G) proteins. Trx-G proteins function as transcriptional activators and have been shown to accumulate in the oocyte. Deletion of Trx-G members using conventional knockout technology results in embryonic lethality in the majority of the cases analysed to date. Recent studies using conditional knockout mice have revealed that at least one family member is necessary for zygote genome activation. We propose that other Trx-G members may also regulate embryonic genome activation and that the use of oocyte-specific deletor mouse lines will help clarify their roles in this process.
Collapse
Affiliation(s)
- Claudia Andreu-Vieyra
- Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | | |
Collapse
|
36
|
Novel gene expression patterns along the proximo-distal axis of the mouse embryo before gastrulation. BMC DEVELOPMENTAL BIOLOGY 2007; 7:8. [PMID: 17302988 PMCID: PMC1821012 DOI: 10.1186/1471-213x-7-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 02/15/2007] [Indexed: 01/29/2023]
Abstract
BACKGROUND To date, the earliest stage at which the orientation of the anterior-posterior axis in the mouse embryo is distinguishable by asymmetric gene expression is shortly after E5.5. At E5.5, prospective anterior markers are expressed at the distal tip of the embryo, whereas prospective posterior markers are expressed more proximally, close to the boundary with the extraembryonic region. RESULTS To contribute to elucidating the mechanisms underlying the events involved in early patterning of the mouse embryo, we have carried out a microarray screen to identify novel genes that are differentially expressed between the distal and proximal parts of the E5.5 embryo. Secondary screening of resulting candidates by in situ hybridisation at E5.5 and E6.5 revealed novel expression patterns for known and previously uncharacterised genes, including Peg10, Ctsz1, Cubilin, Jarid1b, Ndrg1, Sfmbt2, Gjb5, Talia and Plet1. The previously undescribed gene Talia and recently identified Plet1 are expressed specifically in the distal-most part of the extraembryonic ectoderm, adjacent to the epiblast, and are therefore potential candidates for regulating early patterning events. Talia and the previously described gene XE7 define a gene family highly conserved among metazoans and with a predicted protein structure suggestive of a post-transcriptional regulative function, whilst Plet1 appears to be mammal-specific and of unknown function. CONCLUSION Our approach has allowed us to compare expression between dissected parts of the egg cylinder and has identified multiple genes with novel expression patterns at this developmental stage. These genes are potential candidates for regulating tissue interactions following implantation.
Collapse
|
37
|
Kobrossy L, Rastegar M, Featherstone M. Interplay between chromatin and trans-acting factors regulating the Hoxd4 promoter during neural differentiation. J Biol Chem 2006; 281:25926-39. [PMID: 16757478 DOI: 10.1074/jbc.m602555200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Correct patterning of the antero-posterior axis of the embryonic trunk is dependent on spatiotemporally restricted Hox gene expression. In this study, we identified components of the Hoxd4 P1 promoter directing expression in neurally differentiating retinoic acid-treated P19 cells. We mapped three nucleosomes that are subsequently remodeled into an open chromatin state upon retinoic acid-induced Hoxd4 transcription. These nucleosomes spanned the Hoxd4 transcriptional start site in addition to a GC-rich positive regulatory element located 3' to the initiation site. We further identified two major cis-acting regulatory elements. An autoregulatory element was shown to recruit HOXD4 and its cofactor PBX1 and to positively regulate Hoxd4 expression in differentiating P19 cells. Conversely, the Polycomb group (PcG) protein Ying-Yang 1 (YY1) binds to an internucleosomal linker and represses Hoxd4 transcription before and during transcriptional activation. Sequential chromatin immunoprecipitation studies revealed that the PcG protein MEL18 was co-recruited with YY1 only in undifferentiated P19 cells, suggesting a role for MEL18 in silencing Hoxd4 transcription in undifferentiated P19 cells. This study links for the first time local chromatin remodeling events that take place during transcriptional activation with the dynamics of transcription factor association and DNA accessibility at a Hox regulatory region.
