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Vukic M, Chouaref J, Della Chiara V, Dogan S, Ratner F, Hogenboom JZM, Epp TA, Chawengsaksophak K, Vonk KKD, Breukel C, Ariyurek Y, San Leon Granado D, Kloet SL, Daxinger L. CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses. SCIENCE ADVANCES 2024; 10:eadk3384. [PMID: 38335290 PMCID: PMC10857554 DOI: 10.1126/sciadv.adk3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Disruption of cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting the deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that affected large gene clusters. In the brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3), and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Serkan Dogan
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Fallon Ratner
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Trevor A. Epp
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kallayanee Chawengsaksophak
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kelly K. D. Vonk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Cor Breukel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Susan L. Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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2
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Berger F, Muegge K, Richards EJ. Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin. Semin Cell Dev Biol 2023; 135:93-101. [PMID: 35249811 PMCID: PMC9440159 DOI: 10.1016/j.semcdb.2022.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/04/2023]
Abstract
Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA.
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3
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The Chromatin Remodeler HELLS: A New Regulator in DNA Repair, Genome Maintenance, and Cancer. Int J Mol Sci 2022; 23:ijms23169313. [PMID: 36012581 PMCID: PMC9409174 DOI: 10.3390/ijms23169313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 02/06/2023] Open
Abstract
Robust, tightly regulated DNA repair is critical to maintaining genome stability and preventing cancer. Eukaryotic DNA is packaged into chromatin, which has a profound, yet incompletely understood, regulatory influence on DNA repair and genome stability. The chromatin remodeler HELLS (helicase, lymphoid specific) has emerged as an important epigenetic regulator of DNA repair, genome stability, and multiple cancer-associated pathways. HELLS belongs to a subfamily of the conserved SNF2 ATP-dependent chromatin-remodeling complexes, which use energy from ATP hydrolysis to alter nucleosome structure and packaging of chromatin during the processes of DNA replication, transcription, and repair. The mouse homologue, LSH (lymphoid-specific helicase), plays an important role in the maintenance of heterochromatin and genome-wide DNA methylation, and is crucial in embryonic development, gametogenesis, and maturation of the immune system. Human HELLS is abundantly expressed in highly proliferating cells of the lymphoid tissue, skin, germ cells, and embryonic stem cells. Mutations in HELLS cause the human immunodeficiency syndrome ICF (Immunodeficiency, Centromeric instability, Facial anomalies). HELLS has been implicated in many types of cancer, including retinoblastoma, colorectal cancer, hepatocellular carcinoma, and glioblastoma. Here, we review and summarize accumulating evidence highlighting important roles for HELLS in DNA repair, genome maintenance, and key pathways relevant to cancer development, progression, and treatment.
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4
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Kohzaki M. Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies. Front Mol Biosci 2022; 9:934042. [PMID: 36032672 PMCID: PMC9403131 DOI: 10.3389/fmolb.2022.934042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/01/2022] Open
Abstract
Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.
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5
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He C, Liu L. Hsa_circ_0072008 regulates cell proliferation, migration, and invasion in cervical squamous cell carcinoma via miR-1305/helicase, lymphoid specific (HELLS) axis. Bioengineered 2022; 13:8311-8322. [PMID: 35311456 PMCID: PMC9161871 DOI: 10.1080/21655979.2022.2048945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cervical squamous cell carcinoma (CESC) is one of the most common cancers in women. Recent studies have proved that circular RNAs (circRNAs) could regulate the progress of CESC, but the mechanism is still indistinct. In this work, we explored the roles of circ_0072008 in CESC. The expression levels of circ_0072008, microRNA-1305 (miR-1305) and mRNA of HELLS (helicase, lymphoid specific) were detected by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) in CESC tissues. Meanwhile, the level of HELLS was quantified by western blot analysis. Besides, the cell functions were examined by colony formation assay, 5-Ethynyl-2’-deoxyuridine (EdU) assay, wound healing assay, flow cytometry assay and western blot. Furthermore, the interaction between miR-1305 and circ_0072008 or HELLS was detected by dual-luciferase reporter assay. The function of circ_0072008 in CESC has also been further verified in vivo by xenograft model experiments. The levels of circ_0072008 and HELLS were upregulated, and the miR-1305 level was decreased in CESC tissues in contrast to that in normal tissues. For functional analysis, silencing circ_0072008 inhibited cell proliferation and cell migration, whereas enhanced cell apoptosis in CESC cells. In mechanism, circ_0072008 acted as a miR-1305 sponge to regulate the level of HELLS. Moreover, miR-1305 was confirmed to repress the progression of CESC cells by suppressing HELLS. Meanwhile, knockdown of circ_0072008 inhibited CESC cells growth in vivo. In conclusion, circ_0072008 facilitated CESC cell proliferation, migration, and invasion through increasing HELLS expression by regulating miR-1305, which also offered an underlying targeted therapy for CESC treatment.
