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Li T, Li W, Li F, Lin J, Zhang Y, Zhang Q, Sun Y, Chen X, Zhou S, Li Q. Effects of two chd2-knockout strains on the morphology and behavior in zebrafish. Dev Genes Evol 2024:10.1007/s00427-024-00721-5. [PMID: 39190085 DOI: 10.1007/s00427-024-00721-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/19/2024] [Indexed: 08/28/2024]
Abstract
The chromodomain helicase DNA binding domain 2 (CHD2) gene is an ATPase and a member of the SNF2-like family of helicase-related enzymes. CHD2 plays critical roles in human brain development and function, and homozygous mutation of Chd2 in mice results in perinatal lethality. To further elucidate the effects of chd2, we used CRISPR/Cas9 to create two chd2-knockout strains (fdu901, 11,979-11982delGGGT, and fdu902, 27350delG) in zebrafish. We found that the deformity and mortality rates of fdu901 and fdu902 were higher than those of the wild type. Developmental delay was more obvious and embryo mortality was higher in fdu901 than in fdu902. However, the embryo deformity rate in fdu902 was higher than that in fdu901. Although there were no significant differences in behavior between the two knockout zebrafish and wild-type zebrafish at 7 days post fertilization (dpf), fdu901 and fdu902 zebrafish showed different alterations. The excitability of fdu902 was higher than that of fdu901. Overall, our data demonstrate that two homozygous chd2 knockout mutations were survivable and could be stably inherited and that fdu901 and fdu902 zebrafish differed in behavior and morphology. These two models might be good tools for understanding the functions of the different domains of chd2.
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Affiliation(s)
- Tingting Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Wenhui Li
- Department of Neurology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Fei Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Jia Lin
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yinglan Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Qi Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yanhe Sun
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Xudong Chen
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Shuizhen Zhou
- Department of Neurology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
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You C, Xu L, Zhu L, Qiu S, Xu N, Wang Y, Yang L. Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy. Seizure 2024; 121:38-44. [PMID: 39068850 DOI: 10.1016/j.seizure.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
INTRODUCTION Increasing evidence reveals critical roles for CHD2 in children with developmental and epileptic encephalopathy. OBJECTIVES The aim was to present clinical analysis results of five cases with CHD2 mutations and 157 reported cases with non-copy number variations (non-CNV) of CHD2. METHODS This study recruited pediatric epilepsy patients with CHD2 mutations and clinical data from November 2016 to October 2023 in the Linyi People's Hospital, China. Whole-exome and gene panel sequencing were employed to find mutations. The HGMD and PubMed databases were examined for documented cases that had CHD2 mutations. RESULTS This study reports five cases with CHD2 mutations: c.3543T > A, c.1850A > G, c.2536C > T, c.4233_4236del, c.3782G > C. Three novel mutations (c.3543T > A, c.1850A > G, c.2536C > T) have never been reported. c.4233_4236del has been reported in three cases, indicating that this locus may be a mutation hotspot. c.3782G > C has been reported in one case. All five patients had seizures before the age of four. Three patients had varying degrees of developmental delay, and four patients had varying degrees of intellectual disability. All of them had controlled seizures after Valproic acid (VPA) monotherapy or VPA in combination with other medications. Furthermore, we reviewed 157 reported cases having non-CNV mutations of CHD2. Most mutations of these cases were de novo. Epilepsy, developmental delay, and intellectual disability were the typical clinical phenotypes. We also found a significant clustering of the mutations near the C-terminus of the CHD2 protein (P < 0.001). CONCLUSION This study reports new CHD2 genotypes and analyzes reported CHD2 mutation cases. Given its significance in epileptic encephalopathies, research on the CHD2 gene may provide new insights into epileptogenesis.
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Affiliation(s)
- Cuiping You
- Central Laboratory, Linyi People's Hospital, Linyi, Shandong, China
| | - Liyun Xu
- Shandong Medical College, Linyi, China
| | - Liping Zhu
- Department of Pediatrics, Linyi People's Hospital, Linyi, China
| | - Shiyan Qiu
- Department of Pediatrics, Linyi People's Hospital, Linyi, China
| | - Na Xu
- Department of Pediatrics, Linyi People's Hospital, Linyi, China
| | - Yanyan Wang
- Department of Laboratory Medicine, Linyi People's Hospital, Linyi, China; Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China; Shandong Provincial Medicine and Health Key Laboratory for Precise Diagnosis of Hereditary Rare Diseases, Linyi People's Hospital, Linyi, China
| | - Li Yang
- Department of Pediatrics, Linyi People's Hospital, Linyi, China.
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Gao Y, Wu Q, Wang G, Zhang S, Ma W, Shi X, Liu H, Wu L, Tian X, Li X, Ma X. Histomorphic analysis and expression of mRNA and miRNA in embryonic gonadal differentiation in Chinese soft-shelled turtle (Pelodiscus sinensis). Gene 2024; 893:147913. [PMID: 37866663 DOI: 10.1016/j.gene.2023.147913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/07/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
The Chinese soft-shelled turtle (Pelodiscus sinensis) is extensively cultured in Asia for its nutritional and medical value. Gonadal differentiation is fantastic in turtles, whereas morphologic, mRNA, and miRNA expressions were insufficient in the turtle. In this study, ovaries and testes histomorphology analysis of 14-23 stage embryos were performed, and mRNA and miRNA expression profiles were analyzed. Histomorphology analysis revealed that gonads were undifferentiated at embryonic stage 14. Ovarian morphological differentiation became evident from stage 15, which was characterized by the development of the cortical region and degeneration of the medullary region. Concurrently, testicular morphological differentiation was apparent from stage 15, marked by the development of the medullary region and degeneration of the cortical region. qRT-PCR results showed that Cyp19a1 and Foxl2 exhibited female-specific expression at stage 15 and the expression increased throughout most of the embryonic development. Dmrt1, Amh, and Sox9 displayed male-specific expression at stage 15 and tended to increase substantially at later developmental stages. The expression of miR-8356 and miR-3299 in ZZ gonads were significantly higher than that in ZW gonads at stage 15, 17 and 19, and they had the highest expression at stage 15. While the expression of miR-8085 and miR-7982 had the highest expression at stage 19. Furthermore, chromatin remodeler genes showed differential expression in female and male P. sinensis gonads. These results of master sex-differentiation genes and morphological characteristics would provide a reference for the research of sex differentiation and sex reversal in turtles. Additionally, the expression of chromatin remodeler genes indicated they might be involved in gonadal differentiation of P. sinensis.
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Affiliation(s)
- Yijie Gao
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Qisheng Wu
- Fisheries Research Institute of Fujian, Xiamen 361000, China.
| | - Guiyu Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Shufang Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Wenge Ma
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xi Shi
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Huifen Liu
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Limin Wu
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xue Tian
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xiao Ma
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
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Kohzaki M. Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies. Front Mol Biosci 2022; 9:934042. [PMID: 36032672 PMCID: PMC9403131 DOI: 10.3389/fmolb.2022.934042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/01/2022] Open
Abstract
Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.
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Niu X, Huang Y, Lu H, Li S, Huang S, Ran X, Wang J. CircRNAs in Xiang pig ovaries among diestrus and estrus stages. Porcine Health Manag 2022; 8:29. [PMID: 35739583 PMCID: PMC9219244 DOI: 10.1186/s40813-022-00270-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fecundity of sows is a trait of major economic in pig industry. The molecular regulation of estrus cycles can affect the fecundity of female animals. Compared with the other pig breeds, Xiang pig exhibits the special estrus behaviors. CircRNAs are thought to involve in regulation of multiple biological processes. However, the potential roles of circRNAs in ovary regulation on Xiang pig estrus are largely unknown. RESULTS 8,937 circRNAs were identified from eight libraries constructed from the ovarian samples of Xiang pig at estrus and diestrus stages by RNA sequencing method. Of which, 1,995 were high confidence circRNAs detected at least two junction reads in each ovary sample and seven circRNAs were validated by RT-PCR method. Furthermore, we identified 290 upregulated and 15 downregulated circRNAs in estrus ovaries. These differentially expressed circRNAs (DECs) derived from 273 host genes. And 207 miRNAs were identified to be targets sponged by 156 DECs with 432 binding sites, containing more than one miRNA binding site in each circRNA. Function enrichment analysis revealed that the host genes and the targets of miRNAs sponged by DECs were enriched in several reproduction-related signaling pathways, such as ovarian steroidogenesis, oocyte maturation, circadian rhythm, estrogen signaling pathway, GnRH signaling pathway, circadian entrainment, and oocyte meiosis. The circRNA-miRNA-mRNA networks revealed that 153 miRNAs interacting with 122 DECs and 86 miRNAs interacting with 84 DECs were involved in ovarian functions and ovarian circadian entrainment and circadian rhythm respectively. The DEC-miRNA-DEG (differentially expressed gene, DEG) networks associated with reproduction-related signaling pathways contained 22 DECs,18 miRNAs and 7 DEGs. 22 DECs were recognized as hub circRNAs during the estrus phase of Xiang pigs. CONCLUSIONS The circRNAs that function as miRNA sponges could play a key role in post-transcriptional regulation of gene expression during Xiang pig's estrus cycle.
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Affiliation(s)
- Xi Niu
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China
| | - Yali Huang
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China
| | - Huan Lu
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China
| | - Sheng Li
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China
| | - Shihui Huang
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China.
| | - Jiafu Wang
- Institute of Agro-Bioengineering / Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550055, China.
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Trujillo JT, Long J, Aboelnour E, Ogas J, Wisecaver JH. CHD chromatin remodeling protein diversification yields novel clades and domains absent in classic model organisms. Genome Biol Evol 2022; 14:6582301. [PMID: 35524943 PMCID: PMC9113485 DOI: 10.1093/gbe/evac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Chromatin remodelers play a fundamental role in the assembly of chromatin, regulation of transcription, and DNA repair. Biochemical and functional characterizations of the CHD family of chromatin remodelers from a variety of model organisms have shown that these remodelers participate in a wide range of activities. However, because the evolutionary history of CHD homologs is unclear, it is difficult to predict which of these activities are broadly conserved and which have evolved more recently in individual eukaryotic lineages. Here, we performed a comprehensive phylogenetic analysis of 8,042 CHD homologs from 1,894 species to create a model for the evolution of this family across eukaryotes with a particular focus on the timing of duplications that gave rise to the diverse copies observed in plants, animals, and fungi. Our analysis confirms that the three major subfamilies of CHD remodelers originated in the eukaryotic last common ancestor, and subsequent losses occurred independently in different lineages. Improved taxon sampling identified several subfamilies of CHD remodelers in plants that were absent or highly divergent in the model plant Arabidopsis thaliana. Whereas the timing of CHD subfamily expansions in vertebrates corresponds to whole genome duplication events, the mechanisms underlying CHD diversification in land plants appear more complicated. Analysis of protein domains reveals that CHD remodeler diversification has been accompanied by distinct transitions in domain architecture, contributing to the functional differences observed between these remodelers. This study demonstrates the importance of proper taxon sampling when studying ancient evolutionary events to prevent misinterpretation of subsequent lineage-specific changes and provides an evolutionary framework for functional and comparative analysis of this critical chromatin remodeler family across eukaryotes.
