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van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 DOI: 10.1042/bst20230770] [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: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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2
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The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1. Sci Rep 2022; 12:22425. [PMID: 36575212 PMCID: PMC9794786 DOI: 10.1038/s41598-022-23614-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/02/2022] [Indexed: 12/28/2022] Open
Abstract
The chromodomain helicase DNA-binding protein CHD8 is the most frequently mutated gene in autism spectrum disorder. Despite its prominent disease involvement, little is known about its molecular function in the human brain. CHD8 is a chromatin regulator which binds to the promoters of actively transcribed genes through genomic targeting mechanisms which have yet to be fully defined. By generating a conditional loss-of-function and an endogenously tagged allele in human pluripotent stem cells, we investigated the molecular function and the interaction of CHD8 with chromatin in human neurons. Chromatin accessibility analysis and transcriptional profiling revealed that CHD8 functions as a transcriptional activator at its target genes in human neurons. Furthermore, we found that CHD8 chromatin targeting is cell context-dependent. In human neurons, CHD8 preferentially binds at ETS motif-enriched promoters. This enrichment is particularly prominent on the promoters of genes whose expression significantly changes upon the loss of CHD8. Indeed, among the ETS transcription factors, we identified ELK1 as being most highly correlated with CHD8 expression in primary human fetal and adult cortical neurons and most highly expressed in our stem cell-derived neurons. Remarkably, ELK1 was necessary to recruit CHD8 specifically to ETS motif-containing sites. These findings imply that ELK1 and CHD8 functionally cooperate to regulate gene expression and chromatin states at MAPK/ERK target genes in human neurons. Our results suggest that the MAPK/ERK/ELK1 axis potentially contributes to the pathogenesis caused by CHD8 mutations in human neurodevelopmental disorders.
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3
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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4
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Zhang Y, Wang J, Liu X, Liu H. Exploring the role of RALYL in Alzheimer's disease reserve by network-based approaches. Alzheimers Res Ther 2020; 12:165. [PMID: 33298176 PMCID: PMC7724892 DOI: 10.1186/s13195-020-00733-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/23/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) reserve theory is based on specific individual characteristics that are associated with a higher resilience against neurodegeneration and its symptoms. A given degree of AD pathology may contribute to varying cognitive decline levels in different individuals. Although this phenomenon is attributed to reserve, the biological mechanisms that underpin it remain elusive, which restricts translational medicine research and treatment strategy development. METHODS Network-based approaches were integrated to identify AD reserve related genes. Then, AD brain transcriptomics data were clustered into co-expression modules, and a Bayesian network was developed using these modules plus AD reserve related phenotypes. The directed acyclic graph suggested that the module was strongly associated with AD reserve. The hub gene of the module of interest was filtered using the topological method. Validation was performed in the multi-AD brain transcriptomic dataset. RESULTS We revealed that the RALYL (RALY RNA Binding Protein-like) is the hub gene of the module which was highly associated with AD reserve related phenotypes. Pseudo-time projections of RALYL revealed the changes in relative expression drivers in the AD and control subjects over pseudo-time had distinct transcriptional states. Notably, the expression of RALYL decreased with the gradual progression of AD, and this corresponded to MMSE decline. Subjects with AD reserve exhibited significantly higher RALYL expression than those without AD reserve. CONCLUSION The present study suggests that RALYL may be associated with AD reserve, and it provides novel insights into the mechanisms of AD reserve and highlights the potential role of RALYL in this process.
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Affiliation(s)
- Yixuan Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
| | - Jiali Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
| | - Xiaoquan Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
| | - Haochen Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009 People’s Republic of China
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5
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Huning L, Kunkel GR. The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure. Gene 2020; 769:145205. [PMID: 33031894 DOI: 10.1016/j.gene.2020.145205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Zinc Finger Protein 143 (ZNF143) is a pervasive C2H2 zinc-finger transcriptional activator protein regulating the efficiency of eukaryotic promoter regions. ZNF143 is able to activate transcription at both protein coding genes and small RNA genes transcribed by either RNA polymerase II or RNA polymerase III. Target genes regulated by ZNF143 are involved in an array of different cellular processes including both cancer and development. Although a key player in regulating eukaryotic genes, the molecular mechanism by with ZNF143 binds and activates genes transcribed by two different polymerases is still relatively unknown. In addition to its role as a transcriptional regulator, recent genomics experiments have implicated ZNF143 as a potential co-factor involved in chromatin looping and establishing higher order structure within the genome. This review focuses primarily on possible activation mechanisms of promoters by ZNF143, with less emphasis on the role of ZNF143 in cancer and development, and its function in establishing higher order chromatin contacts within the genome.
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Affiliation(s)
- Laura Huning
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Gary R Kunkel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette's Disorder and Autism. Biol Psychiatry 2020; 87:1035-1044. [PMID: 31771860 PMCID: PMC7160031 DOI: 10.1016/j.biopsych.2019.09.029] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 08/01/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Obsessive-compulsive disorder (OCD) is a debilitating neuropsychiatric disorder with a genetic risk component, yet identification of high-confidence risk genes has been challenging. In recent years, risk gene discovery in other complex psychiatric disorders has been achieved by studying rare de novo (DN) coding variants. METHODS We performed whole-exome sequencing in 222 OCD parent-child trios (184 trios after quality control), comparing DN variant frequencies with 777 previously sequenced unaffected trios. We estimated the contribution of DN mutations to OCD risk and the number of genes involved. Finally, we looked for gene enrichment in other datasets and canonical pathways. RESULTS DN likely gene disrupting and predicted damaging missense variants are enriched in OCD probands (rate ratio, 1.52; p = .0005) and contribute to risk. We identified 2 high-confidence risk genes, each containing 2 DN damaging variants in unrelated probands: CHD8 and SCUBE1. We estimate that 34% of DN damaging variants in OCD contribute to risk and that DN damaging variants in approximately 335 genes contribute to risk in 22% of OCD cases. Furthermore, genes harboring DN damaging variants in OCD are enriched for those reported in neurodevelopmental disorders, particularly Tourette's disorder and autism spectrum disorder. An exploratory network analysis reveals significant functional connectivity and enrichment in canonical pathways, biological processes, and disease networks. CONCLUSIONS Our findings show a pathway toward systematic gene discovery in OCD via identification of DN damaging variants. Sequencing larger cohorts of OCD parent-child trios will reveal more OCD risk genes and will provide needed insights into underlying disease biology.
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Ibn-Salem J, Andrade-Navarro MA. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. BMC Genomics 2019; 20:777. [PMID: 31653198 PMCID: PMC6814980 DOI: 10.1186/s12864-019-6088-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. RESULTS While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training. CONCLUSION 7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC .
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Affiliation(s)
- Jonas Ibn-Salem
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128, Mainz, Germany.
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8
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Suetterlin P, Hurley S, Mohan C, Riegman KLH, Pagani M, Caruso A, Ellegood J, Galbusera A, Crespo-Enriquez I, Michetti C, Yee Y, Ellingford R, Brock O, Delogu A, Francis-West P, Lerch JP, Scattoni ML, Gozzi A, Fernandes C, Basson MA. Altered Neocortical Gene Expression, Brain Overgrowth and Functional Over-Connectivity in Chd8 Haploinsufficient Mice. Cereb Cortex 2019; 28:2192-2206. [PMID: 29668850 PMCID: PMC6018918 DOI: 10.1093/cercor/bhy058] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 12/13/2022] Open
Abstract
Truncating CHD8 mutations are amongst the highest confidence risk factors for autism spectrum disorder (ASD) identified to date. Here, we report that Chd8 heterozygous mice display increased brain size, motor delay, hypertelorism, pronounced hypoactivity, and anomalous responses to social stimuli. Whereas gene expression in the neocortex is only mildly affected at midgestation, over 600 genes are differentially expressed in the early postnatal neocortex. Genes involved in cell adhesion and axon guidance are particularly prominent amongst the downregulated transcripts. Resting-state functional MRI identified increased synchronized activity in cortico-hippocampal and auditory-parietal networks in Chd8 heterozygous mutant mice, implicating altered connectivity as a potential mechanism underlying the behavioral phenotypes. Together, these data suggest that altered brain growth and diminished expression of important neurodevelopmental genes that regulate long-range brain wiring are followed by distinctive anomalies in functional brain connectivity in Chd8+/- mice. Human imaging studies have reported altered functional connectivity in ASD patients, with long-range under-connectivity seemingly more frequent. Our data suggest that CHD8 haploinsufficiency represents a specific subtype of ASD where neuropsychiatric symptoms are underpinned by long-range over-connectivity.