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Affiliation(s)
- Chunhua He
- Department of Gynecology, Jingmen NO. 1 People's Hospital, Jingmen, Hubei, China
| | - Leng Liu
- Department of Gynecology, Jingmen NO. 1 People's Hospital, Jingmen, Hubei, China
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6
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Chen X, Li Y, Rubio K, Deng B, Li Y, Tang Q, Mao C, Liu S, Xiao D, Barreto G, Tao Y. Lymphoid-specific helicase in epigenetics, DNA repair and cancer. Br J Cancer 2022; 126:165-173. [PMID: 34493821 PMCID: PMC8770686 DOI: 10.1038/s41416-021-01543-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/26/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
Lymphoid-specific helicase (LSH) is a member of the SNF2 helicase family of chromatin-remodelling proteins. Dysfunctions or mutations in LSH causes an autosomal recessive disease known as immunodeficiency-centromeric instability-facial anomaly (ICF) syndrome. Interestingly, LSH participates in various aspects of epigenetic regulation, including nucleosome remodelling, DNA methylation, histone modifications and heterochromatin formation. Further, LSH plays a crucial role during DNA-damage repair, specifically during double-strand break (DSB) repair, since murine LSH was shown to be essential for non-homologous end joining (NHEJ) and homologous recombination (HR). Accordingly, overexpression of LSH drives tumorigenesis and malignancy. On the other hand, LSH homologs stabilise the genome. Thus, LSH might be implemented as a biomarker for various cancer types and potential target molecule to develop therapeutic strategies against them. In this review, we focus on the role of LSH in orchestrating chromatin rearrangements, such as DNA methylation and histone modifications, as well as in DNA-damage repair. Changes in chromatin structure may facilitate gene expression signatures that cause malignant transformation. We summarise recent findings of LSH in cancers and raise critical open questions for further studies.
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Affiliation(s)
- Xiangyu Chen
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yamei Li
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Karla Rubio
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, Nancy, France
- Univ Paris Est Creteil, Gly-CRRET, Brain and Lung Epigenetics (BLUE), Creteil, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- International Laboratory EPIGEN, Universidad de la Salud del Estado de Puebla, Puebla, Mexico
| | - Bi Deng
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yuyi Li
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Qinwei Tang
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Chao Mao
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China.
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China.
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, Nancy, France.
- Univ Paris Est Creteil, Gly-CRRET, Brain and Lung Epigenetics (BLUE), Creteil, France.
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- International Laboratory EPIGEN, Universidad de la Salud del Estado de Puebla, Puebla, Mexico.
| | - Yongguang Tao
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China.
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China.
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer and Second Xiangya Hospital, Central South University, Changsha, China.
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7
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Long J, Liu J, Xia A, Springer NM, He Y. Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin. THE PLANT CELL 2021; 33:2183-2196. [PMID: 33779761 PMCID: PMC8364229 DOI: 10.1093/plcell/koab098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/25/2021] [Indexed: 06/01/2023]
Abstract
DNA methylation plays vital roles in repressing transposable element activity and regulating gene expression. The chromatin-remodeling factor Decrease in DNA methylation 1 (DDM1) is crucial for maintaining DNA methylation across diverse plant species, and is required for RNA-directed DNA methylation (RdDM) to maintain mCHH islands in maize (Zea mays). However, the mechanisms by which DDM1 is involved in RdDM are not well understood. In this work, we used chromatin immunoprecipitation coupled with high-throughput sequencing to ascertain the genome-wide occupancy of ZmDDM1 in the maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 co-purified with Argonaute 4 (ZmAGO4) proteins, providing further evidence that ZmDDM1 is a component of RdDM complexes in planta. Consistent with this, the vast majority of ZmDDM1-targeted regions co-localized with ZmAGO4-bound genomic sites. Overall, our results suggest a model that ZmDDM1 may be recruited to euchromatic regions via recognition of a GC-rich motif, thereby remodeling chromatin to provide access for RdDM activities in maize.