Collapse
Affiliation(s)
- Laila Kobrossy
- McGill Cancer Centre, McGill University, Montréal, Québec H3G 1Y6 Canada
| | | | | |
Collapse
|
38
|
Okada A, Fujiwara M. Molecular approaches to developmental malformations using analogous forms of valproic acid. Congenit Anom (Kyoto) 2006; 46:68-75. [PMID: 16732764 DOI: 10.1111/j.1741-4520.2006.00105.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The teratogenic potential of valproic acid has been well established both in experimental models and in human clinical studies. Evidence from many previous studies has shown that VPA is an appropriate drug model for studying chemical structure-teratogenicity relationships. Using molecular techniques of DNA microarray (GeneChip system) or quantitative real-time polymerase chain reaction with low teratogenic VPA analogs as comparative control drugs, we attempted to identify the genes involved with the molecular mechanisms of VPA teratogenicity in the neural tube and the axial skeleton of the mouse embryo. The recent development of DNA microarray enables a genome-wide approach to the identification of genes correlated with the teratogenicity of chemicals (teratogenomics). The VPA-induced changes in gene expression seen during mouse embryogenesis provides information for understanding how VPA disrupts normal embryonic development, and also provides leads for the development of safer medicines.
Collapse
Affiliation(s)
- Akinobu Okada
- Drug Safety Research Laboratories, Astellas Pharma, Yodogawa-ku, Osaka, Japan.
| | | |
Collapse
|
39
|
Wang J, Lee CHJ, Lin S, Lee T. Steroid hormone-dependent transformation ofpolyhomeoticmutant neurons in theDrosophilabrain. Development 2006; 133:1231-40. [PMID: 16495309 DOI: 10.1242/dev.02299] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polyhomeotic (Ph), which forms complexes with other Polycomb-group (PcG)proteins, is widely required for maintenance of cell identity by ensuring differential gene expression patterns in distinct types of cells. Genetic mosaic screens in adult fly brains allow for recovery of a mutation that simultaneously disrupts the tandemly duplicated Drosophila phtranscriptional units. Distinct clones of neurons normally acquire different characteristic projection patterns and can be differentially labeled using various subtype-specific drivers in mosaic brains. Such neuronal diversity is lost without Ph. In response to ecdysone, ph mutant neurons are transformed into cells with unidentifiable projection patterns and indistinguishable gene expression profiles during early metamorphosis. Some subtype-specific neuronal drivers become constitutively activated, while others are constantly suppressed. By contrast, loss of other PcG proteins,including Pc and E(z), causes different neuronal developmental defects; and,consistent with these phenomena, distinct Hox genes are differentially misexpressed in different PcG mutant clones. Taken together, Drosophila Ph is essential for governing neuronal diversity,especially during steroid hormone signaling.
Collapse
Affiliation(s)
- Jian Wang
- Department of Entomology, University of Maryland, College Park, 20742, USA
| | | | | | | |
Collapse
|
40
|
Bloor AJC, Kotsopoulou E, Hayward P, Champion BR, Green AR. RFP represses transcriptional activation by bHLH transcription factors. Oncogene 2005; 24:6729-36. [PMID: 16007160 DOI: 10.1038/sj.onc.1208828] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors play a pivotal role in the regulation of tumorigenesis, and also in a wide range of other developmental processes in diverse species from yeast to humans. Here we demonstrate for the first time that Ret finger protein (RFP), a member of the TRIM family of proteins initially identified as a recombined transforming gene from a human lymphoma, is a novel interaction partner for four different bHLH proteins (SCL, E47, MyoD and mASH-1), but does not interact with GATA-1 or PU.1. Interaction with SCL required the B-box and first coiled-coil region of RFP together with the bHLH domain of SCL. RFP was able to repress transcriptional activation by E47, MyoD and mASH-1, but not by members of several other transcription factor families. Transcriptional repression by RFP was trichostatin A sensitive and did not involve an Id-like mechanism or ubiquitination with subsequent degradation of bHLH proteins. Instead, our results suggest that bHLH transcription factors are regulated by a previously undescribed interaction with RFP, which functions to recruit HDAC and/or Polycomb proteins and thus repress target genes of bHLH proteins. These results reveal an unexpected link between the bHLH and TRIM protein families.