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Affiliation(s)
- Philipp Suetterlin
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Shaun Hurley
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Conor Mohan
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Kimberley L H Riegman
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Marco Pagani
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems @ UniTn, 38068 Rovereto, TN, Italy
| | - Angela Caruso
- Research Coordination and Support Service, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Jacob Ellegood
- Department of Medical Biophysics, University of Toronto, Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada M5T 3H7
| | - Alberto Galbusera
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems @ UniTn, 38068 Rovereto, TN, Italy
| | - Ivan Crespo-Enriquez
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Caterina Michetti
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, 16132 Genova, Italy
| | - Yohan Yee
- Department of Medical Biophysics, University of Toronto, Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada M5T 3H7
| | - Robert Ellingford
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Olivier Brock
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9NU, UK
| | - Alessio Delogu
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9NU, UK
| | - Philippa Francis-West
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Jason P Lerch
- Department of Medical Biophysics, University of Toronto, Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada M5T 3H7
| | - Maria Luisa Scattoni
- Research Coordination and Support Service, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Alessandro Gozzi
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems @ UniTn, 38068 Rovereto, TN, Italy
| | - Cathy Fernandes
- MRC Social, Genetic & Developmental Psychiatry Centre, PO82, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London SE5 8AF, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
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9
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Wade AA, Lim K, Catta-Preta R, Nord AS. Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency. Front Mol Neurosci 2019; 11:481. [PMID: 30692911 PMCID: PMC6339895 DOI: 10.3389/fnmol.2018.00481] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/11/2018] [Indexed: 01/26/2023] Open
Abstract
The packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Case sequencing studies have revealed mutations to proteins that regulate chromatin state, known as chromatin remodeling factors, with causal roles in neurodevelopmental disorders. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor with among the highest de novo loss-of-function mutation rates in patients with autism spectrum disorder (ASD). However, mechanisms associated with CHD8 pathology have yet to be elucidated. We analyzed published transcriptomic data across CHD8 in vitro and in vivo knockdown and knockout models and CHD8 binding across published ChIP-seq datasets to identify convergent mechanisms of gene regulation by CHD8. Differentially expressed genes (DEGs) across models varied, but overlap was observed between downregulated genes involved in neuronal development and function, cell cycle, chromatin dynamics, and RNA processing, and between upregulated genes involved in metabolism and immune response. Considering the variability in transcriptional changes and the cells and tissues represented across ChIP-seq analysis, we found a surprisingly consistent set of high-affinity CHD8 genomic interactions. CHD8 was enriched near promoters of genes involved in basic cell functions and gene regulation. Overlap between high-affinity CHD8 targets and DEGs shows that reduced dosage of CHD8 directly relates to decreased expression of cell cycle, chromatin organization, and RNA processing genes, but only in a subset of studies. This meta-analysis verifies CHD8 as a master regulator of gene expression and reveals a consistent set of high-affinity CHD8 targets across human, mouse, and rat in vivo and in vitro studies. These conserved regulatory targets include many genes that are also implicated in ASD. Our findings suggest a model where perturbation to dosage-sensitive CHD8 genomic interactions with a highly-conserved set of regulatory targets leads to model-specific downstream transcriptional impacts.
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Affiliation(s)
- A Ayanna Wade
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, United States.,Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA, United States
| | - Kenneth Lim
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, United States.,Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA, United States
| | - Rinaldo Catta-Preta
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, United States.,Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA, United States
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, United States.,Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA, United States
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10
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Guiro J, Murphy S. Regulation of expression of human RNA polymerase II-transcribed snRNA genes. Open Biol 2018; 7:rsob.170073. [PMID: 28615474 PMCID: PMC5493778 DOI: 10.1098/rsob.170073] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3′ end formation of the transcripts.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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11
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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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12
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Patra P, Izawa T, Pena-Castillo L. REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1270-1283. [PMID: 27019499 DOI: 10.1109/tcbb.2015.2453948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pathway analysis has been extensively applied to aid in the interpretation of the results of genome-wide transcription profiling studies, and has been shown to successfully find associations between the biological phenomena under study and biological pathways. There are two widely used approaches of pathway analysis: over-representation analysis, and gene set analysis. Recently genome-wide transcription factor binding data has become widely available allowing for the application of pathway analysis to this type of data. In this work, we developed regulatory enrichment pathway analysis (REPA) to apply gene set analysis to genome-wide transcription factor binding data to infer associations between transcription factors and biological pathways. We used the transcription factor binding data generated by the ENCODE project, and gene sets from the Molecular Signatures and KEGG databases. Our results showed that 54 percent of the predictions examined have literature support and that REPA's recall is roughly 54 percent. This level of precision is promising as several of REPA's predictions are expected to be novel and can be used to guide new research avenues. In addition, the results of our case studies showed that REPA enhances the interpretation of genome-wide transcription profiling studies by suggesting putative regulators behind the observed transcriptional responses.
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13
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Gao Z, Herrera-Carrillo E, Berkhout B. RNA Polymerase II Activity of Type 3 Pol III Promoters. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:135-145. [PMID: 30195753 PMCID: PMC6023835 DOI: 10.1016/j.omtn.2018.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022]
Abstract
In eukaryotes, three RNA polymerases (Pol I, II, and III) are responsible for the transcription of distinct subsets of genes. Gene-external type 3 Pol III promoters use defined transcription start and termination sites, and they are, therefore, widely used for small RNA expression, including short hairpin RNAs in RNAi applications and guide RNAs in CRISPR-Cas systems. We report that all three commonly used human Pol III promoters (7SK, U6, and H1) mediate luciferase reporter gene expression, which indicates Pol II activity, but to a different extent (H1 ≫ U6 > 7SK). We demonstrate that these promoters can recruit Pol II for transcribing extended messenger transcripts. Intriguingly, selective inhibition of Pol II stimulates the Pol III activity and vice versa, suggesting that two polymerase complexes compete for promoter usage. Pol II initiates transcription at the regular Pol III start site on the 7SK and U6 promoters, but Pol II transcription on the most active H1 promoter starts 8 nt upstream of the Pol III start site. This study provides functional evidence for the close relationship of Pol II and Pol III transcription. These mechanistic insights are important for optimal use of Pol III promoters, and they offer additional flexibility for biotechnology applications of these genetic elements.
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Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
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14
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Didychuk AL, Butcher SE, Brow DA. The life of U6 small nuclear RNA, from cradle to grave. RNA (NEW YORK, N.Y.) 2018; 24:437-460. [PMID: 29367453 PMCID: PMC5855946 DOI: 10.1261/rna.065136.117] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Removal of introns from precursor messenger RNA (pre-mRNA) and some noncoding transcripts is an essential step in eukaryotic gene expression. In the nucleus, this process of RNA splicing is carried out by the spliceosome, a multi-megaDalton macromolecular machine whose core components are conserved from yeast to humans. In addition to many proteins, the spliceosome contains five uridine-rich small nuclear RNAs (snRNAs) that undergo an elaborate series of conformational changes to correctly recognize the splice sites and catalyze intron removal. Decades of biochemical and genetic data, along with recent cryo-EM structures, unequivocally demonstrate that U6 snRNA forms much of the catalytic core of the spliceosome and is highly dynamic, interacting with three snRNAs, the pre-mRNA substrate, and >25 protein partners throughout the splicing cycle. This review summarizes the current state of knowledge on how U6 snRNA is synthesized, modified, incorporated into snRNPs and spliceosomes, recycled, and degraded.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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15
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Kunkel GR, Tracy JA, Jalufka FL, Lekven AC. CHD8short, a naturally-occurring truncated form of a chromatin remodeler lacking the helicase domain, is a potent transcriptional coregulator. Gene 2018; 641:303-309. [DOI: 10.1016/j.gene.2017.10.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/02/2017] [Accepted: 10/20/2017] [Indexed: 12/27/2022]
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16
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Hong S, Kim D. Computational characterization of chromatin domain boundary-associated genomic elements. Nucleic Acids Res 2017; 45:10403-10414. [PMID: 28977568 PMCID: PMC5737353 DOI: 10.1093/nar/gkx738] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/14/2017] [Indexed: 02/06/2023] Open
Abstract
Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region. We found that consensus CTCF-binding sites were strongly associated with TAD boundaries as well as with the transcription factors (TFs) Zinc finger protein (ZNF)143 and Yin Yang (YY)1. TAD boundary-associated genomic elements include DNase I-hypersensitive sites, H3K36 trimethylation, TSSs, RNA polymerase II, and TFs such as Specificity protein 1, ZNF274 and SIX homeobox 5. Computational modeling with these genomic elements suggests that they have distinct roles in TAD boundary formation. We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation.