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Affiliation(s)
- Joshua T Trujillo
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jiaxin Long
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Erin Aboelnour
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Joseph Ogas
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Luo X, Sun X, Wang Y, Lin L, Yuan F, Wang S, Zhang W, Ji X, Liu M, Wu S, Lan X, Zhang J, Yan J, Zeng F, Chen Y. Clinical Study of 8 Cases of CHD2 Gene Mutation–Related Neurological Diseases and Their Mechanisms. Front Cell Dev Biol 2022; 10:853127. [PMID: 35386198 PMCID: PMC8977407 DOI: 10.3389/fcell.2022.853127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 01/15/2023] Open
Abstract
Background: The chromodomain helicase DNA-binding protein 2 (CHD2) gene, is an ATPase and part of the CHD family of chromatin remodelers. Mutations in the CHD2 gene are inherited in an autosomal-dominant manner and can lead to intellectual disability, epilepsy, and autism. We investigated the clinical characteristics of CHD2-related conditions and their possible pathogenesis. Methods: We collected and analysed the clinical data of patients that were identified as having CHD2 mutations. Genetic testing was performed using targeted sequencing or whole-exome sequencing. We analysed the expression of CHD2 and repressor element 1-silencing transcription factor (REST) in blood samples using quantitative PCR and the conservation of the mutations. The CHD2 mutations we identified were compared with the known mutations reported in the CHD2-related literature. Results: Eight patients with CHD2 gene mutations were analysed. Six mutations were identified; four were unreported previously (c.670C>T; c.4012A>C; c.2416dup; c.1727–1728insAT), and two were known mutations: c.5035C>T (two cases) and c.4173dup (two cases). Among these mutations, seven were de novo mutations, and one could not be determined because the parents refused genetic testing. The clinical manifestations included mild or severe intellectual disability, epilepsy, and behavioural abnormalities. Quantitative PCR showed that the CHD2 gene expression levels among the patients, parents, and the controls were not significantly different. The levels of REST gene expression in the patients were significantly higher than those of the controls; thus, mutation of the CHD2 gene led to an increase in the expression level of the REST gene. The mutations reported were all located in conserved positions in different species. Among the various medications administered for treatment, valproate showed the best results for the treatment of epilepsy caused by CHD2 gene mutation. Conclusion: Mutation in CHD2 did not lead to a significant decrease in its expression level, indicating that the clinical phenotype was unrelated to its expression level, and the mutant protein may retain some function. Most of the mutations relatively stable. In addition, the clinical manifestations from the same mutation in the CHD2 gene were different among the known cases; this may be related to the regulation of REST or other regulatory factors.
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Affiliation(s)
- Xiaona Luo
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Xiaoang Sun
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Yilin Wang
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Longlong Lin
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Fang Yuan
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Simei Wang
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Wenjing Zhang
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Xiaobing Ji
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Meiyan Liu
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Shengnan Wu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoping Lan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhang
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Jingbin Yan
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fanyi Zeng
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yucai Chen
- Department of Neurology, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
- *Correspondence: Yucai Chen,
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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9
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Cerase A, Young AN, Ruiz NB, Buness A, Sant GM, Arnold M, Di Giacomo M, Ascolani M, Kumar M, Hierholzer A, Trigiante G, Marzi SJ, Avner P. Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression. Commun Biol 2021; 4:485. [PMID: 33859315 PMCID: PMC8050208 DOI: 10.1038/s42003-021-01945-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 02/25/2021] [Indexed: 01/22/2023] Open
Abstract
Female mammals achieve dosage compensation by inactivating one of their two X chromosomes during development, a process entirely dependent on Xist, an X-linked long non-coding RNA (lncRNA). At the onset of X chromosome inactivation (XCI), Xist is up-regulated and spreads along the future inactive X chromosome. Contextually, it recruits repressive histone and DNA modifiers that transcriptionally silence the X chromosome. Xist regulation is tightly coupled to differentiation and its expression is under the control of both pluripotency and epigenetic factors. Recent evidence has suggested that chromatin remodelers accumulate at the X Inactivation Center (XIC) and here we demonstrate a new role for Chd8 in Xist regulation in differentiating ES cells, linked to its control and prevention of spurious transcription factor interactions occurring within Xist regulatory regions. Our findings have a broader relevance, in the context of complex, developmentally-regulated gene expression.
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Affiliation(s)
- Andrea Cerase
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy.
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Alexander N Young
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nerea Blanes Ruiz
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Andreas Buness
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
- Core Unit for Bioinformatics Data Analysis Universitätsklinikum Bonn, Bonn, Germany
| | - Gabrielle M Sant
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Mirjam Arnold
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
| | | | - Michela Ascolani
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
| | - Manish Kumar
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
- Department of Allied Health Science, Shri B. M. Patil Medical College, Hospital and Research Centre, BLDE, Vijaypura, Karnataka, India
| | - Andreas Hierholzer
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Giuseppe Trigiante
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
| | - Philip Avner
- EMBL-Rome, Epigenetics and Neurobiology Unit, Monterotondo, Italy.
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10
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Wilson MM, Henshall DC, Byrne SM, Brennan GP. CHD2-Related CNS Pathologies. Int J Mol Sci 2021; 22:E588. [PMID: 33435571 PMCID: PMC7827033 DOI: 10.3390/ijms22020588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/08/2023] Open
Abstract
Epileptic encephalopathies (EE) are severe epilepsy syndromes characterized by multiple seizure types, developmental delay and even regression. This class of disorders are increasingly being identified as resulting from de novo genetic mutations including many identified mutations in the family of chromodomain helicase DNA binding (CHD) proteins. In particular, several de novo pathogenic mutations have been identified in the gene encoding chromodomain helicase DNA binding protein 2 (CHD2), a member of the sucrose nonfermenting (SNF-2) protein family of epigenetic regulators. These mutations in the CHD2 gene are causative of early onset epileptic encephalopathy, abnormal brain function, and intellectual disability. Our understanding of the mechanisms by which modification or loss of CHD2 cause this condition remains poorly understood. Here, we review what is known and still to be elucidated as regards the structure and function of CHD2 and how its dysregulation leads to a highly variable range of phenotypic presentations.
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Affiliation(s)
- Marc-Michel Wilson
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - David C. Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - Susan M. Byrne
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- Department of Paediatrics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland
- Department of Paediatric Neurology, Our Ladies Children’s Hospital Crumlin, Dublin 12, Ireland
| | - Gary P. Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 04, Ireland
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11
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Yoo H, La H, Lee EJ, Choi HJ, Oh J, Thang NX, Hong K. ATP-Dependent Chromatin Remodeler CHD9 Controls the Proliferation of Embryonic Stem Cells in a Cell Culture Condition-Dependent Manner. BIOLOGY 2020; 9:biology9120428. [PMID: 33261017 PMCID: PMC7760864 DOI: 10.3390/biology9120428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/23/2022]
Abstract
Emerging evidence suggests that chromodomain-helicase-DNA-binding (CHD) proteins are involved in stem cell maintenance and differentiation via the coordination of chromatin structure and gene expression. However, the molecular function of some CHD proteins in stem cell regulation is still poorly understood. Herein, we show that Chd9 knockdown (KD) in mouse embryonic stem cells (ESCs) cultured in normal serum media, not in 2i-leukemia inhibitory factor (LIF) media, causes rapid cell proliferation. This is caused by transcriptional regulation related to the cell cycle and the response to growth factors. Our analysis showed that, unlike the serum cultured-Chd9 KD ESCs, the 2i-LIF-cultured-Chd9 KO ESCs displayed elevated levels of critical G1 phase regulators such as p21 and p27. Consistently, the DNA binding sites of CHD9 overlap with some transcription factor DNA motifs that are associated with genes regulating the cell cycle and growth pathways. These transcription factors include the cycle gene homology region (CHR), Arid5a, and LIN54. Collectively, our results provide new insights into CHD9-mediated gene transcription for controlling the cell cycle of ESCs.
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12
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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13
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Shahin Varnoosfaderani F, Palau A, Dong W, Persson J, Durand-Dubief M, Svensson JP, Lennartsson A. A regulatory role for CHD2 in myelopoiesis. Epigenetics 2020; 15:702-714. [PMID: 31900031 PMCID: PMC7574388 DOI: 10.1080/15592294.2019.1710913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcriptional program that dictates haematopoietic cell fate and differentiation requires an epigenetic regulatory and memory function, provided by a network of epigenetic factors that regulate DNA methylation, post-translational histone modifications and chromatin structure. Disturbed epigenetic regulation causes perturbations in the blood cell differentiation program that results in various types of haematopoietic disorders. Thus, accurate epigenetic regulation is essential for functional haematopoiesis. In this study, we used a CRISPR-Cas9 screening approach to identify new epigenetic regulators in myeloid differentiation. We designed a Chromatin-UMI CRISPR guide library targeting 1092 epigenetic regulators. Phorbol 12-myristate 13-acetate (PMA) treatment of the chronic myeloid leukaemia cell line K-562 was used as a megakaryocytic myeloid differentiation model. Both previously described developmental epigenetic regulators and novel factors were identified in our screen. In this study, we validated and characterized a role for the chromatin remodeller CHD2 in myeloid proliferation and megakaryocytic differentiation.
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Affiliation(s)
| | - Anna Palau
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Wenbo Dong
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Jenna Persson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, Sweden.,High Throughput Genome Engineering, Science for Life Laboratory , Stockholm, Sweden
| | - Mickaël Durand-Dubief
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet , Stockholm, Sweden
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14
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Rom A, Melamed L, Gil N, Goldrich MJ, Kadir R, Golan M, Biton I, Perry RBT, Ulitsky I. Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability. Nat Commun 2019; 10:5092. [PMID: 31704914 PMCID: PMC6841665 DOI: 10.1038/s41467-019-13075-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Chromodomain helicase DNA binding protein 2 (Chd2) is a chromatin remodeller implicated in neurological disease. Here we show that Chaserr, a highly conserved long noncoding RNA transcribed from a region near the transcription start site of Chd2 and on the same strand, acts in concert with the CHD2 protein to maintain proper Chd2 expression levels. Loss of Chaserr in mice leads to early postnatal lethality in homozygous mice, and severe growth retardation in heterozygotes. Mechanistically, loss of Chaserr leads to substantially increased Chd2 mRNA and protein levels, which in turn lead to transcriptional interference by inhibiting promoters found downstream of highly expressed genes. We further show that Chaserr production represses Chd2 expression solely in cis, and that the phenotypic consequences of Chaserr loss are rescued when Chd2 is perturbed as well. Targeting Chaserr is thus a potential strategy for increasing CHD2 levels in haploinsufficient individuals.