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Affiliation(s)
- Jincheng Long
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Jinghan Liu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Aiai Xia
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
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8
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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9
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LSH mediates gene repression through macroH2A deposition. Nat Commun 2020; 11:5647. [PMID: 33159050 PMCID: PMC7648012 DOI: 10.1038/s41467-020-19159-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The human Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is a severe disease with increased mortality caused by mutation in the LSH gene. Although LSH belongs to a family of chromatin remodeling proteins, it remains unknown how LSH mediates its function on chromatin in vivo. Here, we use chemical-induced proximity to rapidly recruit LSH to an engineered locus and find that LSH specifically induces macroH2A1.2 and macroH2A2 deposition in an ATP-dependent manner. Tethering of LSH induces transcriptional repression and silencing is dependent on macroH2A deposition. Loss of LSH decreases macroH2A enrichment at repeat sequences and results in transcriptional reactivation. Likewise, reduction of macroH2A by siRNA interference mimicks transcriptional reactivation. ChIP-seq analysis confirmed that LSH is a major regulator of genome-wide macroH2A distribution. Tethering of ICF4 mutations fails to induce macroH2A deposition and ICF4 patient cells display reduced macroH2A deposition and transcriptional reactivation supporting a pathogenic role for altered marcoH2A deposition. We propose that LSH is a major chromatin modulator of the histone variant macroH2A and that its ability to insert marcoH2A into chromatin and transcriptionally silence is disturbed in the ICF4 syndrome. The human ICF 4 syndrome is caused by mutation of the chromatin remodeller LSH. Here, the authors show that LSH depletion disrupts the ability of histone variant macroH2A to insert into chromatin and silence transcription.
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10
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Imai Y, Biot M, Clément JA, Teragaki M, Urbach S, Robert T, Baudat F, Grey C, de Massy B. PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment. eLife 2020; 9:57117. [PMID: 33047671 PMCID: PMC7599071 DOI: 10.7554/elife.57117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) at specific genomic locations that correspond to PRDM9-binding sites. The molecular steps occurring from PRDM9 binding to DSB formation are unknown. Using proteomic approaches to find PRDM9 partners, we identified HELLS, a member of the SNF2-like family of chromatin remodelers. Upon functional analyses during mouse male meiosis, we demonstrated that HELLS is required for PRDM9 binding and DSB activity at PRDM9 sites. However, HELLS is not required for DSB activity at PRDM9-independent sites. HELLS is also essential for 5-hydroxymethylcytosine (5hmC) enrichment at PRDM9 sites. Analyses of 5hmC in mice deficient for SPO11, which catalyzes DSB formation, and in PRDM9 methyltransferase deficient mice reveal that 5hmC is triggered at DSB-prone sites upon PRDM9 binding and histone modification, but independent of DSB activity. These findings highlight the complex regulation of the chromatin and epigenetic environments at PRDM9-specified hotspots.
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Affiliation(s)
- Yukiko Imai
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Mathilde Biot
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Julie Aj Clément
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Mariko Teragaki
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Thomas Robert
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Corinne Grey
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
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11
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Liu N, Yang R, Shi Y, Chen L, Liu Y, Wang Z, Liu S, Ouyang L, Wang H, Lai W, Mao C, Wang M, Cheng Y, Liu S, Wang X, Zhou H, Cao Y, Xiao D, Tao Y. The cross-talk between methylation and phosphorylation in lymphoid-specific helicase drives cancer stem-like properties. Signal Transduct Target Ther 2020; 5:197. [PMID: 32994405 PMCID: PMC7524730 DOI: 10.1038/s41392-020-00249-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/20/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
Posttranslational modifications (PTMs) of proteins, including chromatin modifiers, play crucial roles in the dynamic alteration of various protein properties and functions including stem-cell properties. However, the roles of Lymphoid-specific helicase (LSH), a DNA methylation modifier, in modulating stem-like properties in cancer are still not clearly clarified. Therefore, exploring PTMs modulation of LSH activity will be of great significance to further understand the function and activity of LSH. Here, we demonstrate that LSH is capable to undergo PTMs, including methylation and phosphorylation. The arginine methyltransferase PRMT5 can methylate LSH at R309 residue, meanwhile, LSH could as well be phosphorylated by MAPK1 kinase at S503 residue. We further show that the accumulation of phosphorylation of LSH at S503 site exhibits downregulation of LSH methylation at R309 residue, which eventually promoting stem-like properties in lung cancer. Whereas, phosphorylation-deficient LSH S503A mutant promotes the accumulation of LSH methylation at R309 residue and attenuates stem-like properties, indicating the critical roles of LSH PTMs in modulating stem-like properties. Thus, our study highlights the importance of the crosstalk between LSH PTMs in determining its activity and function in lung cancer stem-cell maintenance.