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Affiliation(s)
- Seungpyo Hong
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
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17
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Gonzalez D, Luyten A, Bartholdy B, Zhou Q, Kardosova M, Ebralidze A, Swanson KD, Radomska HS, Zhang P, Kobayashi SS, Welner RS, Levantini E, Steidl U, Chong G, Collombet S, Choi MH, Friedman AD, Scott LM, Alberich-Jorda M, Tenen DG. ZNF143 protein is an important regulator of the myeloid transcription factor C/EBPα. J Biol Chem 2017; 292:18924-18936. [PMID: 28900037 DOI: 10.1074/jbc.m117.811109] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 12/21/2022] Open
Abstract
The transcription factor C/EBPα is essential for myeloid differentiation and is frequently dysregulated in acute myeloid leukemia. Although studied extensively, the precise regulation of its gene by upstream factors has remained largely elusive. Here, we investigated its transcriptional activation during myeloid differentiation. We identified an evolutionarily conserved octameric sequence, CCCAGCAG, ∼100 bases upstream of the CEBPA transcription start site, and demonstrated through mutational analysis that this sequence is crucial for C/EBPα expression. This sequence is present in the genes encoding C/EBPα in humans, rodents, chickens, and frogs and is also present in the promoters of other C/EBP family members. We identified that ZNF143, the human homolog of the Xenopus transcriptional activator STAF, specifically binds to this 8-bp sequence to activate C/EBPα expression in myeloid cells through a mechanism that is distinct from that observed in liver cells and adipocytes. Altogether, our data suggest that ZNF143 plays an important role in the expression of C/EBPα in myeloid cells.
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Affiliation(s)
- David Gonzalez
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore.,the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Annouck Luyten
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore
| | - Boris Bartholdy
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Qiling Zhou
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore
| | - Miroslava Kardosova
- the Institute of Molecular Genetics of the ASCR, Prague 142 20, Czech Republic.,the Childhood Leukaemia Investigation Prague, Second Faculty of Medicine Charles University, University Hospital Motol, Prague 150 06, Czech Republic
| | - Alex Ebralidze
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Kenneth D Swanson
- the Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Hanna S Radomska
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115.,The Ohio State University, Comprehensive Cancer Center, Columbus, Ohio 43210, and
| | - Pu Zhang
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Susumu S Kobayashi
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115.,the Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Robert S Welner
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115.,the Hematology/Oncology Department, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Elena Levantini
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115.,the Institute of Biomedical Technologies, National Research Council, 56124 Pisa, Italy
| | - Ulrich Steidl
- the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115.,the Department of Cell Biology, and Department of Medicine (Oncology), Albert Einstein College of Medicine, New York, New York 10461
| | - Gilbert Chong
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore
| | - Samuel Collombet
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore
| | - Min Hee Choi
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore
| | | | - Linda M Scott
- the The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Meritxell Alberich-Jorda
- the Institute of Molecular Genetics of the ASCR, Prague 142 20, Czech Republic, .,the Childhood Leukaemia Investigation Prague, Second Faculty of Medicine Charles University, University Hospital Motol, Prague 150 06, Czech Republic
| | - Daniel G Tenen
- From the Cancer Science Institute, National University of Singapore, 117599 Singapore, .,the Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115
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18
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Pupavac M, Watkins D, Petrella F, Fahiminiya S, Janer A, Cheung W, Gingras AC, Pastinen T, Muenzer J, Majewski J, Shoubridge EA, Rosenblatt DS. Inborn Error of Cobalamin Metabolism Associated with the Intracellular Accumulation of Transcobalamin-Bound Cobalamin and Mutations in ZNF143, Which Codes for a Transcriptional Activator. Hum Mutat 2016; 37:976-82. [PMID: 27349184 DOI: 10.1002/humu.23037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/09/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022]
Abstract
Vitamin B12 (cobalamin, Cbl) cofactors adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) are required for the activity of the enzymes methylmalonyl-CoA mutase (MCM) and methionine synthase (MS). Inborn errors of Cbl metabolism are rare Mendelian disorders associated with hematological and neurological manifestations, and elevations of methylmalonic acid and/or homocysteine in the blood and urine. We describe a patient whose fibroblasts had decreased functional activity of MCM and MS and decreased synthesis of AdoCbl and MeCbl (3.4% and 1.0% of cellular Cbl, respectively). The defect in cultured patient fibroblasts complemented those from all known complementation groups. Patient cells accumulated transcobalamin-bound-Cbl, a complex which usually dissociates in the lysosome to release free Cbl. Whole-exome sequencing identified putative disease-causing variants c.851T>G (p.L284*) and c.1019C>T (p.T340I) in transcription factor ZNF143. Proximity biotinylation analysis confirmed the interaction between ZNF143 and HCFC1, a protein that regulates expression of the Cbl trafficking enzyme MMACHC. qRT-PCR analysis revealed low MMACHC expression levels both in patient fibroblasts, and in control fibroblasts incubated with ZNF143 siRNA.
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Affiliation(s)
- Mihaela Pupavac
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David Watkins
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Francis Petrella
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Janer
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Warren Cheung
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Sinai Health System and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Joseph Muenzer
- University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Eric A Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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19
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Barnard RA, Pomaville MB, O'Roak BJ. Mutations and Modeling of the Chromatin Remodeler CHD8 Define an Emerging Autism Etiology. Front Neurosci 2015; 9:477. [PMID: 26733790 PMCID: PMC4681771 DOI: 10.3389/fnins.2015.00477] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/26/2015] [Indexed: 12/13/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a common neurodevelopmental disorder with a strong but complex genetic component. Recent family based exome-sequencing strategies have identified recurrent de novo mutations at specific genes, providing strong evidence for ASD risk, but also highlighting the extreme genetic heterogeneity of the disorder. However, disruptions in these genes converge on key molecular pathways early in development. In particular, functional enrichment analyses have found that there is a bias toward genes involved in transcriptional regulation, such as chromatin modifiers. Here we review recent genetic, animal model, co-expression network, and functional genomics studies relating to the high confidence ASD risk gene, CHD8. CHD8, a chromatin remodeling factor, may serve as a "master regulator" of a common ASD etiology. Individuals with a CHD8 mutation show an ASD subtype that includes similar physical characteristics, such as macrocephaly and prolonged GI problems including recurrent constipation. Similarly, animal models of CHD8 disruption exhibit enlarged head circumference and reduced gut motility phenotypes. Systems biology approaches suggest CHD8 and other candidate ASD risk genes are enriched during mid-fetal development, which may represent a critical time window in ASD etiology. Transcription and CHD8 binding site profiles from cell and primary tissue models of early development indicate that CHD8 may also positively regulate other candidate ASD risk genes through both direct and indirect means. However, continued study is needed to elucidate the mechanism of regulation as well as identify which CHD8 targets are most relevant to ASD risk. Overall, these initial studies suggest the potential for common ASD etiologies and the development of personalized treatments in the future.
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Affiliation(s)
- Rebecca A Barnard
- Department of Molecular & Medical Genetics, Oregon Health & Science University Portland, OR, USA
| | - Matthew B Pomaville
- Department of Molecular & Medical Genetics, Oregon Health & Science UniversityPortland, OR, USA; Department of Biology, California State UniversityFresno, CA, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University Portland, OR, USA
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20
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Lee B, Duz MB, Sagong B, Koparir A, Lee KY, Choi JY, Seven M, Yuksel A, Kim UK, Ozen M. Revealing the function of a novel splice-site mutation of CHD7 in CHARGE syndrome. Gene 2015; 576:776-81. [PMID: 26551301 DOI: 10.1016/j.gene.2015.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/24/2015] [Accepted: 11/04/2015] [Indexed: 11/27/2022]
Abstract
Most cases of CHARGE syndrome are sporadic and autosomal dominant. CHD7 is a major causative gene of CHARGE syndrome. In this study, we screened CHD7 in two Turkish patients demonstrating symptoms of CHARGE syndrome such as coloboma, heart defect, choanal atresia, retarded growth, genital abnomalities and ear anomalies. Two mutations of CHD7 were identified including a novel splice-site mutation (c.2443-2A>G) and a previously known frameshift mutation (c.2504_2508delATCTT). We performed exon trapping analysis to determine the effect of the c.2443-2A>G mutation at the transcriptional level, and found that it caused a complete skip of exon 7 and splicing at a cryptic splice acceptor site. Our current study is the second study demonstrating an exon 7 deficit in CHD7. Results of previous studies suggest that the c.2443-2A>G mutation affects the formation of nasal tissues and the neural retina during early development, resulting in choanal atresia and coloboma, respectively. The findings of the present study will improve our understanding of the genetic causes of CHARGE syndrome.