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Affiliation(s)
- Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Liliya Melamed
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rotem Kadir
- National Institute for Biotechnology in the Negev and Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Matan Golan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inbal Biton
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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15
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Abstract
Mutations in the chromodomain helicase DNA-binding 2 (CHD2) gene have been found in patients with a range of neurodevelopmental disorders. In this issue of Neuron, Kim et al. (2018) showed that Chd2 haploinsufficiency compromises cortical development, synaptic function, and memory in mice.
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Affiliation(s)
- Vanesa Nieto-Estevez
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jenny Hsieh
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA.
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16
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Kim YJ, Khoshkhoo S, Frankowski JC, Zhu B, Abbasi S, Lee S, Wu YE, Hunt RF. Chd2 Is Necessary for Neural Circuit Development and Long-Term Memory. Neuron 2018; 100:1180-1193.e6. [PMID: 30344048 PMCID: PMC6479120 DOI: 10.1016/j.neuron.2018.09.049] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 07/31/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022]
Abstract
Considerable evidence suggests loss-of-function mutations in the chromatin remodeler CHD2 contribute to a broad spectrum of human neurodevelopmental disorders. However, it is unknown how CHD2 mutations lead to impaired brain function. Here we report mice with heterozygous mutations in Chd2 exhibit deficits in neuron proliferation and a shift in neuronal excitability that included divergent changes in excitatory and inhibitory synaptic function. Further in vivo experiments show that Chd2+/- mice displayed aberrant cortical rhythmogenesis and severe deficits in long-term memory, consistent with phenotypes observed in humans. We identified broad, age-dependent transcriptional changes in Chd2+/- mice, including alterations in neurogenesis, synaptic transmission, and disease-related genes. Deficits in interneuron density and memory caused by Chd2+/- were reproduced by Chd2 mutation restricted to a subset of inhibitory neurons and corrected by interneuron transplantation. Our results provide initial insight into how Chd2 haploinsufficiency leads to aberrant cortical network function and impaired memory.
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Affiliation(s)
- Young J Kim
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Sattar Khoshkhoo
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Brigham and Women's Hospital and Massachusetts General Hospital, Harvard University, Boston, MA 02115, USA
| | - Jan C Frankowski
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Bingyao Zhu
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Saad Abbasi
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Sunyoung Lee
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ye Emily Wu
- Department of Biological Chemistry and Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert F Hunt
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA 92697, USA.
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17
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Kasah S, Oddy C, Basson MA. Autism-linked CHD gene expression patterns during development predict multi-organ disease phenotypes. J Anat 2018; 233:755-769. [PMID: 30277262 DOI: 10.1111/joa.12889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
Recent large-scale exome sequencing studies have identified mutations in several members of the CHD (Chromodomain Helicase DNA-binding protein) gene family in neurodevelopmental disorders. Mutations in the CHD2 gene have been linked to developmental delay, intellectual disability, autism and seizures, CHD8 mutations to autism and intellectual disability, whereas haploinsufficiency of CHD7 is associated with executive dysfunction and intellectual disability. In addition to these neurodevelopmental features, a wide range of other developmental defects are associated with mutants of these genes, especially with regards to CHD7 haploinsufficiency, which is the primary cause of CHARGE syndrome. Whilst the developmental expression of CHD7 has been reported previously, limited information on the expression of CHD2 and CHD8 during development is available. Here, we compare the expression patterns of all three genes during mouse development directly. We find high, widespread expression of these genes at early stages of development that gradually becomes restricted during later developmental stages. Chd2 and Chd8 are widely expressed in the developing central nervous system (CNS) at all stages of development, with moderate expression remaining in the neocortex, hippocampus, olfactory bulb and cerebellum of the postnatal brain. Similarly, Chd7 expression is seen throughout the CNS during late embryogenesis and early postnatal development, with strong enrichment in the cerebellum, but displays low expression in the cortex and neurogenic niches in early life. In addition to expression in the brain, novel sites of Chd2 and Chd8 expression are reported. These findings suggest additional roles for these genes in organogenesis and predict that mutation of these genes may predispose individuals to a range of other, non-neurological developmental defects.
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Affiliation(s)
- Sahrunizam Kasah
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Christopher Oddy
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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18
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G-quadruplexes in the BAP1 promoter positively regulate its expression. Exp Cell Res 2018; 369:147-157. [DOI: 10.1016/j.yexcr.2018.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/23/2018] [Accepted: 05/17/2018] [Indexed: 12/13/2022]
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19
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Lamar KMJ, Carvill GL. Chromatin Remodeling Proteins in Epilepsy: Lessons From CHD2-Associated Epilepsy. Front Mol Neurosci 2018; 11:208. [PMID: 29962935 PMCID: PMC6013553 DOI: 10.3389/fnmol.2018.00208] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/25/2018] [Indexed: 12/24/2022] Open
Abstract
The chromodomain helicase DNA-binding (CHD) family of proteins are ATP-dependent chromatin remodelers that contribute to the reorganization of chromatin structure and deposition of histone variants necessary to regulate gene expression. CHD proteins play an important role in neurodevelopment, as pathogenic variants in CHD1, CHD2, CHD4, CHD7 and CHD8 have been associated with a range of neurological phenotypes, including autism spectrum disorder (ASD), intellectual disability (ID) and epilepsy. Pathogenic variants in CHD2 are associated with developmental epileptic encephalopathy (DEE) in humans, however little is known about how these variants contribute to this disorder. Of the nine CHD family members, CHD2 is the only one that leads to a brain-restricted phenotype when disrupted in humans. This suggests that despite being expressed ubiquitously, CHD2 has a unique role in human brain development and function. In this review, we will discuss the phenotypic spectrum of patients with pathogenic variants in CHD2, current animal models of CHD2 deficiency, and the role of CHD2 in proliferation, neurogenesis, neuronal differentiation, chromatin remodeling and DNA-repair. We also consider how CHD2 depletion can affect each of these biological mechanisms and how these defects may underpin neurodevelopmental disorders including epilepsy.
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Affiliation(s)
- Kay-Marie J Lamar
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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20
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Moccia A, Martin DM. Nervous system development and disease: A focus on trithorax related proteins and chromatin remodelers. Mol Cell Neurosci 2018; 87:46-54. [PMID: 29196188 PMCID: PMC5828982 DOI: 10.1016/j.mcn.2017.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/08/2017] [Accepted: 11/27/2017] [Indexed: 01/12/2023] Open
Abstract
The nervous system comprises many different cell types including neurons, glia, macrophages, and immune cells, each of which is defined by specific patterns of gene expression, morphology, function, and anatomical location. Establishment of these complex and highly regulated cell fates requires spatial and temporal coordination of gene transcription. Open chromatin (euchromatin) allows transcription factors to interact with gene promoters and activate lineage specific genes, whereas closed chromatin (heterochromatin) remains inaccessible to transcriptional activation. Changes in the genome-wide distribution of euchromatin accompany transcriptional plasticity that allows the diversity of mature cell fates to be generated during development. In the past 20years, many new genes and gene families have been identified to participate in regulation of chromatin accessibility. These genes include chromatin remodelers that interact with Trithorax group (TrxG) and Polycomb group (PcG) proteins to activate or repress transcription, respectively. Here we review the role of TrxG proteins in neurodevelopment and disease.
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Affiliation(s)
- Amanda Moccia
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Donna M Martin
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Pediatrics and Communicable Diseases, The University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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21
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Cabot B, Cabot RA. Chromatin remodeling in mammalian embryos. Reproduction 2018; 155:R147-R158. [PMID: 29339454 DOI: 10.1530/rep-17-0488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/12/2018] [Indexed: 12/28/2022]
Abstract
The mammalian embryo undergoes a dramatic amount of epigenetic remodeling during the first week of development. In this review, we discuss several epigenetic changes that happen over the course of cleavage development, focusing on covalent marks (e.g., histone methylation and acetylation) and non-covalent remodeling (chromatin remodeling via remodeling complexes; e.g., SWI/SNF-mediated chromatin remodeling). Comparisons are also drawn between remodeling events that occur in embryos from a variety of mammalian species.
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Affiliation(s)
- Birgit Cabot
- Department of Animal SciencesPurdue University, West Lafayette, Indiana, USA
| | - Ryan A Cabot
- Department of Animal SciencesPurdue University, West Lafayette, Indiana, USA
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22
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Regulatory networks specifying cortical interneurons from human embryonic stem cells reveal roles for CHD2 in interneuron development. Proc Natl Acad Sci U S A 2017; 114:E11180-E11189. [PMID: 29229852 DOI: 10.1073/pnas.1712365115] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cortical interneurons (cINs) modulate excitatory neuronal activity by providing local inhibition. During fetal development, several cIN subtypes derive from the medial ganglionic eminence (MGE), a transient ventral telencephalic structure. While altered cIN development contributes to neurodevelopmental disorders, the inaccessibility of human fetal brain tissue during development has hampered efforts to define molecular networks controlling this process. Here, we modified protocols for directed differentiation of human embryonic stem cells, obtaining efficient, accelerated production of MGE-like progenitors and MGE-derived cIN subtypes with the expected electrophysiological properties. We defined transcriptome changes accompanying this process and integrated these data with direct transcriptional targets of NKX2-1, a transcription factor controlling MGE specification. This analysis defined NKX2-1-associated genes with enriched expression during MGE specification and cIN differentiation, including known and previously unreported transcription factor targets with likely roles in MGE specification, and other target classes regulating cIN migration and function. NKX2-1-associated peaks were enriched for consensus binding motifs for NKX2-1, LHX, and SOX transcription factors, suggesting roles in coregulating MGE gene expression. Among the NKX2-1 direct target genes with cIN-enriched expression was CHD2, which encodes a chromatin remodeling protein mutated to cause human epilepsies. Accordingly, CHD2 deficiency impaired cIN specification and altered later electrophysiological function, while CHD2 coassociated with NKX2-1 at cis-regulatory elements and was required for their transactivation by NKX2-1 in MGE-like progenitors. This analysis identified several aspects of gene-regulatory networks underlying human MGE specification and suggested mechanisms by which NKX2-1 acts with chromatin remodeling activities to regulate gene expression programs underlying cIN development.