Collapse
Affiliation(s)
- Adrian J C Bloor
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Hills Road, Cambridge CB2 2XY, UK
| | | | | | | | | |
Collapse
|
41
|
Neves N, Delgado M, Silva M, Caperta A, Morais-Cecílio L, Viegas W. Ribosomal DNA heterochromatin in plants. Cytogenet Genome Res 2005; 109:104-11. [PMID: 15753565 DOI: 10.1159/000082388] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 02/19/2004] [Indexed: 11/19/2022] Open
Abstract
The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.
Collapse
Affiliation(s)
- N Neves
- Secção de Genética, Centro de Botânica Aplicada à Agricultura, Instituto Superior de Agronomia, Lisboa, Portugal
| | | | | | | | | | | |
Collapse
|
42
|
Akin ZN, Nazarali AJ. Hox genes and their candidate downstream targets in the developing central nervous system. Cell Mol Neurobiol 2005; 25:697-741. [PMID: 16075387 DOI: 10.1007/s10571-005-3971-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Accepted: 04/14/2004] [Indexed: 12/14/2022]
Abstract
1. Homeobox (Hox) genes were originally discovered in the fruit fly Drosophila, where they function through a conserved homeodomain as transcriptional regulators to control embryonic morphogenesis. Since then over 1000 homeodomain proteins have been identified in several species. In vertebrates, 39 Hox genes have been identified as homologs of the original Drosophila complex, and like their Drosophila counterparts they are organized within chromosomal clusters. Vertebrate Hox genes have also been shown to play a critical role in embryonic development as transcriptional regulators. 2. Both the Drosophila and vertebrate Hox genes have been shown to interact with various cofactors, such as the TALE homeodomain proteins, in recognition of consensus sequences within regulatory elements of their target genes. These protein-protein interactions are believed to contribute to enhancing the specificity of target gene recognition in a cell-type or tissue- dependent manner. The regulatory activity of a particular Hox protein on a specific regulatory element is highly variable and dependent on its interacting partners within the transcriptional complex. 3. In vertebrates, Hox genes display spatially restricted patterns of expression within the developing CNS, both along the anterioposterior and dorsoventral axis of the embryo. Their restricted gene expression is suggestive of a regulatory role in patterning of the CNS, as well as in cell specification. Determining the precise function of individual Hox genes in CNS morphogenesis through classical mutational analyses is complicated due to functional redundancy between Hox genes. 4. Understanding the precise mechanisms through which Hox genes mediate embryonic morphogenesis requires the identification of their downstream target genes. Although Hox genes have been implicated in the regulation of several pathways, few target genes have been shown to be under their direct regulatory control. Development of methodologies used for the isolation of target genes and for the analysis of putative targets will be beneficial in establishing the genetic pathways controlled by Hox factors. 5. Within the developing CNS various cell adhesion molecules and signaling molecules have been identified as candidate downstream target genes of Hox proteins. These targets play a role in processes such as cell migration and differentiation, and are implicated in contributing to neuronal processes such as plasticity and/or specification. Hence, Hox genes not only play a role in patterning of the CNS during early development, but may also contribute to cell specification and identity.
Collapse
Affiliation(s)
- Z N Akin
- Laboratory of Molecular Biology, College of Pharmacy and Nutrition, University of Saskatchewan, 116 Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada
| | | |
Collapse
|
43
|
Armstrong JA, Sperling AS, Deuring R, Manning L, Moseley SL, Papoulas O, Piatek CI, Doe CQ, Tamkun JW. Genetic screens for enhancers of brahma reveal functional interactions between the BRM chromatin-remodeling complex and the delta-notch signal transduction pathway in Drosophila. Genetics 2005; 170:1761-74. [PMID: 15944353 PMCID: PMC1449748 DOI: 10.1534/genetics.105.041327] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Drosophila trithorax group gene brahma (brm) encodes the ATPase subunit of a 2-MDa chromatin-remodeling complex. brm was identified in a screen for transcriptional activators of homeotic genes and subsequently shown to play a global role in transcription by RNA polymerase II. To gain insight into the targeting, function, and regulation of the BRM complex, we screened for mutations that genetically interact with a dominant-negative allele of brm (brm(K804R)). We first screened for dominant mutations that are lethal in combination with a brm(K804R) transgene under control of the brm promoter. In a distinct but related screen, we identified dominant mutations that modify eye defects resulting from expression of brm(K804R) in the eye-antennal imaginal disc. Mutations in three classes of genes were identified in our screens: genes encoding subunits of the BRM complex (brm, moira, and osa), other proteins directly involved in transcription (zerknullt and RpII140), and signaling molecules (Delta and vein). Expression of brm(K804R) in the adult sense organ precursor lineage causes phenotypes similar to those resulting from impaired Delta-Notch signaling. Our results suggest that signaling pathways may regulate the transcription of target genes by regulating the activity of the BRM complex.