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Affiliation(s)
- Byeonghyeon Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Mehmet Bugrahan Duz
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Asuman Koparir
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Mehmet Seven
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Adnan Yuksel
- Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea.
| | - Mustafa Ozen
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey; Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey; Department of Pathology & Immunology, Baylor College of Medicine, Michael E. DeBakey VAMC, Houston, TX, United States.
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21
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Dumay-Odelot H, Durrieu-Gaillard S, El Ayoubi L, Parrot C, Teichmann M. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription. Transcription 2015; 5:e27526. [PMID: 25764111 DOI: 10.4161/trns.27526] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcription factors and to the definition of minimal promoter sequences for human RNA polymerase III transcription.
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Affiliation(s)
- Hélène Dumay-Odelot
- a INSERM U869; University of Bordeaux; Institut Européen de Chimie et Biologie (IECB); 33607 Pessac, France
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22
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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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23
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Serruya R, Orlovetskie N, Reiner R, Dehtiar-Zilber Y, Wesolowski D, Altman S, Jarrous N. Human RNase P ribonucleoprotein is required for formation of initiation complexes of RNA polymerase III. Nucleic Acids Res 2015; 43:5442-50. [PMID: 25953854 PMCID: PMC4477669 DOI: 10.1093/nar/gkv447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 04/24/2015] [Indexed: 12/12/2022] Open
Abstract
Human RNase P is implicated in transcription of small non-coding RNA genes by RNA polymerase III (Pol III), but the precise role of this ribonucleoprotein therein remains unknown. We here show that targeted destruction of HeLa nuclear RNase P inhibits transcription of 5S rRNA genes in whole cell extracts, if this precedes the stage of initiation complex formation. Biochemical purification analyses further reveal that this ribonucleoprotein is recruited to 5S rRNA genes as a part of proficient initiation complexes and the activity persists at reinitiation. Knockdown of RNase P abolishes the assembly of initiation complexes by preventing the formation of the initiation sub-complex of Pol III. Our results demonstrate that the structural intactness, but not the endoribonucleolytic activity per se, of RNase P is critical for the function of Pol III in cells and in extracts.
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Affiliation(s)
- Raphael Serruya
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Natalie Orlovetskie
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Robert Reiner
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yana Dehtiar-Zilber
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Donna Wesolowski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Nayef Jarrous
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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24
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Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M, Reyes JC. The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PLoS Genet 2015; 11:e1005174. [PMID: 25894978 PMCID: PMC4403880 DOI: 10.1371/journal.pgen.1005174] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 03/25/2015] [Indexed: 01/01/2023] Open
Abstract
While the importance of gene enhancers in transcriptional regulation is well established, the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled. Recent studies have shown that progesterone receptor (PR) binds regions that display typical features of gene enhancers. Here, we show by ChIP-seq experiments that the chromatin remodeler CHD8 mostly binds promoters under proliferation conditions. However, upon progestin stimulation, CHD8 re-localizes to PR enhancers also enriched in p300 and H3K4me1. Consistently, CHD8 depletion severely impairs progestin-dependent gene regulation. CHD8 binding is PR-dependent but independent of the pioneering factor FOXA1. The SWI/SNF chromatin-remodelling complex is required for PR-dependent gene activation. Interestingly, we show that CHD8 interacts with the SWI/SNF complex and that depletion of BRG1 and BRM, the ATPases of SWI/SNF complex, impairs CHD8 recruitment. We also show that CHD8 is not required for H3K27 acetylation, but contributes to increase accessibility of the enhancer to DNaseI. Furthermore, CHD8 was required for RNAPII recruiting to the enhancers and for transcription of enhancer-derived RNAs (eRNAs). Taken together our data demonstrate that CHD8 is involved in late stages of PR enhancers activation. A lot of research has been devoted during the last decades to understand the mechanisms that control gene promoters activity, however, much less is known about enhancers. Only recently, the use of genome-wide chromatin immunoprecipitation techniques has revealed the existence of more than 400,000 enhancers in the human genome. We are starting to understand the importance of these regulatory elements and how they are activated or repressed. In this work we discover that the chromatin remodeler CHD8 is recruited to Progesteron Receptor-dependent enhancers upon hormone treatment. CHD8 is required for late steps in the activation of these enhancers, including transcription of the enhancers and synthesis of eRNA (long noncoding RNAs derived form the enhancers).
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Affiliation(s)
- María Ceballos-Chávez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Alicia Subtil-Rodríguez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- * E-mail: (ASR); (JCR)
| | - Eugenia G. Giannopoulou
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, New York, New York, United States of America
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, United States of America
| | - Daniel Soronellas
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elena Vázquez-Chávez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Guillermo P. Vicent
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York, United States of America
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - José C. Reyes
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- * E-mail: (ASR); (JCR)
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25
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Sadeghifar F, Böhm S, Vintermist A, Östlund Farrants AK. The B-WICH chromatin-remodelling complex regulates RNA polymerase III transcription by promoting Max-dependent c-Myc binding. Nucleic Acids Res 2015; 43:4477-90. [PMID: 25883140 PMCID: PMC4482074 DOI: 10.1093/nar/gkv312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/27/2015] [Indexed: 01/11/2023] Open
Abstract
The chromatin-remodelling complex B-WICH, comprised of William syndrome transcription factor, the ATPase SNF2h and nuclear myosin, specifically activates RNA polymerase III transcription of the 5S rRNA and 7SL genes. However, the underlying mechanism is unknown. Using high-resolution MN walking we demonstrate here that B-WICH changes the chromatin structure in the vicinity of the 5S rRNA and 7SL RNA genes during RNA polymerase III transcription. The action of B-WICH is required for the binding of the RNA polymerase machinery and the regulatory factors c-Myc at the 5S rRNA and 7SL RNA genes. In addition to the c-Myc binding site at the 5S genes, we have revealed a novel c-Myc and Max binding site in the intergenic spacer of the 5S rDNA. This region also contains a region remodelled by B-WICH. We demonstrate that c-Myc binds to both sites in a Max-dependent way, and thereby activate transcription by acetylating histone H3. The novel binding patterns of c-Myc and Max link transcription of 5S rRNA to the Myc/Max/Mxd network. Since B-WICH acts prior to c-Myc and other factors, we propose a model in which the B-WICH complex is required to maintain an open chromatin structure at these RNA polymerase III genes. This is a prerequisite for the binding of additional regulatory factors.
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Affiliation(s)
- Fatemeh Sadeghifar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Stefanie Böhm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Anna Vintermist
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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26
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Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun 2015; 6:6404. [PMID: 25752243 PMCID: PMC4355952 DOI: 10.1038/ncomms7404] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/22/2015] [Indexed: 01/09/2023] Open
Abstract
Recent studies implicate chromatin modifiers in autism spectrum disorder (ASD) through the identification of recurrent de novo loss of function mutations in affected individuals. ASD risk genes are co-expressed in human midfetal cortex, suggesting that ASD risk genes converge in specific regulatory networks during neurodevelopment. To elucidate such networks, we identify genes targeted by CHD8, a chromodomain helicase strongly associated with ASD, in human midfetal brain, human neural stem cells (hNSCs) and embryonic mouse cortex. CHD8 targets are strongly enriched for other ASD risk genes in both human and mouse neurodevelopment, and converge in ASD-associated co-expression networks in human midfetal cortex. CHD8 knockdown in hNSCs results in dysregulation of ASD risk genes directly targeted by CHD8. Integration of CHD8-binding data into ASD risk models improves detection of risk genes. These results suggest loss of CHD8 contributes to ASD by perturbing an ancient gene regulatory network during human brain development.