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23
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Semba Y, Harada A, Maehara K, Oki S, Meno C, Ueda J, Yamagata K, Suzuki A, Onimaru M, Nogami J, Okada S, Akashi K, Ohkawa Y. Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells. Nucleic Acids Res 2017; 45:8758-8772. [PMID: 28549158 PMCID: PMC5587750 DOI: 10.1093/nar/gkx475] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/15/2017] [Indexed: 12/21/2022] Open
Abstract
Chromatin reorganization is necessary for pluripotent stem cells, including embryonic stem cells (ESCs), to acquire lineage potential. However, it remains unclear how ESCs maintain their characteristic chromatin state for appropriate gene expression upon differentiation. Here, we demonstrate that chromodomain helicase DNA-binding domain 2 (Chd2) is required to maintain the differentiation potential of mouse ESCs. Chd2-depleted ESCs showed suppressed expression of developmentally regulated genes upon differentiation and subsequent differentiation defects without affecting gene expression in the undifferentiated state. Furthermore, chromatin immunoprecipitation followed by sequencing revealed alterations in the nucleosome occupancy of the histone variant H3.3 for developmentally regulated genes in Chd2-depleted ESCs, which in turn led to elevated trimethylation of the histone H3 lysine 27. These results suggest that Chd2 is essential in preventing suppressive chromatin formation for developmentally regulated genes and determines subsequent effects on developmental processes in the undifferentiated state.
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Affiliation(s)
- Yuichiro Semba
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Jun Ueda
- Center of Education in Laboratory Animal Research, Chubu University, Aichi 487-8501, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, KINDAI University, Wakayama 649-6493, Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mitsuho Onimaru
- Pathophysiological and Experimental Pathology, Department of Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Seiji Okada
- Department of Advanced Medical Initiatives, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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24
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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25
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Mills AA. The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026450. [PMID: 28096241 DOI: 10.1101/cshperspect.a026450] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A plethora of mutations in chromatin regulators in diverse human cancers is emerging, attesting to the pivotal role of chromatin dynamics in tumorigenesis. A recurrent theme is inactivation of the chromodomain helicase DNA-binding (CHD) family of proteins-ATP-dependent chromatin remodelers that govern the cellular machinery's access to DNA, thereby controlling fundamental processes, including transcription, proliferation, and DNA damage repair. This review highlights what is currently known about how genetic and epigenetic perturbation of CHD proteins and the pathways that they regulate set the stage for cancer, providing new insight for designing more effective anti-cancer therapies.
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Affiliation(s)
- Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
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26
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Festuccia N, Gonzalez I, Navarro P. The Epigenetic Paradox of Pluripotent ES Cells. J Mol Biol 2016; 429:1476-1503. [PMID: 27988225 DOI: 10.1016/j.jmb.2016.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
The propagation and maintenance of gene expression programs are at the foundation of the preservation of cell identity. A large and complex set of epigenetic mechanisms enables the long-term stability and inheritance of transcription states. A key property of authentic epigenetic regulation is being independent from the instructive signals used for its establishment. This makes epigenetic regulation, particularly epigenetic silencing, extremely robust and powerful to lock regulatory states and stabilise cell identity. In line with this, the establishment of epigenetic silencing during development restricts cell potency and maintains the cell fate choices made by transcription factors (TFs). However, how more immature cells that have not yet established their definitive fate maintain their transitory identity without compromising their responsiveness to signalling cues remains unclear. A paradigmatic example is provided by pluripotent embryonic stem (ES) cells derived from a transient population of cells of the blastocyst. Here, we argue that ES cells represent an interesting "epigenetic paradox": even though they are captured in a self-renewing state characterised by extremely efficient maintenance of their identity, which is a typical manifestation of robust epigenetic regulation, they seem not to heavily rely on classical epigenetic mechanisms. Indeed, self-renewal strictly depends on the TFs that previously instructed their undifferentiated identity and relies on a particular signalling-dependent chromatin state where repressive chromatin marks play minor roles. Although this "epigenetic paradox" may underlie their exquisite responsiveness to developmental cues, it suggests that alternative mechanisms to faithfully propagate gene regulatory states might be prevalent in ES cells.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France.
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27
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Shen T, Ji F, Yuan Z, Jiao J. CHD2 is Required for Embryonic Neurogenesis in the Developing Cerebral Cortex. Stem Cells 2016; 33:1794-806. [PMID: 25786798 DOI: 10.1002/stem.2001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 02/02/2015] [Accepted: 02/06/2015] [Indexed: 11/08/2022]
Abstract
Chromodomain helicase DNA-binding protein 2 (CHD2) has been associated with a broad spectrum of neurodevelopmental disorders, such as autism spectrum disorders and intellectual disability. However, it is largely unknown whether and how CHD2 is involved in brain development. Here, we demonstrate that CHD2 is predominantly expressed in Pax6(+) radial glial cells (RGs) but rarely expressed in Tbr2(+) intermediate progenitors (IPs). Importantly, the suppression of CHD2 expression inhibits the self-renewal of RGs and increases the generation of IPs and the production of neurons. CHD2 mediates these functions by directly binding to the genomic region of repressor element 1-silencing transcription factor (REST), thereby regulating the expression of REST. Furthermore, the overexpression of REST rescues the defect in neurogenesis caused by CHD2 knockdown. Taken together, these findings demonstrate an essential role of CHD2 in the maintenance of the RGs self-renewal levels, the subsequent generation of IPs, and neuronal output during neurogenesis in cerebral cortical development, suggesting that inactivation of CHD2 during neurogenesis might contribute to abnormal neurodevelopment.
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Affiliation(s)
- Tianjin Shen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Fen Ji
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zengqiang Yuan
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jianwei Jiao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
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28
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Wille A, Maurer V, Piatti P, Whittle N, Rieder D, Singewald N, Lusser A. Impaired Contextual Fear Extinction Learning is Associated with Aberrant Regulation of CHD-Type Chromatin Remodeling Factors. Front Behav Neurosci 2015; 9:313. [PMID: 26635563 PMCID: PMC4649039 DOI: 10.3389/fnbeh.2015.00313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/03/2015] [Indexed: 02/04/2023] Open
Abstract
Successful attenuation of fearful memories is a cognitive process requiring initiation of highly coordinated transcription programs. Chromatin-modulating mechanisms such as DNA methylation and histone modifications, including acetylation, are key regulators of these processes. However, knowledge concerning the role of ATP-dependent chromatin remodeling factors (ChRFs) being required for successful fear extinction is lacking. Underscoring the potential importance of these factors that alter histone-DNA contacts within nucleosomes are recent genome-wide association studies linking several ChRFs to various human cognitive and psychiatric disorders. To better understand the role of ChRFs in the brain, and since to date little is known about ChRF expression in the brain, we performed a comprehensive survey of expression levels of 24 ATP-dependent remodelers across different brain areas, and we identified several distinct high molecular weight complexes by chromatographic methods. We next aimed to gain novel insight into the potential regulation of ChRFs in different brain regions in association with normal and impaired fear extinction learning. To this end, we established the 129S1/SvImJ (S1) laboratory mouse strain as a model for compromised contextual fear extinction learning that can be rescued by dietary zinc restriction (ZnR). Using this model along with genetically related but fear extinction-competent 129S6/SvEv (S6) mice as controls, we found that impaired fear extinction in S1 was associated with enhanced ventral hippocampal expression of CHD1 and reduced expression of CHD5 that was normalized following successful rescue of impaired fear extinction. Moreover, a select reduction in CHD3 expression was observed in the ventral hippocampus (vHC) following successful rescue of fear extinction in S1 mice. Taken together, these data provide novel insight into the regulation of specific ChRFs following an impaired cognitive process and its rescue, and they suggest that imbalance of CHD-type remodeler levels, which consequently may lead to changes of transcriptional programs, may be an underlying mechanism involved in impaired fear extinction learning and its therapeutic rescue.
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Affiliation(s)
- Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Verena Maurer
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Nigel Whittle
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck Innsbruck, Austria
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, Institute of Chemistry and Pharmacy, Leopold-Franzens University of Innsbruck Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck Innsbruck, Austria
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29
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De Rubeis S, Buxbaum JD. Genetics and genomics of autism spectrum disorder: embracing complexity. Hum Mol Genet 2015; 24:R24-31. [PMID: 26188008 PMCID: PMC4675826 DOI: 10.1093/hmg/ddv273] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/02/2015] [Accepted: 07/09/2015] [Indexed: 01/19/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) characterized by impairments in social communication and social interaction and the presence of repetitive behaviors and/or restricted interests. ASD has profound etiological and clinical heterogeneity, which has impeded the identification of risk factors and pathophysiological processes underlying the disorder. A constellation of (i) types of genetic variation, (ii) modes of inheritance and (iii) specific genomic loci and genes have all recently been implicated in ASD risk, and these findings are currently being extended with functional analyses in model organisms and genotype-phenotype correlation studies. The overlap of risk loci between ASD and other NDDs raises intriguing questions around the mechanisms of risk. In this review, we will touch upon these aspects of ASD and how they might be addressed.
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Affiliation(s)
- Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA and The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA
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30
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Ogden KK, Ozkan ED, Rumbaugh G. Prioritizing the development of mouse models for childhood brain disorders. Neuropharmacology 2015; 100:2-16. [PMID: 26231830 DOI: 10.1016/j.neuropharm.2015.07.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 07/18/2015] [Accepted: 07/22/2015] [Indexed: 12/20/2022]
Abstract
Mutations in hundreds of genes contribute to cognitive and behavioral dysfunction associated with developmental brain disorders (DBDs). Due to the sheer number of risk factors available for study combined with the cost of developing new animal models, it remains an open question how genes should be prioritized for in-depth neurobiological investigations. Recent reviews have argued that priority should be given to frequently mutated genes commonly found in sporadic DBD patients. Intrigued by this idea, we explored to what extent "high priority" risk factors have been studied in animals in an effort to assess their potential for generating valuable preclinical models capable of advancing the neurobiological understanding of DBDs. We found that in-depth whole animal studies are lacking for many high priority genes, with relatively few neurobiological studies performed in construct valid animal models aimed at understanding the pathological substrates associated with disease phenotypes. However, some high priority risk factors have been extensively studied in animal models and they have generated novel insights into DBD patho-neurobiology while also advancing early pre-clinical therapeutic treatment strategies. We suggest that prioritizing model development toward genes frequently mutated in non-specific DBD populations will accelerate the understanding of DBD patho-neurobiology and drive novel therapeutic strategies. This article is part of the Special Issue entitled 'Synaptopathy--from Biology to Therapy'.