Collapse
Affiliation(s)
- Jennifer A Armstrong
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
The E2 factor (E2F) family of transcription factors are downstream targets of the retinoblastoma protein. E2F factors have been known for several years to be important regulators of S-phase entry. Recent studies have improved our understanding of the molecular mechanisms of action used by this transcriptional network. In addition, they have given us an appreciation of the fact that E2F has functions that reach beyond G1/S control and impact cell proliferation in several different ways. The discovery of new family members with unusual properties, the unexpected phenotypes of mutant animals, a diverse collection of biological activities, a large number of new putative target genes and the new modes of transcriptional regulation have all contributed to an increasingly complex view of E2F function. In this review, we will discuss these recent developments and describe how they are beginning to shape a new and revised picture of the E2F transcriptional program.
Collapse
|
45
|
Okada A, Aoki Y, Kushima K, Kurihara H, Bialer M, Fujiwara M. Polycomb homologs are involved in teratogenicity of valproic acid in mice. ACTA ACUST UNITED AC 2005; 70:870-9. [PMID: 15523661 DOI: 10.1002/bdra.20085] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Valproic acid (VPA) is widely used to treat epilepsy and bipolar disorder and is also a potent teratogen, but its teratogenic mechanisms are unknown. We have attempted to describe a fundamental role of the Polycomb group (Pc-G) in VPA-induced transformations of the axial skeleton. METHODS Pregnant NMRI mice were given a single subcutaneous injection of vehicle or VPA (800 mg/kg) on gestation day (GD) 8. The expression of genes encoding Polycomb and trithorax groups was measured by quantitative real-time RT-PCR using total RNA isolated from the embryos exposed to vehicle or VPA for 1, 3, and 6 hr. In addition, the use of two less teratogenic antiepileptic chemicals valpromide (VPD) and valnoctamide (VCD) provide reliable evidence to support the relationship between VPA teratogenicity and the Polycomb group. RESULTS At a teratogenic level, VPA inhibits the expression of the Polycomb group genes, including Eed, Ezh2, Zfp144, Bmi1, Cbx2, Rnf2, and YY1 in the mouse embryos. In contrast, neither VPD nor VCD have significant effects on the expression of those genes affected by VPA. The trithorax group (trx-G) gene MLL, which is known to be required to maintain homeobox gene expression such as the Polycomb gene, is not affected by a teratogenic dose of VPA. CONCLUSIONS We propose that, during embryonic development, VPA may affect the gene silencing pathway mediated by the Polycomb group complex. The epigenetic mechanism of VPA teratogenicity on anteroposterior patterning is suspected.
Collapse
Affiliation(s)
- Akinobu Okada
- Safety Research Laboratories, Yamanouchi Pharmaceutical Co., Ltd., Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
46
|
Isono K, Mizutani-Koseki Y, Komori T, Schmidt-Zachmann MS, Koseki H. Mammalian polycomb-mediated repression of Hox genes requires the essential spliceosomal protein Sf3b1. Genes Dev 2005; 19:536-41. [PMID: 15741318 PMCID: PMC551574 DOI: 10.1101/gad.1284605] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polycomb group (PcG) proteins are responsible for the stable repression of homeotic (Hox) genes by forming multimeric protein complexes. We show (1) physical interaction between components of the U2 small nuclear ribonucleoprotein particle (U2 snRNP), including Sf3b1 and PcG proteins Zfp144 and Rnf2; and (2) that Sf3b1 heterozygous mice exhibit skeletal transformations concomitant with ectopic Hox expressions. These alterations are enhanced by Zfp144 mutation but repressed by Mll mutation (a trithorax-group gene). Importantly, the levels of Sf3b1 in PcG complexes were decreased in Sf3b1-heterozygous embryos. These findings suggest that Sf3b1-PcG protein interaction is essential for true PcG-mediated repression of Hox genes.