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Affiliation(s)
- Justin Cotney
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Rebecca A. Muhle
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Child Study Center, Yale School of Medicine, 230S. Frontage Road, New Haven, Connecticut 06519, USA
| | - Stephan J. Sanders
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Department of Psychiatry, University of California, 401 Parnassus Avenue, San Francisco, California 94143, USA
| | - Li Liu
- Department of Statistics, Carnegie Mellon University, Baker Hall 228B, Pittsburgh, Pennsylvania 15213, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Department of Psychiatry, University of California, 401 Parnassus Avenue, San Francisco, California 94143, USA
| | - Wei Niu
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Child Study Center, Yale School of Medicine, 230S. Frontage Road, New Haven, Connecticut 06519, USA
| | - Wenzhong Liu
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, Pennsylvania 15213, USA
| | - Jing Lei
- Department of Statistics, Carnegie Mellon University, Baker Hall 228B, Pittsburgh, Pennsylvania 15213, USA
| | - Jun Yin
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Andrew T. Tebbenkamp
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Candace Bichsel
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Mihovil Pletikos
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Nenad Sestan
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Baker Hall 228B, Pittsburgh, Pennsylvania 15213, USA
- Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Matthew W. State
- Department of Psychiatry, University of California, 401 Parnassus Avenue, San Francisco, California 94143, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, Pennsylvania 15213, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
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Subtil-Rodríguez A, Vázquez-Chávez E, Ceballos-Chávez M, Rodríguez-Paredes M, Martín-Subero JI, Esteller M, Reyes JC. The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes. Nucleic Acids Res 2013; 42:2185-96. [PMID: 24265227 PMCID: PMC3936757 DOI: 10.1093/nar/gkt1161] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The precise regulation of S-phase-specific genes is critical for cell proliferation. How the repressive chromatin configuration mediated by the retinoblastoma protein and repressor E2F factors changes at the G1/S transition to allow transcription activation is unclear. Here we show ChIP-on-chip studies that reveal that the chromatin remodeller CHD8 binds ∼ 2000 transcriptionally active promoters. The spectrum of CHD8 target genes was enriched in E2F-dependent genes. We found that CHD8 binds E2F-dependent promoters at the G1/S transition but not in quiescent cells. Consistently, CHD8 was required for G1/S-specific expression of these genes and for cell cycle re-entry on serum stimulation of quiescent cells. We also show that CHD8 interacts with E2F1 and, importantly, loading of E2F1 and E2F3, but not E2F4, onto S-specific promoters, requires CHD8. However, CHD8 recruiting is independent of these factors. Recruiting of MLL histone methyltransferase complexes to S-specific promoters was also severely impaired in the absence of CHD8. Furthermore, depletion of CHD8 abolished E2F1 overexpression-dependent S-phase stimulation of serum-starved cells, highlighting the essential role of CHD8 in E2F-dependent transcription activation.
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Affiliation(s)
- Alicia Subtil-Rodríguez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Av. Americo Vespucio 41092 Seville, Spain, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Spain and Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Spain
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O'Reilly D, Kuznetsova OV, Laitem C, Zaborowska J, Dienstbier M, Murphy S. Human snRNA genes use polyadenylation factors to promote efficient transcription termination. Nucleic Acids Res 2013; 42:264-75. [PMID: 24097444 PMCID: PMC3874203 DOI: 10.1093/nar/gkt892] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase II transcribes both protein coding and non-coding RNA genes and, in yeast, different mechanisms terminate transcription of the two gene types. Transcription termination of mRNA genes is intricately coupled to cleavage and polyadenylation, whereas transcription of small nucleolar (sno)/small nuclear (sn)RNA genes is terminated by the RNA-binding proteins Nrd1, Nab3 and Sen1. The existence of an Nrd1-like pathway in humans has not yet been demonstrated. Using the U1 and U2 genes as models, we show that human snRNA genes are more similar to mRNA genes than yeast snRNA genes with respect to termination. The Integrator complex substitutes for the mRNA cleavage and polyadenylation specificity factor complex to promote cleavage and couple snRNA 3′-end processing with termination. Moreover, members of the associated with Pta1 (APT) and cleavage factor I/II complexes function as transcription terminators for human snRNA genes with little, if any, role in snRNA 3′-end processing. The gene-specific factor, proximal sequence element-binding transcription factor (PTF), helps clear the U1 and U2 genes of nucleosomes, which provides an easy passage for pol II, and the negative elongation factor facilitates termination at the end of the genes where nucleosome levels increase. Thus, human snRNA genes may use chromatin structure as an additional mechanism to promote efficient transcription termination in vivo.
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Affiliation(s)
- Dawn O'Reilly
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK and CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
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29
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Epigenetic regulation of transcription by RNA polymerase III. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1015-25. [DOI: 10.1016/j.bbagrm.2013.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/11/2013] [Accepted: 05/15/2013] [Indexed: 01/11/2023]
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30
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Sawada G, Ueo H, Matsumura T, Uchi R, Ishibashi M, Mima K, Kurashige J, Takahashi Y, Akiyoshi S, Sudo T, Sugimachi K, Doki Y, Mori M, Mimori K. CHD8 is an independent prognostic indicator that regulates Wnt/β-catenin signaling and the cell cycle in gastric cancer. Oncol Rep 2013; 30:1137-42. [PMID: 23835524 DOI: 10.3892/or.2013.2597] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/25/2013] [Indexed: 01/23/2023] Open
Abstract
The chromodomain helicase DNA-binding (CHD) family comprises a class of chromatin remodeling enzymes. Previous studies suggest that CHD8 may negatively regulate various genes and signaling pathways, such as the Wnt/β‑catenin pathway. However, few studies have investigated the role of CHD8 in cancer cells. We analyzed the expression of CHD8 in cancer lesions and corresponding non-cancerous tissues to demonstrate the prognostic significance of CHD8 expression in 101 cases of gastric cancer. We also investigated the functional implications of aberrant CHD8 expression by conducting gene set enrichment analysis (GSEA). Expression of CHD8 mRNA was significantly lower in gastric cancer tissues compared to that in corresponding normal tissues (P=0.003). In multivariate analysis for overall survival, we found that CHD8 expression was an independent prognostic factor in gastric cancer. Moreover, GSEA revealed that CHD8 was significantly associated with genes involved in the Wnt/β‑catenin pathway and in the cell cycle. In addition, knockdown of CHD8 expression in the gastric cancer cell lines, MKN45 and NUGC4, promoted proliferation. In conclusion, the present study suggests that loss of CHD8 expression may be a novel indicator for biological aggressiveness in gastric cancer.
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Affiliation(s)
- Genta Sawada
- Department of Surgery, Beppu Hospital, Kyushu University, Beppu 874-0838, Japan
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31
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The dynamics of HCF-1 modulation of herpes simplex virus chromatin during initiation of infection. Viruses 2013; 5:1272-91. [PMID: 23698399 PMCID: PMC3712308 DOI: 10.3390/v5051272] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 12/30/2022] Open
Abstract
Successful infection of herpes simplex virus is dependent upon chromatin modulation by the cellular coactivator host cell factor-1 (HCF-1). This review focuses on the multiple chromatin modulation components associated with HCF-1 and the chromatin-related dynamics mediated by this coactivator that lead to the initiation of herpes simplex virus (HSV) immediate early gene expression.
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32
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Michaud J, Praz V, James Faresse N, Jnbaptiste CK, Tyagi S, Schütz F, Herr W. HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy. Genome Res 2013; 23:907-16. [PMID: 23539139 PMCID: PMC3668359 DOI: 10.1101/gr.150078.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In human transcriptional regulation, DNA-sequence-specific factors can associate with intermediaries that orchestrate interactions with a diverse set of chromatin-modifying enzymes. One such intermediary is HCFC1 (also known as HCF-1). HCFC1, first identified in herpes simplex virus transcription, has a poorly defined role in cellular transcriptional regulation. We show here that, in HeLa cells, HCFC1 is observed bound to 5400 generally active CpG-island promoters. Examination of the DNA sequences underlying the HCFC1-binding sites revealed three sequence motifs associated with the binding of (1) ZNF143 and THAP11 (also known as Ronin), (2) GABP, and (3) YY1 sequence-specific transcription factors. Subsequent analysis revealed colocalization of HCFC1 with these four transcription factors at ∼90% of the 5400 HCFC1-bound promoters. These studies suggest that a relatively small number of transcription factors play a major role in HeLa-cell transcriptional regulation in association with HCFC1.
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Affiliation(s)
- Joëlle Michaud
- Center for Integrative Genomics, University of Lausanne, Génopode, 1015 Lausanne, Switzerland
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33
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James Faresse N, Canella D, Praz V, Michaud J, Romascano D, Hernandez N. Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators. PLoS Genet 2012; 8:e1003028. [PMID: 23166507 PMCID: PMC3499247 DOI: 10.1371/journal.pgen.1003028] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 08/24/2012] [Indexed: 12/23/2022] Open
Abstract
SNAPc is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAPc-dependent promoters in human cells, we have localized genome-wide four SNAPc subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAPc and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAPc-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAPc-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo. SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and others RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find a surprisingly small number of them, some 70 promoters. Among these, the large majority is bound by either RNA polymerase II or RNA polymerase III, as expected, but one gene hitherto considered an RNA polymerase III gene is also occupied by significant levels of RNA polymerase II. Both RNA polymerase II and RNA polymerase III SNAPc-dependent promoters use a largely overlapping set of a few transcription activators, including GABP, a novel factor implicated in snRNA gene transcription.