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Affiliation(s)
- Kevin K Ogden
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Emin D Ozkan
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gavin Rumbaugh
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
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31
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Li W, Mills AA. Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 2015; 6:381-95. [PMID: 25333848 DOI: 10.2217/epi.14.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chromatin is vital to normal cells, and its deregulation contributes to a spectrum of human ailments. An emerging concept is that aberrant chromatin regulation culminates in gene expression programs that set the stage for the seemingly diverse pathologies of cancer, developmental disorders and neurological syndromes. However, the mechanisms responsible for such common etiology have been elusive. Recent evidence has implicated lesions affecting chromatin-remodeling proteins in cancer, developmental disorders and neurological syndromes, suggesting a common source for these different pathologies. Here, we focus on the chromodomain helicase DNA binding chromatin-remodeling family and the recent evidence for its deregulation in diverse pathological conditions, providing a new perspective on the underlying mechanisms and their implications for these prevalent human diseases.
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Affiliation(s)
- Wangzhi Li
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724, USA
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32
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Mutations in CHD2 cause defective association with active chromatin in chronic lymphocytic leukemia. Blood 2015; 126:195-202. [PMID: 26031915 DOI: 10.1182/blood-2014-10-604959] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/26/2015] [Indexed: 12/20/2022] Open
Abstract
Great progress has recently been achieved in the understanding of the genomic alterations driving chronic lymphocytic leukemia (CLL). Nevertheless, the specific molecular mechanisms governing chromatin remodeling in CLL are unknown. Here we report the genetic and functional characterization of somatic mutations affecting the chromatin remodeler CHD2, one of the most frequently mutated genes in CLL (5.3%) and in monoclonal B lymphocytosis (MBL, 7%), a B-cell expansion that can evolve to CLL. Most of the mutations affecting CHD2, identified by whole-exome sequencing of 456 CLL and 43 MBL patients, are either truncating or affect conserved residues in functional domains, thus supporting a putative role for CHD2 as a tumor suppressor gene. CHD2 mutants show altered nuclear distribution, and a chromodomain helicase DNA binding protein 2 (CHD2) mutant affected in its DNA-binding domain exhibits defective association with active chromatin. Clinicobiological analyses show that most CLL patients carrying CHD2 mutations also present mutated immunoglobulin heavy chain variable region genes (IGHVs), being the most frequently mutated gene in this prognostic subgroup. This is the first study providing functional evidence supporting CHD2 as a cancer driver and opens the way to further studies of the role of this chromatin remodeler in CLL.
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33
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Galizia EC, Myers CT, Leu C, de Kovel CGF, Afrikanova T, Cordero-Maldonado ML, Martins TG, Jacmin M, Drury S, Krishna Chinthapalli V, Muhle H, Pendziwiat M, Sander T, Ruppert AK, Møller RS, Thiele H, Krause R, Schubert J, Lehesjoki AE, Nürnberg P, Lerche H, Palotie A, Coppola A, Striano S, Gaudio LD, Boustred C, Schneider AL, Lench N, Jocic-Jakubi B, Covanis A, Capovilla G, Veggiotti P, Piccioli M, Parisi P, Cantonetti L, Sadleir LG, Mullen SA, Berkovic SF, Stephani U, Helbig I, Crawford AD, Esguerra CV, Kasteleijn-Nolst Trenité DGA, Koeleman BPC, Mefford HC, Scheffer IE, Sisodiya SM. CHD2 variants are a risk factor for photosensitivity in epilepsy. Brain 2015; 138:1198-207. [PMID: 25783594 PMCID: PMC4407192 DOI: 10.1093/brain/awv052] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/07/2015] [Indexed: 12/24/2022] Open
Abstract
Photosensitivity in epilepsy is common and has high heritability, but its genetic basis remains uncertain. Galizia et al. reveal an overrepresentation of unique variants of CHD2 — which encodes the transcriptional regulator ‘chromodomain helicase DNA-binding protein 2’ — in photosensitive epilepsies, and show that chd2 knockdown in zebrafish causes photosensitivity. Photosensitivity is a heritable abnormal cortical response to flickering light, manifesting as particular electroencephalographic changes, with or without seizures. Photosensitivity is prominent in a very rare epileptic encephalopathy due to de novo CHD2 mutations, but is also seen in epileptic encephalopathies due to other gene mutations. We determined whether CHD2 variation underlies photosensitivity in common epilepsies, specific photosensitive epilepsies and individuals with photosensitivity without seizures. We studied 580 individuals with epilepsy and either photosensitive seizures or abnormal photoparoxysmal response on electroencephalography, or both, and 55 individuals with photoparoxysmal response but no seizures. We compared CHD2 sequence data to publicly available data from 34 427 individuals, not enriched for epilepsy. We investigated the role of unique variants seen only once in the entire data set. We sought CHD2 variants in 238 exomes from familial genetic generalized epilepsies, and in other public exome data sets. We identified 11 unique variants in the 580 individuals with photosensitive epilepsies and 128 unique variants in the 34 427 controls: unique CHD2 variation is over-represented in cases overall (P = 2·17 × 10−5). Among epilepsy syndromes, there was over-representation of unique CHD2 variants (3/36 cases) in the archetypal photosensitive epilepsy syndrome, eyelid myoclonia with absences (P = 3·50 × 10−4). CHD2 variation was not over-represented in photoparoxysmal response without seizures. Zebrafish larvae with chd2 knockdown were tested for photosensitivity. Chd2 knockdown markedly enhanced mild innate zebrafish larval photosensitivity. CHD2 mutation is the first identified cause of the archetypal generalized photosensitive epilepsy syndrome, eyelid myoclonia with absences. Unique CHD2 variants are also associated with photosensitivity in common epilepsies. CHD2 does not encode an ion channel, opening new avenues for research into human cortical excitability.
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Affiliation(s)
- Elizabeth C Galizia
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
| | | | - Costin Leu
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
| | - Carolien G F de Kovel
- 4 Department of Medical Genetics Research, University Medical Centre Utrecht, The Netherlands
| | - Tatiana Afrikanova
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Teresa G Martins
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Maxime Jacmin
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Suzanne Drury
- 6 North East Thames Regional Genetics Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - V Krishna Chinthapalli
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
| | - Hiltrud Muhle
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Manuela Pendziwiat
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Thomas Sander
- 8 Cologne Centre for Genomics, University of Cologne, Cologne, Germany
| | | | - Rikke S Møller
- 9 Danish Epilepsy Centre, Dianalund, Denmark 10 Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Holger Thiele
- 8 Cologne Centre for Genomics, University of Cologne, Cologne, Germany
| | - Roland Krause
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Julian Schubert
- 11 Deptartment of Neurology and Epileptology, Hertie Institut for Clinical Brain Research, Tübingen, Germany
| | - Anna-Elina Lehesjoki
- 12 Folkhälsan Institute of Genetics and Neuroscience Centre, University of Helsinki, Helsinki, Finland 13 Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Peter Nürnberg
- 8 Cologne Centre for Genomics, University of Cologne, Cologne, Germany
| | - Holger Lerche
- 11 Deptartment of Neurology and Epileptology, Hertie Institut for Clinical Brain Research, Tübingen, Germany
| | | | - Aarno Palotie
- 14 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK 15 Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland 16 Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, USA
| | - Antonietta Coppola
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK 17 Epilepsy Centre, Neurology Department, Federico II University of Naples, Naples, Italy
| | - Salvatore Striano
- 17 Epilepsy Centre, Neurology Department, Federico II University of Naples, Naples, Italy
| | - Luigi Del Gaudio
- 17 Epilepsy Centre, Neurology Department, Federico II University of Naples, Naples, Italy
| | - Christopher Boustred
- 6 North East Thames Regional Genetics Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Amy L Schneider
- 18 Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Nicholas Lench
- 6 North East Thames Regional Genetics Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Bosanka Jocic-Jakubi
- 19 Department of Child Neurology, Paediatric Clinic, Clinical Centre Nis, Serbia 20 Department of Paediatric Neurology, Paediatric Clinic, Al Sabah Hospital, Kuwait
| | - Athanasios Covanis
- 21 Neurology Department, The Children's Hospital Agia Sophia, Athens, Greece
| | | | - Pierangelo Veggiotti
- 23 Department of Child Neurology and Psychiatry C. Mondino National Neurological Institute, Via Mondino, 2, 27100, Pavia, Italy 24 Brain and Behaviour Department, University of Pavia, Pavia, Italy
| | - Marta Piccioli
- 25 Neurophysiopathology Unit, San Filippo Neri Hospital, Rome, Italy
| | - Pasquale Parisi
- 26 Child Neurology, NESMOS Department, Faculty of Medicine and Psychology, Sapienza University, Rome, Italy
| | - Laura Cantonetti
- 27 Neurorehabilitation Unit, Department of Neuroscience and Neurorehabilitation, IRCCS, Bambino Gesu' Children's Hospital, Rome, Italy
| | - Lynette G Sadleir
- 28 Department of Paediatrics and Child Health, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Saul A Mullen
- 29 Florey Institute of Neurosciences and Mental Health, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Samuel F Berkovic
- 18 Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
| | - Ulrich Stephani
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Ingo Helbig
- 7 Department of Neuropaediatrics, University Medical Centre Schleswig-Holstein and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander D Crawford
- 5 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camila V Esguerra
- 30 Chemical Neuroscience Group, Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway 31 Laboratory for Molecular Biodiscovery, University of Leuven, Leuven, Belgium
| | | | - Bobby P C Koeleman
- 4 Department of Medical Genetics Research, University Medical Centre Utrecht, The Netherlands
| | | | - Ingrid E Scheffer
- 18 Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia 29 Florey Institute of Neurosciences and Mental Health, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Sanjay M Sisodiya
- 1 NIHR Biomedical Research Centre Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK 2 Epilepsy Society, Bucks, UK
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34
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Micucci JA, Sperry ED, Martin DM. Chromodomain helicase DNA-binding proteins in stem cells and human developmental diseases. Stem Cells Dev 2015; 24:917-26. [PMID: 25567374 DOI: 10.1089/scd.2014.0544] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dynamic regulation of gene expression is vital for proper cellular development and maintenance of differentiated states. Over the past 20 years, chromatin remodeling and epigenetic modifications of histones have emerged as key controllers of rapid reversible changes in gene expression. Mutations in genes encoding enzymes that modify chromatin have also been identified in a variety of human neurodevelopmental disorders, ranging from isolated intellectual disability and autism spectrum disorder to multiple congenital anomaly conditions that affect major organ systems and cause severe morbidity and mortality. In this study, we review recent evidence that chromodomain helicase DNA-binding (CHD) proteins regulate stem cell proliferation, fate, and differentiation in a wide variety of tissues and organs. We also highlight known roles of CHD proteins in human developmental diseases and present current unanswered questions about the pleiotropic effects of CHD protein complexes, their genetic targets, nucleosome sliding functions, and enzymatic effects in cells and tissues.