Collapse
Affiliation(s)
- Kyoichi Isono
- Developmental Genetics Group, RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama 230-0045, Japan
| | | | | | | | | |
Collapse
|
47
|
Srinivasan S, Armstrong JA, Deuring R, Dahlsveen IK, McNeill H, Tamkun JW. The Drosophila trithorax group protein Kismet facilitates an early step in transcriptional elongation by RNA Polymerase II. Development 2005; 132:1623-35. [PMID: 15728673 DOI: 10.1242/dev.01713] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Drosophila trithorax group gene kismet (kis) was identified in a screen for extragenic suppressors of Polycomb (Pc) and subsequently shown to play important roles in both segmentation and the determination of body segment identities. One of the two major proteins encoded by kis (KIS-L) is related to members of the SWI2/SNF2 and CHD families of ATP-dependent chromatin-remodeling factors. To clarify the role of KIS-L in gene expression, we examined its distribution on larval salivary gland polytene chromosomes. KIS-L is associated with virtually all sites of transcriptionally active chromatin in a pattern that largely overlaps that of RNA Polymerase II (Pol II). The levels of elongating Pol II and the elongation factors SPT6 and CHD1 are dramatically reduced on polytene chromosomes from kis mutant larvae. By contrast, the loss of KIS-L function does not affect the binding of PC to chromatin or the recruitment of Pol II to promoters. These data suggest that KIS-L facilitates an early step in transcriptional elongation by Pol II.
Collapse
Affiliation(s)
- Shrividhya Srinivasan
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | | | | | | | | |
Collapse
|
48
|
Sung S, Amasino RM. Remembering winter: toward a molecular understanding of vernalization. ANNUAL REVIEW OF PLANT BIOLOGY 2005; 56:491-508. [PMID: 15862105 DOI: 10.1146/annurev.arplant.56.032604.144307] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Exposure to the prolonged cold of winter is an important environmental cue that favors flowering in the spring in many types of plants. The process by which exposure to cold promotes flowering is known as vernalization. In Arabidopsis and certain cereals, the block to flowering in plants that have not been vernalized is due to the expression of flowering repressors. The promotion of flowering is due to the cold-mediated suppression of these repressors. Recent work has demonstrated that covalent modifications of histones in the chromatin of target loci are part of the molecular mechanism by which certain repressors are silenced during vernalization.
Collapse
Affiliation(s)
- Sibum Sung
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
| | | |
Collapse
|
49
|
Rahman M, Miyamoto H, Chang C. Androgen receptor coregulators in prostate cancer: mechanisms and clinical implications. Clin Cancer Res 2004; 10:2208-19. [PMID: 15073094 DOI: 10.1158/1078-0432.ccr-0746-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Mujib Rahman
- George Whipple Laboratory for Cancer Research, Department of Biochemistry, and the Cancer Center, University of Rochester Medical Center, Rochester, New York 14642, USA
| | | | | |
Collapse
|
50
|
Abstract
HOX genes are a family of regulatory molecules that encode conserved transcription factors controlling aspects of morphogenesis and cell differentiation during normal embryonic development. All metazoans possess a common genetic system for embryonic patterning, and this system is also used in the reproductive tract. Hox genes are also expressed in the adult uterus. Hox genes are essential both for the development of mullerian tract in the embryonic period and adult function. Sex steroids regulate Hox gene expression during embryonic and endometrial development in the menstrual cycle. EMX2 and beta(3)-integrin acting downstream of Hoxa10 gene are likely involved in both these developmental processes. This article reviews the role and molecular regulation of Hox genes in reproductive tract development.
Collapse
Affiliation(s)
- Hongling DU
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology, Yale University School of Medicine, 333 Cedar Street, P.O. Box 2008063, New Haven, CT 06520, USA
| | | |
Collapse
|