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Affiliation(s)
- Nicole James Faresse
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Donatella Canella
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joëlle Michaud
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - David Romascano
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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34
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Shanks MO, Lund LM, Manni S, Russell M, Mauban JRH, Bond M. Chromodomain helicase binding protein 8 (Chd8) is a novel A-kinase anchoring protein expressed during rat cardiac development. PLoS One 2012; 7:e46316. [PMID: 23071553 PMCID: PMC3468582 DOI: 10.1371/journal.pone.0046316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
A-kinase anchoring proteins (AKAPs) bind the regulatory subunits of protein kinase A (PKA) and localize the holoenzyme to discrete signaling microdomains in multiple subcellular compartments. Despite emerging evidence for a nuclear pool of PKA that rapidly responds to activation of the PKA signaling cascade, only a few AKAPs have been identified that localize to the nucleus. Here we show a PKA-binding domain in the amino terminus of Chd8, and demonstrate subcellular colocalization of Chd8 with RII. RII overlay and immunoprecipitation assays demonstrate binding between Chd8-S and RIIα. Binding is abrogated upon dephosphorylation of RIIα. By immunofluorescence, we identified nuclear and perinuclear pools of Chd8 in HeLa cells and rat neonatal cardiomyocytes. We also show high levels of Chd8 mRNA in RNA extracted from post-natal rat hearts. These data add Chd8 to the short list of known nuclear AKAPs, and implicate a function for Chd8 in post-natal rat cardiac development.
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Affiliation(s)
- Maureen O. Shanks
- Department of Physiology, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Linda M. Lund
- Department of Biochemistry, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Sabrina Manni
- Department of Medicine, Clinical Immunology and Hematology Branches, University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Mary Russell
- Department of Biological Sciences, Trumbull Campus, Kent State University, Warren, Ohio, United States of America
| | - Joseph R. H. Mauban
- Department of Physiology, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - Meredith Bond
- Department of Physiology, University of Maryland Baltimore, Baltimore, Maryland, United States of America
- College of Sciences and Health Professions, Cleveland State University, Cleveland, Ohio, United States of America
- * E-mail:
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35
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Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren A, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris D, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 2012; 149:525-37. [PMID: 22521361 PMCID: PMC3340505 DOI: 10.1016/j.cell.2012.03.028] [Citation(s) in RCA: 425] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/27/2012] [Accepted: 03/28/2012] [Indexed: 01/18/2023]
Abstract
Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We sequenced BCAs in patients with autism or related NDDs, revealing disruption of 33 loci in four general categories: (1) genes previously associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, and CDKL5), (2) single-gene contributors to microdeletion syndromes (MBD5, SATB2, EHMT1, and SNURF-SNRPN), (3) novel risk loci (e.g., CHD8, KIRREL3, and ZNF507), and (4) genes associated with later-onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3). We also discovered among neurodevelopmental cases a profoundly increased burden of copy-number variants from these 33 loci and a significant enrichment of polygenic risk alleles from genome-wide association studies of autism and schizophrenia. Our findings suggest a polygenic risk model of autism and reveal that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages.
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Affiliation(s)
- Michael E. Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | | | - Ian Blumenthal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Colby Chiang
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Adrian Heilbut
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Carl Ernst
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Carrie Hanscom
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Elizabeth Rossin
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Amelia Lindgren
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
| | - Shahrin Pereira
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
| | - Douglas Ruderfer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Andrew Kirby
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Stephan Ripke
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - David Harris
- Division of Clinical Genetics, Children’s Hospital of Boston, Boston, MA
| | - Ji-Hyun Lee
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Kyungsoo Ha
- Cancer Research Center, Georgia Health Sciences University, Augusta, GA
| | - Hyung-Goo Kim
- Department of OB/GYN, IMMAG, Georgia Health Sciences University, Augusta, GA
| | - Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Andrea L. Gropman
- Department of Neurology, Children’s National Medical Center, Washington, DC, USA
- Department of Neurology, George Washington University of Health Sciences, Washington, DC, USA
| | - Diane Lucente
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Katherine Sims
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | - Toshiro K. Ohsumi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Mark L. Borowsky
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | | | - Bradley Quade
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Kasper Lage
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Pediatric Surgical Research Laboratories, MassGeneral Hospital for Children, Massachusetts General Hospital, Boston, MA, USA
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Judith Miles
- Departments of Pediatrics, Medical Genetics & Pathology, The Thompson Center for Autism & Neurodevelopmental Disorders, University of Missouri Hospitals and Clinics, Columbia, MO
| | - Bai-Lin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA
- Children’s Hospital and Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Yiping Shen
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Benjamin Neale
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Lisa G. Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA
| | - Mark J. Daly
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Autism Consortium of Boston, Boston, MA
| | - Cynthia C. Morton
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Autism Consortium of Boston, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
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36
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Halbig KM, Lekven AC, Kunkel GR. The transcriptional activator ZNF143 is essential for normal development in zebrafish. BMC Mol Biol 2012; 13:3. [PMID: 22268977 PMCID: PMC3282657 DOI: 10.1186/1471-2199-13-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/23/2012] [Indexed: 12/25/2022] Open
Abstract
Background ZNF143 is a sequence-specific DNA-binding protein that stimulates transcription of both small RNA genes by RNA polymerase II or III, or protein-coding genes by RNA polymerase II, using separable activating domains. We describe phenotypic effects following knockdown of this protein in developing Danio rerio (zebrafish) embryos by injection of morpholino antisense oligonucleotides that target znf143 mRNA. Results The loss of function phenotype is pleiotropic and includes a broad array of abnormalities including defects in heart, blood, ear and midbrain hindbrain boundary. Defects are rescued by coinjection of synthetic mRNA encoding full-length ZNF143 protein, but not by protein lacking the amino-terminal activation domains. Accordingly, expression of several marker genes is affected following knockdown, including GATA-binding protein 1 (gata1), cardiac myosin light chain 2 (cmlc2) and paired box gene 2a (pax2a). The zebrafish pax2a gene proximal promoter contains two binding sites for ZNF143, and reporter gene transcription driven by this promoter in transfected cells is activated by this protein. Conclusions Normal development of zebrafish embryos requires ZNF143. Furthermore, the pax2a gene is probably one example of many protein-coding gene targets of ZNF143 during zebrafish development.
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Affiliation(s)
- Kari M Halbig
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
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Histone H1 recruitment by CHD8 is essential for suppression of the Wnt-β-catenin signaling pathway. Mol Cell Biol 2011; 32:501-12. [PMID: 22083958 DOI: 10.1128/mcb.06409-11] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Members of the chromodomain helicase DNA-binding (CHD) family of proteins are thought to regulate gene expression. Among mammalian CHD proteins, CHD8 was originally isolated as a negative regulator of the Wnt-β-catenin signaling pathway that binds directly to β-catenin and suppresses its transactivation activity. The mechanism by which CHD8 inhibits β-catenin-dependent transcription has been unclear, however. Here we show that CHD8 promotes the association of β-catenin and histone H1, with formation of the trimeric complex on chromatin being required for inhibition of β-catenin-dependent transactivation. A CHD8 mutant that lacks the histone H1 binding domain did not show such inhibitory activity, indicating that histone H1 recruitment is essential for the inhibitory effect of CHD8. Furthermore, either depletion of histone H1 or expression of a dominant negative mutant of this protein resulted in enhancement of the response to Wnt signaling. These observations reveal a new mode of regulation of the Wnt signaling pathway by CHD8, which counteracts β-catenin function through recruitment of histone H1 to Wnt target genes. Given that CHD8 is expressed predominantly during embryogenesis, it may thus contribute to setting a threshold for responsiveness to Wnt signaling that operates in a development-dependent manner.