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Affiliation(s)
- Joseph A Micucci
- 1 Division of Hematology, Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
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35
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Piatti P, Lim CY, Nat R, Villunger A, Geley S, Shue YT, Soratroi C, Moser M, Lusser A. Embryonic stem cell differentiation requires full length Chd1. Sci Rep 2015; 5:8007. [PMID: 25620209 PMCID: PMC4306112 DOI: 10.1038/srep08007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/22/2014] [Indexed: 12/28/2022] Open
Abstract
The modulation of chromatin dynamics by ATP-dependent chromatin remodeling factors has been recognized as an important mechanism to regulate the balancing of self-renewal and pluripotency in embryonic stem cells (ESCs). Here we have studied the effects of a partial deletion of the gene encoding the chromatin remodeling factor Chd1 that generates an N-terminally truncated version of Chd1 in mouse ESCs in vitro as well as in vivo. We found that a previously uncharacterized serine-rich region (SRR) at the N-terminus is not required for chromatin assembly activity of Chd1 but that it is subject to phosphorylation. Expression of Chd1 lacking this region in ESCs resulted in aberrant differentiation properties of these cells. The self-renewal capacity and ESC chromatin structure, however, were not affected. Notably, we found that newly established ESCs derived from Chd1(Δ2/Δ2) mutant mice exhibited similar differentiation defects as in vitro generated mutant ESCs, even though the N-terminal truncation of Chd1 was fully compatible with embryogenesis and post-natal life in the mouse. These results underscore the importance of Chd1 for the regulation of pluripotency in ESCs and provide evidence for a hitherto unrecognized critical role of the phosphorylated N-terminal SRR for full functionality of Chd1.
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Affiliation(s)
- Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Chin Yan Lim
- Epithelial Epigenetics and Development Laboratory, Institute of Medical Biology, A*Star, Singapore
| | - Roxana Nat
- Institute for Neuroscience, Medical University of Innsbruck, Austria
| | - Andreas Villunger
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Stephan Geley
- Division of Molecular Pathophysiology, Biocenter, Medical University of Innsbruck, Austria
| | - Yan Ting Shue
- Epithelial Epigenetics and Development Laboratory, Institute of Medical Biology, A*Star, Singapore
| | - Claudia Soratroi
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Markus Moser
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Austria
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36
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Siggens L, Cordeddu L, Rönnerblad M, Lennartsson A, Ekwall K. Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions. Epigenetics Chromatin 2015; 8:4. [PMID: 25621013 PMCID: PMC4305392 DOI: 10.1186/1756-8935-8-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/23/2014] [Indexed: 01/31/2023] Open
Abstract
Background CHD1 and CHD2 chromatin remodeling enzymes play important roles in development, cancer and differentiation. At a molecular level, the mechanisms are not fully understood but include transcriptional regulation, nucleosome organization and turnover. Results Here we show human CHD1 and CHD2 enzymes co-occupy active chromatin regions associated with transcription start sites (TSS), enhancer like regions and active tRNA genes. We demonstrate that their recruitment is transcription-coupled. CHD1 and CHD2 show distinct binding profiles across active TSS regions. Depletion of CHD1 influences chromatin accessibility at TSS and enhancer-like chromatin regions. CHD2 depletion causes increased histone H3 and reduced histone variant H3.3 occupancy. Conclusions We conclude that transcription-coupled recruitment of CHD1 and CHD2 occurs at transcribed gene TSSs and at intragenic and intergenic enhancer-like sites. The recruitment of CHD1 and CHD2 regulates the architecture of active chromatin regions through chromatin accessibility and nucleosome disassembly. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lee Siggens
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Lina Cordeddu
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Michelle Rönnerblad
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
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Liu JC, Ferreira CG, Yusufzai T. Human CHD2 is a chromatin assembly ATPase regulated by its chromo- and DNA-binding domains. J Biol Chem 2014; 290:25-34. [PMID: 25384982 DOI: 10.1074/jbc.m114.609156] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromodomain helicase DNA-binding protein 2 (CHD2) is an ATPase and a member of the SNF2-like family of helicase-related enzymes. Although deletions of CHD2 have been linked to developmental defects in mice and epileptic disorders in humans, little is known about its biochemical and cellular activities. In this study, we investigate the ATP-dependent activity of CHD2 and show that CHD2 catalyzes the assembly of chromatin into periodic arrays. We also show that the N-terminal region of CHD2, which contains tandem chromodomains, serves an auto-inhibitory role in both the DNA-binding and ATPase activities of CHD2. While loss of the N-terminal region leads to enhanced chromatin-stimulated ATPase activity, the N-terminal region is required for ATP-dependent chromatin remodeling by CHD2. In contrast, the C-terminal region, which contains a putative DNA-binding domain, selectively senses double-stranded DNA of at least 40 base pairs in length and enhances the ATPase and chromatin remodeling activities of CHD2. Our study shows that the accessory domains of CHD2 play central roles in both regulating the ATPase domain and conferring selectivity to chromatin substrates.
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Affiliation(s)
- Jessica C Liu
- From the Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215 and Graduate Program: Molecules, Cells, and Organisms, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Catarina G Ferreira
- From the Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215 and
| | - Timur Yusufzai
- From the Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215 and
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Rodgers MJ, Banks DJ, Bradley KA, Young JA. CHD1 and CHD2 are positive regulators of HIV-1 gene expression. Virol J 2014; 11:180. [PMID: 25297984 PMCID: PMC4283154 DOI: 10.1186/1743-422x-11-180] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Retroviruses encode a very limited number of proteins and therefore must exploit a wide variety of host proteins for completion of their lifecycle. METHODS We performed an insertional mutagenesis screen to identify novel cellular regulators of retroviral replication. RESULTS This approach identified the ATP-dependent chromatin remodeler, chromodomain helicase DNA-binding protein 2 (CHD2), as well as the highly related CHD1 protein, as positive regulators of both MLV and HIV-1 replication in rodent and human cells. RNAi knockdown of either CHD2 or the related CHD1 protein, in human cells resulted in a block to infection by HIV-1, specifically at the level of transcription. CONCLUSIONS These results demonstrate that CHD1 and CHD2 can act as positive regulators of HIV-1 gene expression.
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Affiliation(s)
| | | | | | - John At Young
- The Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Graf A, Krebs S, Heininen-Brown M, Zakhartchenko V, Blum H, Wolf E. Genome activation in bovine embryos: Review of the literature and new insights from RNA sequencing experiments. Anim Reprod Sci 2014; 149:46-58. [DOI: 10.1016/j.anireprosci.2014.05.016] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/09/2014] [Accepted: 05/26/2014] [Indexed: 11/30/2022]
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40
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Qin Y, Ji J, Du G, Wu W, Dai J, Hu Z, Sha J, Hang B, Lu C, Xia Y, Wang X. Comprehensive pathway-based analysis identifies associations of BCL2, GNAO1 and CHD2 with non-obstructive azoospermia risk. Hum Reprod 2014; 29:860-866. [PMID: 24549219 DOI: 10.1093/humrep/deu013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024] Open
Abstract
STUDY QUESTION Do genetic variants in known canonical pathways that have been widely suggested to affect spermatogenesis confer susceptibility to non-obstructive azoospermia (NOA)? SUMMARY ANSWER Rs1406714 in CHD2, rs2126986 in GNAO1 and rs7226979 in BCL2 were associated with NOA in Han Chinese men at a significant level after multiple testing corrections. WHAT IS KNOWN ALREADY Previous genome-wide association studies (GWASs) have identified three loci for NOA, whereas less attention has been given to those markers that did not exceed the genome-wide significance threshold. STUDY DESIGN, SIZE, DURATION We conducted a two-stage association study containing 1653 NOA cases and 2329 controls to investigate the susceptibility markers for NOA. PARTICIPANTS/MATERIALS, SETTING, METHODS Imputation and pathway-based approaches can be applied to identify additional causal makers with small effects on NOA. We performed a candidate pathway-based association study using imputed-genotyping data for 24 238 single nucleotide polymorphisms estimated from NOA GWAS. Remarkably, 40 markers were associated with NOA in both imputation analysis and NOA GWAS (Stage 1) after linkage disequilibrium analysis and selected for validation (Stage 2) in another population. MAIN RESULTS AND THE ROLE OF CHANCE Based on the literature, genes from 11 biological pathways known or hypothesized to be important in spermatogenesis were selected. Combined analysis using directly genotyped data for Stages 1 and 2 revealed that rs1406714 in CHD2 was associated with decreased risk of NOA [odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.68-0.89, Pmeta = 1.7E-04], whereas rs2126986 in GNAO1 and rs7226979 in BCL2 were both risk makers for NOA (rs2126986: OR = 1.28, 95% CI = 1.15-1.41, Pmeta = 2.3E-06; rs7226979: OR = 1.21, 95% CI = 1.11-1.33, Pmeta = 4.5E-05). LIMITATIONS, REASONS FOR CAUTION Our analysis of genes in the pathways studied was not exhaustive. WIDER IMPLICATIONS OF THE FINDINGS Our study opens new avenues for the identification of other novel causal markers that are related to NOA. It will also provide a new paradigm for understanding the etiology of male infertility and contribute to the development of targeted therapies.
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Affiliation(s)
- Yufeng Qin
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 818 East Tianyuan Road, Nanjing 211166, China
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Platt JL, Rogers BJ, Rogers KC, Harwood AJ, Kimmel AR. Different CHD chromatin remodelers are required for expression of distinct gene sets and specific stages during development of Dictyostelium discoideum. Development 2014; 140:4926-36. [PMID: 24301467 PMCID: PMC3848188 DOI: 10.1242/dev.099879] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Control of chromatin structure is crucial for multicellular development and regulation of cell differentiation. The CHD (chromodomain-helicase-DNA binding) protein family is one of the major ATP-dependent, chromatin remodeling factors that regulate nucleosome positioning and access of transcription factors and RNA polymerase to the eukaryotic genome. There are three mammalian CHD subfamilies and their impaired functions are associated with several human diseases. Here, we identify three CHD orthologs (ChdA, ChdB and ChdC) in Dictyostelium discoideum. These CHDs are expressed throughout development, but with unique patterns. Null mutants lacking each CHD have distinct phenotypes that reflect their expression patterns and suggest functional specificity. Accordingly, using genome-wide (RNA-seq) transcriptome profiling for each null strain, we show that the different CHDs regulate distinct gene sets during both growth and development. ChdC is an apparent ortholog of the mammalian Class III CHD group that is associated with the human CHARGE syndrome, and GO analyses of aberrant gene expression in chdC nulls suggest defects in both cell-autonomous and non-autonomous signaling, which have been confirmed through analyses of chdC nulls developed in pure populations or with low levels of wild-type cells. This study provides novel insight into the broad function of CHDs in the regulation development and disease, through chromatin-mediated changes in directed gene expression.