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Affiliation(s)
- Na Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China.,Postdoctoral Research Workstation, Department of Neurosurgery, Xiangya Hospital, Central South University, 410078, Hunan, China
| | - Rui Yang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Ying Shi
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Ling Chen
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Yating Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Zuli Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Shouping Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Lianlian Ouyang
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Haiyan Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Weiwei Lai
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Chao Mao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Min Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Yan Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, 410078, Changsha, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Xiang Wang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine; Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, 410011, Changsha, China
| | - Hu Zhou
- Shanghai Institute of Material Medical, Chinese Academy of Sciences (CAS), 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, China
| | - Ya Cao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.
| | - Yongguang Tao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China. .,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine; Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, 410011, Changsha, China.
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12
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He Y, Ren J, Xu X, Ni K, Schwader A, Finney R, Wang C, Sun L, Klarmann K, Keller J, Tubbs A, Nussenzweig A, Muegge K. Lsh/HELLS is required for B lymphocyte development and immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2020; 117:20100-20108. [PMID: 32727902 PMCID: PMC7443918 DOI: 10.1073/pnas.2004112117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutation of HELLS (Helicase, Lymphoid-Specific)/Lsh in human DNA causes a severe immunodeficiency syndrome, but the nature of the defect remains unknown. We assessed here the role of Lsh in hematopoiesis using conditional Lsh knockout mice with expression of Mx1 or Vav Cre-recombinase. Bone marrow transplantation studies revealed that Lsh depletion in hematopoietic stem cells severely reduced B cell numbers and impaired B cell development in a hematopoietic cell-autonomous manner. Lsh-deficient mice without bone marrow transplantation exhibited lower Ig levels in vivo compared to controls despite normal peripheral B cell numbers. Purified B lymphocytes proliferated normally but produced less immunoglobulins in response to in vitro stimulation, indicating a reduced capacity to undergo class switch recombination (CSR). Analysis of germline transcripts, examination of double-stranded breaks using biotin-labeling DNA break assay, and End-seq analysis indicated that the initiation of the recombination process was unscathed. In contrast, digestion-circularization PCR analysis and high-throughput sequencing analyses of CSR junctions and a chromosomal break repair assay indicated an impaired ability of the canonical end-joining pathway in Lsh-deficient B cells. Our data suggest a hematopoietic cell-intrinsic role of Lsh in B cell development and in CSR providing a potential target for immunodeficiency therapy.