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Yamada K, Fukushi D, Ono T, Kondo Y, Kimura R, Nomura N, Kosaki KJ, Yamada Y, Mizuno S, Wakamatsu N. Characterization of a de novo balanced t(4;20)(q33;q12) translocation in a patient with mental retardation. Am J Med Genet A 2011; 152A:3057-67. [PMID: 21086493 DOI: 10.1002/ajmg.a.33174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
CHD6 is an ATP-dependent chromatin-remodeling enzyme, which has been implicated as a crucial component for maintaining and regulating chromatin structure. CHD6 belongs to the largest subfamily, subfamily III (CHD6-9), of the chromodomain helicase DNA (CHD-binding protein) family of enzymes (CHD1-9). Here we report on a female patient with a balanced translocation t(4;20)(q33;q12) presenting with severe mental retardation and brachydactyly of the toes. We identified the translocation breakpoint in intron 27 of CHD6 at 20q12, while the 4q33 breakpoint was intergenic. Northern blot analysis demonstrated the CHD6 mRNA in the patient's lymphoblastoid cells was decreased to ∼50% of the control cells. To investigate the cellular mechanism of diseases resulting from decreased CHD subfamily III proteins, we knocked down CHD6 or CHD7 by RNA interference in HeLa cells and analyzed chromosome alignment. The both CHD6- and CHD7-knockdown cells showed increased frequency of misaligned chromosomes on metaphase plates. Moreover, an elevated frequency of aneuploidy, the major cause of miscarriages and mental retardation, was observed in patients with CHD6 and CHD7 haploinsufficiency. These results suggest that CHD6 and CHD7 play important roles in chromatin assembly during mitosis and that mitotic delay and/or impaired cell proliferation may be associated with pathogenesis of the diseases caused by CHD6 or CHD7 mutations.
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Affiliation(s)
- Kenichiro Yamada
- Department of Genetics, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan
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Rodenberg JM, Hoggatt AM, Chen M, Touw K, Jones R, Herring BP. Regulation of serum response factor activity and smooth muscle cell apoptosis by chromodomain helicase DNA-binding protein 8. Am J Physiol Cell Physiol 2010; 299:C1058-67. [PMID: 20739623 DOI: 10.1152/ajpcell.00080.2010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Serum response factor (SRF) is a widely expressed protein that plays a key role in the regulation of smooth muscle differentiation, proliferation, migration, and apoptosis. It is generally accepted that one mechanism by which SRF regulates these diverse functions is through pathway-specific cofactor interactions. A novel SRF cofactor, chromodomain helicase DNA binding protein 8 (CHD8), was isolated from a yeast two-hybrid screen using SRF as bait. CHD8 is highly expressed in adult smooth muscle tissues. Coimmunoprecipitation assays from A10 smooth muscle cells demonstrated binding of endogenous SRF and CHD8. Data from GST-pulldown assays indicate that the NH(2)-terminus of CHD8 can interact directly with the MADS domain of SRF. Adenoviral-mediated knockdown of CHD8 in smooth muscle cells resulted in attenuated expression of SRF-dependent, smooth muscle-specific genes. Knockdown of CHD8, SRF, or CTCF, a previously described binding partner of CHD8, in A10 VSMCs also resulted in a marked induction of apoptosis. Mechanistically, apoptosis induced by CHD8 knockdown was accompanied by attenuated expression of the anti-apoptotic proteins, Birc5, and CARD10, whereas SRF knockdown attenuated expression of CARD10 and Mcl-1, but not Birc5, and CTCF knockdown attenuated expression of Birc5. These data suggest that CHD8 plays a dual role in smooth muscle cells modulating SRF activity toward differentiation genes and promoting cell survival through interactions with both SRF and CTCF to regulate expression of Birc5 and CARD10.
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Affiliation(s)
- Jennifer M Rodenberg
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5120, USA
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Batsukh T, Pieper L, Koszucka AM, von Velsen N, Hoyer-Fender S, Elbracht M, Bergman JEH, Hoefsloot LH, Pauli S. CHD8 interacts with CHD7, a protein which is mutated in CHARGE syndrome. Hum Mol Genet 2010; 19:2858-66. [PMID: 20453063 DOI: 10.1093/hmg/ddq189] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
CHARGE syndrome is an autosomal dominant disorder caused in about two-third of cases by mutations in the CHD7 gene. For other genetic diseases e.g. hereditary spastic paraplegia, it was shown that interacting partners are involved in the underlying cause of the disease. These data encouraged us to search for CHD7 binding partners by a yeast two-hybrid library screen and CHD8 was identified as an interacting partner. The result was confirmed by a direct yeast two-hybrid analysis, co-immunoprecipitation studies and by a bimolecular fluorescence complementation assay. To investigate the function of CHD7 missense mutations in the CHD7-CHD8 interacting area on the binding capacity of both proteins, we included three known missense mutations (p.His2096Arg, p.Val2102Ile and p.Gly2108Arg) and one newly identified missense mutation (p.Trp2091Arg) in the CHD7 gene and performed both direct yeast two-hybrid and co-immunoprecipitation studies. In the direct yeast two-hybrid system, the CHD7-CHD8 interaction was disrupted by the missense mutations p.Trp2091Arg, p.His2096Arg and p.Gly2108Arg, whereas in the co-immunoprecipitation studies disruption of the CHD7-CHD8 interaction by the mutations could not be observed. The results lead to the hypothesis that CHD7 and CHD8 proteins are interacting directly and indirectly via additional linker proteins. Disruption of the direct CHD7-CHD8 interaction might change the conformation of a putative large CHD7-CHD8 complex and could be a disease mechanism in CHARGE syndrome.
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Affiliation(s)
- Tserendulam Batsukh
- Institute of Human Genetics, University of Göttingen, 37073 Göttingen, Germany
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Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 2010; 17:635-40. [PMID: 20418883 PMCID: PMC3350333 DOI: 10.1038/nsmb.1794] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/25/2010] [Indexed: 12/24/2022]
Abstract
Genome-wide occupancy profiles of five components of the RNA Polymerase III (Pol III) machinery in human cells identified the expected tRNA and non-coding RNA targets and revealed many additional Pol III-associated loci, mostly near SINEs. Several genes are targets of an alternative TFIIIB containing Brf2 instead of Brf1 and have extremely low levels of TFIIIC. Strikingly, expressed Pol III genes, unlike non-expressed Pol III genes, are situated in regions with a pattern of histone modifications associated with functional Pol II promoters. TFIIIC alone associates with numerous ETC loci, via the B box or a novel motif. ETCs are often near CTCF binding sites, suggesting a potential role in chromosome organization. Our results suggest that human Pol III complexes associate preferentially with regions near functional Pol II promoters and that TFIIIC-mediated recruitment of TFIIIB is regulated in a locus-specific manner.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol 2010; 17:620-8. [PMID: 20418882 PMCID: PMC2945309 DOI: 10.1038/nsmb.1801] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 03/10/2010] [Indexed: 12/28/2022]
Abstract
RNA polymerase (Pol) III transcribes many noncoding RNAs (e.g. tRNAs) important for translational capacity and other functions. Here, we localized Pol III, alternative TFIIIB complexes (BRF1/2) and TFIIIC in HeLa cells, determining the Pol III transcriptome, defining gene classes, and revealing ‘TFIIIC-only’ sites. Pol III localization in other transformed and primary cell lines revealed novel and cell-type specific Pol III loci, and one miRNA. Surprisingly, only a fraction of the in silico-predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Remarkably, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. Taken together, active chromatin appears to gate Pol III accessibility to the genome.
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Zentner GE, Layman WS, Martin DM, Scacheri PC. Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome. Am J Med Genet A 2010; 152A:674-86. [PMID: 20186815 DOI: 10.1002/ajmg.a.33323] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CHARGE syndrome [coloboma of the eye, heart defects, atresia of the choanae, retardation of growth and/or development, genital and/or urinary abnormalities, and ear abnormalities (including deafness)] is a genetic disorder characterized by a specific and a recognizable pattern of anomalies. De novo mutations in the gene encoding chromodomain helicase DNA binding protein 7 (CHD7) are the major cause of CHARGE syndrome. Here, we review the clinical features of 379 CHARGE patients who tested positive or negative for mutations in CHD7. We found that CHARGE individuals with CHD7 mutations more commonly have ocular colobomas, temporal bone anomalies (semicircular canal hypoplasia/dysplasia), and facial nerve paralysis compared with mutation negative individuals. We also highlight recent genetic and genomic studies that have provided functional insights into CHD7 and the pathogenesis of CHARGE syndrome.