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Affiliation(s)
- James L Platt
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Karczewski KJ, Snyder M, Altman RB, Tatonetti NP. Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association. PLoS Genet 2014; 10:e1004122. [PMID: 24516403 PMCID: PMC3916285 DOI: 10.1371/journal.pgen.1004122] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 12/03/2013] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) are fundamental controllers of cellular regulation that function in a complex and combinatorial manner. Accurate identification of a transcription factor's targets is essential to understanding the role that factors play in disease biology. However, due to a high false positive rate, identifying coherent functional target sets is difficult. We have created an improved mapping of targets by integrating ChIP-Seq data with 423 functional modules derived from 9,395 human expression experiments. We identified 5,002 TF-module relationships, significantly improved TF target prediction, and found 30 high-confidence TF-TF associations, of which 14 are known. Importantly, we also connected TFs to diseases through these functional modules and identified 3,859 significant TF-disease relationships. As an example, we found a link between MEF2A and Crohn's disease, which we validated in an independent expression dataset. These results show the power of combining expression data and ChIP-Seq data to remove noise and better extract the associations between TFs, functional modules, and disease. Transcription factors (TFs) are crucial to the precise regulation of many cellular processes and thus, are responsible for many human phenotypes and diseases. Now that the ENCODE project has mapped hundreds of TFs to their genomic binding locations, extracting functional biological signals is the next step in understanding their role in disease. In this paper, we present a novel approach to identifying TF targets and use these targets to find regulatory relationships between TFs and diseases. We present a large open dataset of putative TF-TF interactions and TF-disease associations which includes known connections as well as novel ones. We validate the association of one of our novel TF-disease associations, MEF2A and Crohn's disease, suggesting that our approach generates testable disease association hypotheses. Integrating these datasets will be crucial for understanding phenotypes and complex diseases.
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Affiliation(s)
- Konrad J. Karczewski
- Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Russ B. Altman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicholas P. Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, and Department of Medicine, Columbia University, New York, New York, United States of America
- * E-mail:
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Suls A, Jaehn J, Kecskés A, Weber Y, Weckhuysen S, Craiu D, Siekierska A, Djémié T, Afrikanova T, Gormley P, von Spiczak S, Kluger G, Iliescu C, Talvik T, Talvik I, Meral C, Caglayan H, Giraldez B, Serratosa J, Lemke J, Hoffman-Zacharska D, Szczepanik E, Barisic N, Komarek V, Hjalgrim H, Møller R, Linnankivi T, Dimova P, Striano P, Zara F, Marini C, Guerrini R, Depienne C, Baulac S, Kuhlenbäumer G, Crawford A, Lehesjoki AE, de Witte P, Palotie A, Lerche H, Esguerra C, De Jonghe P, Helbig I. De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy sharing features with Dravet syndrome. Am J Hum Genet 2013; 93:967-75. [PMID: 24207121 PMCID: PMC3824114 DOI: 10.1016/j.ajhg.2013.09.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/28/2013] [Accepted: 09/30/2013] [Indexed: 11/18/2022] Open
Abstract
Dravet syndrome is a severe epilepsy syndrome characterized by infantile onset of therapy-resistant, fever-sensitive seizures followed by cognitive decline. Mutations in SCN1A explain about 75% of cases with Dravet syndrome; 90% of these mutations arise de novo. We studied a cohort of nine Dravet-syndrome-affected individuals without an SCN1A mutation (these included some atypical cases with onset at up to 2 years of age) by using whole-exome sequencing in proband-parent trios. In two individuals, we identified a de novo loss-of-function mutation in CHD2 (encoding chromodomain helicase DNA binding protein 2). A third CHD2 mutation was identified in an epileptic proband of a second (stage 2) cohort. All three individuals with a CHD2 mutation had intellectual disability and fever-sensitive generalized seizures, as well as prominent myoclonic seizures starting in the second year of life or later. To explore the functional relevance of CHD2 haploinsufficiency in an in vivo model system, we knocked down chd2 in zebrafish by using targeted morpholino antisense oligomers. chd2-knockdown larvae exhibited altered locomotor activity, and the epileptic nature of this seizure-like behavior was confirmed by field-potential recordings that revealed epileptiform discharges similar to seizures in affected persons. Both altered locomotor activity and epileptiform discharges were absent in appropriate control larvae. Our study provides evidence that de novo loss-of-function mutations in CHD2 are a cause of epileptic encephalopathy with generalized seizures.
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Affiliation(s)
- Arvid Suls
- Neurogenetics group, Department of Molecular Genetics, VIB, 2610 Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Johanna A. Jaehn
- University Medical Center Schleswig-Holstein, Christian-Albrechts University, 24105 Kiel, Germany
| | - Angela Kecskés
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, 3000 Leuven, Belgium
| | - Yvonne Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Sarah Weckhuysen
- Neurogenetics group, Department of Molecular Genetics, VIB, 2610 Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Dana C. Craiu
- Pediatric Neurology Clinic II, Departments of Neurology, Pediatric Neurology, Psychiatry, and Neurosurgery, “Carol Davila” University of Medicine, Sector 4, 050474 Bucharest, Romania
- Pediatric Neurology Clinic, “Professor Doctor Alexandru Obregia” Clinical Hospital, Sector 4, 041914 Bucharest, Romania
| | - Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, 3000 Leuven, Belgium
| | - Tania Djémié
- Neurogenetics group, Department of Molecular Genetics, VIB, 2610 Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Tatiana Afrikanova
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, 3000 Leuven, Belgium
| | - Padhraig Gormley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sarah von Spiczak
- University Medical Center Schleswig-Holstein, Christian-Albrechts University, 24105 Kiel, Germany
| | - Gerhard Kluger
- Neuropädiatrie und Neurologische Rehabilitation, Epilepsiezentrum für Kinder und Jugendliche, Tagesklinik für Neuropädiatrie, Schön Klinik Vogtareuth, 83569 Vogtareuth, Germany
| | - Catrinel M. Iliescu
- Pediatric Neurology Clinic II, Departments of Neurology, Pediatric Neurology, Psychiatry, and Neurosurgery, “Carol Davila” University of Medicine, Sector 4, 050474 Bucharest, Romania
- Pediatric Neurology Clinic, “Professor Doctor Alexandru Obregia” Clinical Hospital, Sector 4, 041914 Bucharest, Romania
| | - Tiina Talvik
- Department of Pediatrics, University of Tartu, 51014 Tartu, Estonia
- Department of Neurology and Neurorehabilitation, Children’s Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Inga Talvik
- Department of Pediatrics, University of Tartu, 51014 Tartu, Estonia
- Department of Neurology and Neurorehabilitation, Children’s Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Cihan Meral
- Department of Pediatric Neurology, GATA Haydarpasa Teaching Hospital, 34668 Istanbul, Turkey
| | - Hande S. Caglayan
- Department of Molecular Biology and Genetics, Bogazici University, 34342 Istanbul, Turkey
| | - Beatriz G. Giraldez
- Epilepsy Unit, Hospital Universitario Fundación Jiménez Diaz and Centro De Investigación Biomédica En Red De Enfermedades Raras, 28040 Madrid, Spain
| | - José Serratosa
- Epilepsy Unit, Hospital Universitario Fundación Jiménez Diaz and Centro De Investigación Biomédica En Red De Enfermedades Raras, 28040 Madrid, Spain
| | - Johannes R. Lemke
- Division of Human Genetics, University Children’s Hospital Inselspital, 3010 Bern, Switzerland
| | | | - Elzbieta Szczepanik
- Clinic of Neurology of Child and Adolescents, Institute of Mother and Child, 01211 Warsaw, Poland
| | - Nina Barisic
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Vladimir Komarek
- Child Neurology Department, University Hospital Motol, 150 06 Praha, Czech Republic
| | - Helle Hjalgrim
- Danish Epilepsy Centre, 4293 Dianalund, Denmark
- Institute for Regional Health research, University of Southern Denmark, 5230 Odense, Denmark
| | | | - Tarja Linnankivi
- Pediatric Neurology, Children’s Hospital, University of Helsinki and Helsinki University Central Hospital, 00029 Helsinki, Finland
| | - Petia Dimova
- Clinic of Child Neurology, St. Naum University Hospital of Neurology and Psychiatry, 1113 Sofia, Bulgaria
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Departments of Neurosciences, Rehabilitation, Ophtalmology, Genetics, and Maternal and Child Health, University of Genova and Gaslini Institute, 16147 Genova, Italy
| | - Federico Zara
- Laboratory of Neurogenetics, Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Gaslini Institute, 16147 Genova, Italy
| | - Carla Marini
- Pediatric Neurology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50132 Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50132 Florence, Italy
| | - Christel Depienne
- Institut National de la Santé et de la Recherche Médicale U975, Centre de Recherche de l’Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, 75013 Paris, France
- Centre National de la Recherche Scientifique 7225, Centre de Recherche de l’Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, 75013 Paris, France
- Département de Génétique et de Cytogénétique, Unité Fonctionnelle de Neurogénétique Moléculaire et Cellulaire, Hôpital Pitié-Salpêtrière, Assistance Publique – Hôpitaux de Paris, 75013 Paris, France
| | - Stéphanie Baulac
- Institut National de la Santé et de la Recherche Médicale U975, Centre de Recherche de l’Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, 75013 Paris, France
- Centre National de la Recherche Scientifique 7225, Centre de Recherche de l’Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, 75013 Paris, France
- Université Pierre et Marie Curie (Paris VI), UMR_S 975, 75013 Paris, France
| | - Gregor Kuhlenbäumer
- Department of Neurology, Institute of Experimental Medicine, Christian-Albrechts University of Kiel, 24105 Kiel, Germany
| | - Alexander D. Crawford
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, 3000 Leuven, Belgium
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
- Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland
| | - Peter A.M. de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, 3000 Leuven, Belgium
| | - Aarno Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Camila V. Esguerra
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, 3000 Leuven, Belgium
| | - Peter De Jonghe
- Neurogenetics group, Department of Molecular Genetics, VIB, 2610 Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Ingo Helbig
- University Medical Center Schleswig-Holstein, Christian-Albrechts University, 24105 Kiel, Germany
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Zhang Y, Yang L, Lin Y, Rong Z, Liu X, Li D. SPATA12 and its possible role in DNA damage induced by ultraviolet-C. PLoS One 2013; 8:e78201. [PMID: 24205157 PMCID: PMC3799742 DOI: 10.1371/journal.pone.0078201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 09/10/2013] [Indexed: 02/03/2023] Open
Abstract
Our previous studies indicated that SPATA12, a novel spermatogenesis-associated gene, might be an inhibitor involved in spermatogenesis and tumorigenesis. To obtain a better understanding of the functions of SPATA12, a yeast two-hybrid screening system was used to search for interacting proteins, and chromodomain helicase DNA binding protein 2 (CHD2) was successfully identified. Bimolecular fluorescence complementation (BiFC) and subcellular co-localization assays further suggested a possible interaction between SPATA12 and CHD2 in the nuclei. CHD2 is known to be involved in the later stage of the DNA damage response pathway by influencing the transcriptional activity of p53. Thus, our hypothesis is that SPATA12 might play a role in DNA damage signaling. Western blotting results showed that SPATA12 expression could be induced in ultraviolet-C (UV-C) irradiated cells. Through reporter gene assays and the activator protein-1 (AP-1) decoy oligodeoxynucleotide method, we demonstrated that SPATA12 promoter activity could be up-regulated in response to UV-C radiation exposure and an AP-1 binding site in the SPATA12 promoter may have a role in transcriptional regulation of SPATA12. Using colony formation and host cell reactivation assays, it was demonstrated that SPATA12 might lead to inhibition of cellular proliferation in UV-C-irradiated DNA damage. Furthermore, SPATA12 was transfected into H1299, MCF-7 and HeLa cells, and flow cytometry (FCM) results suggested that there are some biological association between SPATA12 and p53 in UV-C-irradiated DNA damage. In addition, we investigated whether SPATA12 could up-regulate the expression of p53. Taken together, these findings indicate that SPATA12 could be induced under UV-C stress. During DNA damage process, AP-1 involves in the transcriptional up-regulation of SPATA12 in response to UV-C radiation and p53 involves in growth inhibitory effects of SPATA12 on UV-C irradiated cells.