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Affiliation(s)
- Yafeng He
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Jianke Ren
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Xiaoping Xu
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Kai Ni
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Andrew Schwader
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Richard Finney
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Can Wang
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Lei Sun
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Kimberly Klarmann
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
- Basic Science Program, Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD 21702
| | - Jonathan Keller
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
- Basic Science Program, Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD 21702
| | - Anthony Tubbs
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Kathrin Muegge
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702;
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
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13
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Zocchi L, Mehta A, Wu SC, Wu J, Gu Y, Wang J, Suh S, Spitale RC, Benavente CA. Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression. Oncogenesis 2020; 9:25. [PMID: 32071286 PMCID: PMC7028996 DOI: 10.1038/s41389-020-0210-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Retinoblastoma is an aggressive childhood cancer of the developing retina that initiates by biallelic RB1 gene inactivation. Tumor progression in retinoblastoma is driven by epigenetics, as retinoblastoma genomes are stable, but the mechanism(s) that drive these epigenetic changes remain unknown. Lymphoid-specific helicase (HELLS) protein is an epigenetic modifier directly regulated by the RB/E2F pathway. In this study, we used novel genetically engineered mouse models to investigate the role of HELLS during retinal development and tumorigenesis. Our results indicate that Hells-null retinal progenitor cells divide, undergo cell-fate specification, and give rise to fully laminated retinae with minor bipolar cells defects, but normal retinal function. Despite the apparent nonessential role of HELLS in retinal development, failure to transcriptionally repress Hells during retinal terminal differentiation due to retinoblastoma (RB) family loss significantly contributes to retinal tumorigenesis. Loss of HELLS drastically reduced ectopic division of differentiating cells in Rb1/p107-null retinae, significantly decreased the incidence of retinoblastoma, delayed tumor progression, and increased overall survival. Despite its role in heterochromatin formation, we found no evidence that Hells loss directly affected chromatin accessibility in the retina but functioned as transcriptional co-activator of E2F3, decreasing expression of cell cycle genes. We propose that HELLS is a critical downstream mediator of E2F-dependent ectopic proliferation in RB-null retinae. Together with the nontoxic effect of HELLS loss in the developing retina, our results suggest that HELLS and its downstream pathways could serve as potential therapeutic targets for retinoblastoma.
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Affiliation(s)
- Loredana Zocchi
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Aditi Mehta
- Pediatric Hematology and Pediatric Oncology, Children's Hospital of Orange County, Orange, CA, 92868, USA.,Department of Graduate Medical Education, University of California, Irvine, CA, 92697, USA
| | - Stephanie C Wu
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA
| | - Yijun Gu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Jingtian Wang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Claudia A Benavente
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA. .,Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA. .,Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA.
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14
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Spruce C, Dlamini S, Ananda G, Bronkema N, Tian H, Paigen K, Carter GW, Baker CL. HELLS and PRDM9 form a pioneer complex to open chromatin at meiotic recombination hot spots. Genes Dev 2020; 34:398-412. [PMID: 32001511 PMCID: PMC7050486 DOI: 10.1101/gad.333542.119] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
Abstract
In this study, Spruce et al. investigated access to recombination hot spots during meiosis and show that the chromatin remodeler HELLS and DNA-binding protein PRDM9 function together to open chromatin at hot spots and provide access for the DNA double-strand break (DSB) machinery. Their data provide a model for hot spot activation in which HELLS and PRDM9 form a pioneer complex to create a unique epigenomic environment of open chromatin, permitting correct placement and repair of DSBs. Chromatin barriers prevent spurious interactions between regulatory elements and DNA-binding proteins. One such barrier, whose mechanism for overcoming is poorly understood, is access to recombination hot spots during meiosis. Here we show that the chromatin remodeler HELLS and DNA-binding protein PRDM9 function together to open chromatin at hot spots and provide access for the DNA double-strand break (DSB) machinery. Recombination hot spots are decorated by a unique combination of histone modifications not found at other regulatory elements. HELLS is recruited to hot spots by PRDM9 and is necessary for both histone modifications and DNA accessibility at hot spots. In male mice lacking HELLS, DSBs are retargeted to other sites of open chromatin, leading to germ cell death and sterility. Together, these data provide a model for hot spot activation in which HELLS and PRDM9 form a pioneer complex to create a unique epigenomic environment of open chromatin, permitting correct placement and repair of DSBs.