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Affiliation(s)
- Gabriel E Zentner
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
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Menon T, Yates JA, Bochar DA. Regulation of androgen-responsive transcription by the chromatin remodeling factor CHD8. Mol Endocrinol 2010; 24:1165-74. [PMID: 20308527 DOI: 10.1210/me.2009-0421] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The androgen receptor (AR) mediates the effect of androgens through its transcriptional function during both normal prostate development and in the emergence and progression of prostate cancer. AR is known to assemble coactivator complexes at target promoters to facilitate transcriptional activation in response to androgens. Here we identify the ATP-dependent chromatin remodeling factor chromodomain helicase DNA-binding protein 8 (CHD8) as a novel coregulator of androgen-responsive transcription. We demonstrate that CHD8 directly associates with AR and that CHD8 and AR simultaneously localize to the TMPRSS2 enhancer after androgen treatment. In the LNCaP cell line, reduction of CHD8 levels by small interfering RNA treatment severely diminishes androgen-dependent activation of the TMPRSS2 gene. We demonstrate that the recruitment of AR to the TMPRSS2 promoter in response to androgen treatment requires CHD8. Finally, CHD8 facilitates androgen-stimulated proliferation of LNCaP cells, emphasizing the physiological importance of CHD8. Taken together, we present evidence of a functional role for CHD8 in AR-mediated transcriptional regulation of target genes.
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Affiliation(s)
- Tushar Menon
- The Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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Regulation of HOXA2 gene expression by the ATP-dependent chromatin remodeling enzyme CHD8. FEBS Lett 2010; 584:689-93. [PMID: 20085832 DOI: 10.1016/j.febslet.2010.01.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 12/23/2009] [Accepted: 01/07/2010] [Indexed: 11/23/2022]
Abstract
Chromodomain, helicase, DNA-binding protein 8 (CHD8) is an ATP-dependent chromatin remodeling enzyme that has been demonstrated to exist within a large protein complex which includes WDR5, Ash2L, and RbBP5, members of the Mixed Lineage Leukemia (MLL) histone modifying complexes. Here we show that CHD8 relocalizes to the promoter of the MLL regulated gene HOXA2 upon gene activation. Depletion of CHD8 enhances HOXA2 expression under activating conditions. Furthermore, depletion of CHD8 results in a loss of the WDR5/Ash2L/RbBP5 subcomplex, and consequently H3K4 trimethylation, at the HOXA2 promoter. These studies suggest that CHD8 alters HOXA2 gene expression and regulates the recruitment of chromatin modifying enzymes.
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Kantidakis T, White RJ. Dr1 (NC2) is present at tRNA genes and represses their transcription in human cells. Nucleic Acids Res 2009; 38:1228-39. [PMID: 19965767 PMCID: PMC2831321 DOI: 10.1093/nar/gkp1102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dr1 (also known as NC2β) was identified as a repressor of RNA polymerase (pol) II transcription. It was subsequently shown to inhibit pol III transcription when expressed at high levels in vitro or in yeast cells. However, endogenous Dr1 was not detected at pol III-transcribed genes in growing yeast. In contrast, we demonstrate that endogenous Dr1 is present at pol III templates in human cells, as is its dimerization partner DRAP1 (also called NC2α). Expression of tRNA by pol III is selectively enhanced by RNAi-mediated depletion of endogenous human Dr1, but we found no evidence that DRAP1 influences pol III output in vivo. A stable association was detected between endogenous Dr1 and the pol III-specific transcription factor Brf1. This interaction may recruit Dr1 to pol III templates in vivo, as crosslinking to these sites increases following Brf1 induction. On the basis of these data, we conclude that the physiological functions of human Dr1 include regulation of pol III transcription.
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Affiliation(s)
- Theodoros Kantidakis
- Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
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Rodríguez-Paredes M, Ceballos-Chávez M, Esteller M, García-Domínguez M, Reyes JC. The chromatin remodeling factor CHD8 interacts with elongating RNA polymerase II and controls expression of the cyclin E2 gene. Nucleic Acids Res 2009; 37:2449-60. [PMID: 19255092 PMCID: PMC2677868 DOI: 10.1093/nar/gkp101] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
CHD8 is a chromatin remodeling ATPase of the SNF2 family. We found that depletion of CHD8 impairs cell proliferation. In order to identify CHD8 target genes, we performed a transcriptomic analysis of CHD8-depleted cells, finding out that CHD8 controls the expression of cyclin E2 (CCNE2) and thymidylate synthetase (TYMS), two genes expressed in the G1/S transition of the cell cycle. CHD8 was also able to co-activate the CCNE2 promoter in transient transfection experiments. Chromatin immunoprecipitation experiments demonstrated that CHD8 binds directly to the 5' region of both CCNE2 and TYMS genes. Interestingly, both RNA polymerase II (RNAPII) and CHD8 bind constitutively to the 5' promoter-proximal region of CCNE2, regardless of the cell-cycle phase and, therefore, of the expression of CCNE2. The tandem chromodomains of CHD8 bind in vitro specifically to histone H3 di-methylated at lysine 4. However, CHD8 depletion does not affect the methylation levels of this residue. We also show that CHD8 associates with the elongating form of RNAPII, which is phosphorylated in its carboxy-terminal domain (CTD). Furthermore, CHD8-depleted cells are hypersensitive to drugs that inhibit RNAPII phosphorylation at serine 2, suggesting that CHD8 is required for an early step of the RNAPII transcription cycle.
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Affiliation(s)
- M Rodríguez-Paredes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC, Américo Vespucio s/n, E-41092 Sevilla, Spain
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Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC. Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res 2009; 19:590-601. [PMID: 19251738 DOI: 10.1101/gr.086983.108] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CHD7 is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes. De novo mutation of the CHD7 gene is a major cause of CHARGE syndrome, a genetic disease characterized by a complex constellation of birth defects (Coloboma of the eye, Heart defects, Atresia of the choanae, severe Retardation of growth and development, Genital abnormalities, and Ear abnormalities). To gain insight into the function of CHD7, we mapped the distribution of the CHD7 protein on chromatin using the approach of chromatin immunoprecipitation on tiled microarrays (ChIP-chip). These studies were performed in human colorectal carcinoma cells, human neuroblastoma cells, and mouse embryonic stem (ES) cells before and after differentiation into neural precursor cells. The results indicate that CHD7 localizes to discrete locations along chromatin that are specific to each cell type, and that the cell-specific binding of CHD7 correlates with a subset of histone H3 methylated at lysine 4 (H3K4me). The CHD7 sites change concomitantly with H3K4me patterns during ES cell differentiation, suggesting that H3K4me is part of the epigenetic signature that defines lineage-specific association of CHD7 with specific sites on chromatin. Furthermore, the CHD7 sites are predominantly located distal to transcription start sites, most often contained within DNase hypersensitive sites, frequently conserved, and near genes expressed at relatively high levels. These features are similar to those of gene enhancer elements, raising the possibility that CHD7 functions in enhancer mediated transcription, and that the congenital anomalies in CHARGE syndrome are due to alterations in transcription of tissue-specific genes normally regulated by CHD7 during development.
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Affiliation(s)
- Michael P Schnetz
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Birch JL, Tan BCM, Panov KI, Panova TB, Andersen JS, Owen-Hughes TA, Russell J, Lee SC, Zomerdijk JCBM. FACT facilitates chromatin transcription by RNA polymerases I and III. EMBO J 2009; 28:854-65. [PMID: 19214185 PMCID: PMC2647773 DOI: 10.1038/emboj.2009.33] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 01/21/2009] [Indexed: 01/23/2023] Open
Abstract
Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle. The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III and facilitates their transcription in cells. Our findings indicate that, beyond the established role in Pol II transcription, FACT has physiological functions in chromatin transcription by all three nuclear RNA Pols. Our data also imply that local chromatin dynamics influence transcription of the active rRNA genes by Pol I and of Pol III-transcribed genes.
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Affiliation(s)
- Joanna L Birch
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, UK
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Halbig KM, Lekven AC, Kunkel GR. Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location. Gene 2008; 421:89-94. [PMID: 18619527 DOI: 10.1016/j.gene.2008.06.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/03/2008] [Accepted: 06/03/2008] [Indexed: 11/29/2022]
Abstract
Promoters for vertebrate small nuclear RNA (snRNA) genes contain a relatively simple array of transcriptional control elements, divided into proximal and distal regions. Most of these genes are transcribed by RNA polymerase II (e.g., U1, U2), whereas the U6 gene is transcribed by RNA polymerase III. Previously identified vertebrate U6 snRNA gene promoters consist of a proximal sequence element (PSE) and TATA element in the proximal region, plus a distal region with octamer (OCT) and SphI postoctamer homology (SPH) elements. We have found that zebrafish U6 snRNA promoters contain the SPH element in a novel proximal position immediately upstream of the TATA element. The zebrafish SPH element is recognized by SPH-binding factor/selenocysteine tRNA gene transcription activating factor/zinc finger protein 143 (SBF/Staf/ZNF143) in vitro. Furthermore, a zebrafish U6 promoter with a defective SPH element is inefficiently transcribed when injected into embryos.
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Affiliation(s)
- Kari M Halbig
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
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