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Affiliation(s)
- Yunsheng Zhang
- Department of Life Science, College of Biology, Hunan University, Changsha, P. R. China
| | - Lifang Yang
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, P. R. China
| | - Yiting Lin
- Department of Life Science, College of Biology, Hunan University, Changsha, P. R. China
| | - Zhuoxian Rong
- Department of Life Science, College of Biology, Hunan University, Changsha, P. R. China
| | - Xiaowen Liu
- Department of Life Science, College of Biology, Hunan University, Changsha, P. R. China
| | - Dan Li
- Department of Life Science, College of Biology, Hunan University, Changsha, P. R. China
- * E-mail:
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Keil KP, Altmann HM, Mehta V, Abler LL, Elton EA, Vezina CM. Catalog of mRNA expression patterns for DNA methylating and demethylating genes in developing mouse lower urinary tract. Gene Expr Patterns 2013; 13:413-24. [PMID: 23920106 DOI: 10.1016/j.gep.2013.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/07/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
The mouse prostate develops from a component of the lower urinary tract (LUT) known as the urogenital sinus (UGS). This process requires androgens and signaling between mesenchyme and epithelium. Little is known about DNA methylation during prostate development, including which factors are expressed, whether their expression changes over time, and if DNA methylation contributes to androgen signaling or influences signaling between mesenchyme and epithelium. We used in situ hybridization to evaluate the spatial and temporal expression pattern of mRNAs which encode proteins responsible for establishing, maintaining or remodeling DNA methylation. These include DNA methyltransferases, DNA deaminases, DNA glycosylases, base excision repair and mismatch repair pathway members. The mRNA expression patterns were compared between male and female LUT prior to prostatic bud formation (14.5 days post coitus (dpc)), during prostatic bud formation (17.5 dpc) and during prostatic branching morphogenesis (postnatal day (P) 5). We found dramatic changes in the patterns of these mRNAs over the course of prostate development and identified examples of sexually dimorphic mRNA expression. Future investigation into how DNA methylation patterns are established, maintained and remodeled during the course of embryonic prostatic bud formation may provide insight into prostate morphogenesis and disease.
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Affiliation(s)
- Kimberly P Keil
- Department of Comparative Biosciences, University of Wisconsin-Madison, 1656 Linden Dr., Madison, WI 53706, USA
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Watanabe A, Yamada Y, Yamanaka S. Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120292. [PMID: 23166402 DOI: 10.1098/rstb.2012.0292] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The differentiation and reprogramming of cells are accompanied by drastic changes in the epigenetic profiles of cells. Waddington's classical model clearly describes how differentiating cells acquire their cell identity as the developmental potential of an individual cell population declines towards the terminally differentiated state. The recent discovery of induced pluripotent stem cells as well as of somatic cell nuclear transfer provided evidence that the process of differentiation can be reversed. The identity of somatic cells is strictly protected by an epigenetic barrier, and these cells acquire pluripotency by breaking the epigenetic barrier by reprogramming factors such as Oct3/4, Sox2, Klf4, Myc and LIN28. This review covers the current understanding of the spatio-temporal regulation of epigenetics in pluripotent and differentiated cells, and discusses how cells determine their identity and overcome the epigenetic barrier during the reprogramming process.
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Affiliation(s)
- Akira Watanabe
- Center for iPS Cell Research and Application, Kyoto University
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Gene expression and epigenetic deregulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 792:133-50. [PMID: 24014295 DOI: 10.1007/978-1-4614-8051-8_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The last decade resulted in many scientific discoveries illuminating epigenetic mechanisms of gene regulation and genome organization. DNA methylation emerged as playing a pivotal role in development and cancer. Genome-wide changes in DNA methylation, including hypermethylation of tumor suppressor genes and genome-wide loss of methylation, are two dominant mechanisms that deregulate gene expression and contribute to chromosomal instability. In this chapter we give an overview of how methylation patterns are established during B-cell development and what machinery is necessary to maintain those patterns. We summarize the current state of knowledge of aberrant changes taking place during and contributing to lymphoid transformation in general and to the development of CLL in particular. We discuss key deregulated biomarkers extensively studied using single-gene approaches and give an overview of a wealth of data that became available from genome-wide approaches, focusing on pathways that are critical for lymphomagenesis. We also highlight epigenetic differences between known prognostic groups of CLL.
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Harada A, Okada S, Konno D, Odawara J, Yoshimi T, Yoshimura S, Kumamaru H, Saiwai H, Tsubota T, Kurumizaka H, Akashi K, Tachibana T, Imbalzano AN, Ohkawa Y. Chd2 interacts with H3.3 to determine myogenic cell fate. EMBO J 2012; 31:2994-3007. [PMID: 22569126 DOI: 10.1038/emboj.2012.136] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 04/18/2012] [Indexed: 11/09/2022] Open
Abstract
Cell differentiation is mediated by lineage-determining transcription factors. We show that chromodomain helicase DNA-binding domain 2 (Chd2), a SNF2 chromatin remodelling enzyme family member, interacts with MyoD and myogenic gene regulatory sequences to specifically mark these loci via deposition of the histone variant H3.3 prior to cell differentiation. Directed and genome-wide analysis of endogenous H3.3 incorporation demonstrates that knockdown of Chd2 prevents H3.3 deposition at differentiation-dependent, but not housekeeping, genes and inhibits myogenic gene activation. The data indicate that MyoD determines cell fate and facilitates differentiation-dependent gene expression through Chd2-dependent deposition of H3.3 at myogenic loci prior to differentiation.
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Affiliation(s)
- Akihito Harada
- Department of Advanced Medical Initiatives, JST-CREST, Faculty of Medicine, Kyushu University, Fukuoka, Japan
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Brockschmidt A, Chung B, Weber S, Fischer DC, Kolatsi-Joannou M, Christ L, Heimbach A, Shtiza D, Klaus G, Simonetti GD, Konrad M, Winyard P, Haffner D, Schaefer F, Weber RG. CHD1L: a new candidate gene for congenital anomalies of the kidneys and urinary tract (CAKUT). Nephrol Dial Transplant 2011; 27:2355-64. [PMID: 22146311 DOI: 10.1093/ndt/gfr649] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Recently, we identified a microduplication in chromosomal band 1q21.1 encompassing the CHD1L/ALC1 gene encoding a chromatin-remodelling enzyme in congenital anomalies of the kidneys and urinary tract (CAKUT) patient. METHODS To explore the role of CHD1L in CAKUT, we screened 85 CAKUT patients for mutations in the CHD1L gene and performed functional analyses of the three heterozygous missense variants detected. In addition, we quantitatively determined CHD1L expression in multiple human fetal and adult tissues and analysed expression of CHD1L protein in human embryonal, adult and hydronephrotic kidney sections. RESULTS Two of three novel heterozygous missense variants identified in three patients were not found in >400 control chromosomes. All variants lead to amino acid substitutions in or near the CHD1L macro domain, a poly-ADP-ribose (PAR)-binding module interacting with PAR polymerase 1 (PARP1), and showed decreased interaction with PARP1 by pull-down assay of transfected cell lysates. Quantitative messenger RNA analysis demonstrated high CHD1L expression in human fetal kidneys, and levels were four times higher than in adult kidneys. In the human embryo at 7-11 weeks gestation, CHD1L immunolocalized in the early ureteric bud and the S- and comma-shaped bodies, critical stages of kidney development. In normal postnatal sections, CHD1L was expressed in the cytoplasm of tubular cells in all tubule segments. CHD1L expression appeared higher in the hydronephrotic kidney of one patient with a hypofunctional CHD1L variant than in normal kidneys, recapitulating high fetal levels. CONCLUSION Our data suggest that CHD1L plays a role in kidney development and may be a new candidate gene for CAKUT.
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Affiliation(s)
- Antje Brockschmidt
- Institute of Human Genetics, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
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Jacobs-McDaniels NL, Albertson RC. Chd7 plays a critical role in controlling left-right symmetry during zebrafish somitogenesis. Dev Dyn 2011; 240:2272-80. [PMID: 21901784 DOI: 10.1002/dvdy.22722] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2011] [Indexed: 01/18/2023] Open
Abstract
Somitogenesis is a complex process during early vertebrate development involving interactions between many factors to form a bilateral somite series. A role for chromatin remodelers in somitogenesis has not yet been demonstrated. Here, we investigate the function of chromodomain helicase DNA binding protein 7 (chd7) during zebrafish somitogenesis. We show that Chd7 deficiency leads to asymmetric segmentation of the presomitic mesoderm (PSM), as revealed by expression of the somitogenesis genes, cdx1a, dlc, her7, mespa, and ripply1. Moreover, we show that abrogation of Chd7 results in the loss of asymmetric expression of spaw in the lateral plate mesoderm, which is consistent with more general laterality defects. Based on the observation that insufficient Chd7 leads to left-right asymmetry defects during PSM segmentation, and because CHD7 has been linked to human spinal deformities, we suggest that zebrafish chd7 morphants may be a good in vivo model to examine the pathophysiology of these diseases.
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