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Affiliation(s)
| | | | | | | | - Hui Tian
- The Jackson Laboratory, Bar Harbor, Maine 04660, USA
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15
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Robinson MH, Maximov V, Lallani S, Farooq H, Taylor MD, Read RD, Kenney AM. Upregulation of the chromatin remodeler HELLS is mediated by YAP1 in Sonic Hedgehog Medulloblastoma. Sci Rep 2019; 9:13611. [PMID: 31541170 PMCID: PMC6754407 DOI: 10.1038/s41598-019-50088-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/22/2019] [Indexed: 12/29/2022] Open
Abstract
Medulloblastoma is a malignant pediatric tumor that arises from neural progenitors in the cerebellum. Despite a five-year survival rate of ~70%, nearly all patients incur adverse side effects from current treatment strategies that drastically impact quality of life. Roughly one-third of medulloblastoma are driven by aberrant activation of the Sonic Hedgehog (SHH) signaling pathway. However, the scarcity of genetic mutations in medulloblastoma has led to investigation of other mechanisms contributing to cancer pathogenicity including epigenetic regulation of gene expression. Here, we show that Helicase, Lymphoid Specific (HELLS), a chromatin remodeler with epigenetic functions including DNA methylation and histone modification, is induced by Sonic Hedgehog (SHH) in SHH-dependent cerebellar progenitor cells and the developing murine cerebella. HELLS is also up-regulated in mouse and human SHH medulloblastoma. Others have shown that HELLS activity generally results in a repressive chromatin state. Our results demonstrate that increased expression of HELLS in our experimental systems is regulated by the oncogenic transcriptional regulator YAP1 downstream of Smoothened, the positive transducer of SHH signaling. Elucidation of HELLS as one of the downstream effectors of the SHH pathway may lead to novel targets for precision therapeutics with the promise of better outcomes for SHH medulloblastoma patients.
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Affiliation(s)
- M Hope Robinson
- Department of Pediatric Oncology, Emory University, Atlanta, GA, 30322, USA
- Cancer Biology Graduate Program, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Victor Maximov
- Department of Pediatric Oncology, Emory University, Atlanta, GA, 30322, USA
| | - Shoeb Lallani
- Department of Pharmacology, Emory University, Atlanta, GA, 30322, USA
| | - Hamza Farooq
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Surgery, Department of Laboratory Medicine and Pathobiology, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Surgery, Department of Laboratory Medicine and Pathobiology, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Renee D Read
- Department of Pharmacology, Emory University, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Atlanta, GA, 30322, USA
| | - Anna Marie Kenney
- Department of Pediatric Oncology, Emory University, Atlanta, GA, 30322, USA.
- Winship Cancer Institute, Atlanta, GA, 30322, USA.
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16
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Ren J, Finney R, Ni K, Cam M, Muegge K. The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors. Epigenetics 2019; 14:277-293. [PMID: 30861354 PMCID: PMC6557562 DOI: 10.1080/15592294.2019.1582275] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
Dynamic regulation of chromatin accessibility is a key feature of cellular differentiation during embryogenesis, but the precise factors that control access to chromatin remain largely unknown. Lsh/HELLS is critical for normal development and mutations of Lsh in human cause the ICF (Immune deficiency, Centromeric instability, Facial anomalies) syndrome, a severe immune disorder with multiple organ deficiencies. We report here that Lsh, previously known to regulate DNA methylation level, has a genome wide chromatin remodeling function. Using micrococcal nuclease (MNase)-seq analysis, we demonstrate that Lsh protects MNase accessibility at transcriptional regulatory regions characterized by DNase I hypersensitivity and certain histone 3 (H3) tail modifications associated with enhancers. Using an auxin-inducible degron system, allowing proteolytical degradation of Lsh, we show that Lsh mediated changes in nucleosome occupancy are independent of DNA methylation level and are characterized by reduced H3 occupancy. While Lsh mediated nucleosome occupancy prevents binding sites for transcription factors in wild type cells, depletion of Lsh leads to an increase in binding of ectopically expressed tissue specific transcription factors to their respective binding sites. Our data suggests that Lsh mediated chromatin remodeling can modulate nucleosome positioning at a subset of putative enhancers contributing to the preservation of cellular identity through regulation of accessibility.
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Affiliation(s)
- Jianke Ren
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Richard Finney
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kai Ni
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
- Frederick National Laboratory for Cancer Research, Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
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17
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Rajshekar S, Yao J, Arnold PK, Payne SG, Zhang Y, Bowman TV, Schmitz RJ, Edwards JR, Goll M. Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLife 2018; 7:39658. [PMID: 30484769 PMCID: PMC6261255 DOI: 10.7554/elife.39658] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/04/2018] [Indexed: 12/13/2022] Open
Abstract
Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter). Cells package DNA into structures called chromosomes. When cells divide, each chromosome duplicates, and a structure called a centromere initially holds the copies together. The sequences of DNA on either side of the centromeres are often highly repetitive. In backboned animals, this DNA normally also has extra chemical modifications called methyl groups attached to it. The role that these methyl groups play in this region is not known, although in other DNA regions they often stop the DNA being ‘transcribed’ into molecules of RNA. The cells of people who have a rare human genetic disorder called ICF syndrome, lack the methyl groups near the centromere. The methyl groups may also be lost in old and cancerous cells. Researchers often use ‘model’ animals to investigate the effects of DNA modifications. But, until now, there were no animal models that lose methyl groups from the DNA around centromeres in the same way as seen in ICF syndrome. Rajshekar et al. have developed a new zebrafish model for ICF syndrome that loses the methyl groups around its centromeres over time. Studying the cells of these zebrafish showed that when the methyl groups are missing, the cell starts to transcribe the DNA sequences around the centromeres. The resulting RNA molecules appear to be mistaken by the cell for viral RNA. They activate immune sensors that normally detect RNA viruses, which triggers an immune response. The new zebrafish model can now be used in further studies to help researchers to understand the key features of ICF syndrome. Future work could also investigate whether the loss of methyl groups around the centromeres plays a role in other diseases where the immune system attacks healthy tissues.
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Affiliation(s)
- Srivarsha Rajshekar
- Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Jun Yao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Paige K Arnold
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sara G Payne
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, United States
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, United States
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, United States
| | - John R Edwards
- Department of Medicine, Center for Pharmacogenomics, Washington University in St. Louis School of Medicine, Missouri, United States
| | - Mary Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Genetics, University of Georgia, Georgia, United States
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18
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Unoki M, Funabiki H, Velasco G, Francastel C, Sasaki H. CDCA7 and HELLS mutations undermine nonhomologous end joining in centromeric instability syndrome. J Clin Invest 2018; 129:78-92. [PMID: 30307408 DOI: 10.1172/jci99751] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in CDCA7 and HELLS that respectively encode a CXXC-type zinc finger protein and an SNF2 family chromatin remodeler cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome types 3 and 4. Here, we demonstrate that the classical nonhomologous end joining (C-NHEJ) proteins Ku80 and Ku70, as well as HELLS, coimmunoprecipitated with CDCA7. The coimmunoprecipitation of the repair proteins was sensitive to nuclease treatment and an ICF3 mutation in CDCA7 that impairs its chromatin binding. The functional importance of these interactions was strongly suggested by the compromised C-NHEJ activity and significant delay in Ku80 accumulation at DNA damage sites in CDCA7- and HELLS-deficient HEK293 cells. Consistent with the repair defect, these cells displayed increased apoptosis, abnormal chromosome segregation, aneuploidy, centrosome amplification, and significant accumulation of γH2AX signals. Although less prominent, cells with mutations in the other ICF genes DNMT3B and ZBTB24 (responsible for ICF types 1 and 2, respectively) showed similar defects. Importantly, lymphoblastoid cells from ICF patients shared the same changes detected in the mutant HEK293 cells to varying degrees. Although the C-NHEJ defect alone did not cause CG hypomethylation, CDCA7 and HELLS are involved in maintaining CG methylation at centromeric and pericentromeric repeats. The defect in C-NHEJ may account for some common features of ICF cells, including centromeric instability, abnormal chromosome segregation, and apoptosis.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York, USA
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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19
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Han Y, Ren J, Lee E, Xu X, Yu W, Muegge K. Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells. Sci Rep 2017; 7:1136. [PMID: 28442710 PMCID: PMC5430779 DOI: 10.1038/s41598-017-00804-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022] Open
Abstract
Epigenetic mechanisms are known to exert control over gene expression and determine cell fate. Genetic mutations in epigenetic regulators are responsible for several neurologic disorders. Mutations of the chromatin remodeling protein Lsh/HELLS can cause the human Immunodeficiency, Centromere instability and Facial anomalies (ICF) syndrome, which is associated with neurologic deficiencies. We report here a critical role for Lsh in murine neural development. Lsh depleted neural stem/progenitor cells (NSPCs) display reduced growth, increases in apoptosis and impaired ability of self-renewal. RNA-seq analysis demonstrates differential gene expression in Lsh-/- NSPCs and suggests multiple aberrant pathways. Concentrating on specific genomic targets, we show that ablation of Lsh alters epigenetic states at specific enhancer regions of the key cell cycle regulator Cdkn1a and the stem cell regulator Bmp4 in NSPCs and alters their expression. These results suggest that Lsh exerts epigenetic regulation at key regulators of neural stem cell fate ensuring adequate NSPCs self-renewal and maintenance during development.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Jianke Ren
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Eunice Lee
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Xiaoping Xu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Weishi Yu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA.
- Basic Science Program, Leidos Biomedical Research, Inc., Mouse Cancer Genetics Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA.
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20
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Devos M, Gilbert B, Denecker G, Leurs K, Mc Guire C, Lemeire K, Hochepied T, Vuylsteke M, Lambert J, Van Den Broecke C, Libbrecht L, Haigh J, Berx G, Lippens S, Vandenabeele P, Declercq W. Elevated ΔNp63α Levels Facilitate Epidermal and Biliary Oncogenic Transformation. J Invest Dermatol 2016; 137:494-505. [PMID: 27725202 DOI: 10.1016/j.jid.2016.09.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 09/05/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022]
Abstract
Unlike its family member p53, TP63 is rarely mutated in human cancer. However, ΔNp63α protein levels are often elevated in tumors of epithelial origin, such as squamous cell carcinoma and cholangiocarcinoma. To study the oncogenic properties of ΔNp63α in vivo, we generated transgenic mice overexpressing ΔNp63α from the Rosa26 locus promoter controlled by keratin 5-Cre. We found that these mice spontaneously develop epidermal cysts and ectopic ΔNp63α expression in the bile duct epithelium that leads to dilatation of the intrahepatic biliary ducts, to hepatic cyst formation and bile duct adenoma. Moreover, when subjected to models of 7,12-dimethylbenz[a]anthracene-based carcinogenesis, tumor initiation was increased in ΔNp63α transgenic mice in a gene dosage-dependent manner although ΔNp63α overexpression did not alter the sensitivity to 7,12-dimethylbenz[a]anthracene-induced cytotoxicity in vivo. However, keratinocytes isolated from ΔNp63α transgenic mice displayed increased survival and delayed cellular senescence compared with wild-type keratinocytes, marked by decreased p16Ink4a and p19Arf expression. Taken together, we show that increased ΔNp63α protein levels facilitate oncogenic transformation in the epidermis as well as in the bile duct.
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Affiliation(s)
- Michael Devos
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Barbara Gilbert
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Geertrui Denecker
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular and Cellular Oncology Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Kirsten Leurs
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Conor Mc Guire
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular Signal Transduction in Inflammation Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Inflammation Research Center, VIB, Ghent, Belgium
| | - Tino Hochepied
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Transgenic mice core facility, VIB, Ghent, Belgium
| | | | - Jo Lambert
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | | | - Louis Libbrecht
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jody Haigh
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
| | - Geert Berx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular and Cellular Oncology Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Saskia Lippens
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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21
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Wu H, Thijssen PE, de Klerk E, Vonk KKD, Wang J, den Hamer B, Aytekin C, van der Maarel SM, Daxinger L. Converging disease genes in ICF syndrome: ZBTB24 controls expression of CDCA7 in mammals. Hum Mol Genet 2016; 25:4041-4051. [PMID: 27466202 DOI: 10.1093/hmg/ddw243] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/31/2022] Open
Abstract
For genetically heterogeneous diseases a better understanding of how the underlying gene defects are functionally interconnected will be important for dissecting disease etiology. The Immunodeficiency, Centromeric instability, Facial anomalies (ICF) syndrome is a chromatin disorder characterized by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS Here, we generated a Zbtb24 BTB domain deletion mouse and found that loss of functional Zbtb24 leads to early embryonic lethality. Transcriptome analysis identified Cdca7 as the top down-regulated gene in Zbtb24 homozygous mutant mESCs, which can be restored by ectopic ZBTB24 expression. We further demonstrate enrichment of ZBTB24 at the CDCA7 promoter suggesting that ZBTB24 can function as a transcription factor directly controlling Cdca7 expression. Finally, we show that this regulation is conserved between species and that CDCA7 levels are reduced in patients carrying ZBTB24 nonsense mutations. Together, our findings demonstrate convergence of the two ICF genes ZBTB24 and CDCA7 at the level of transcription.
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Affiliation(s)
- Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Peter E Thijssen
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
- Department of Microbiology and Immunology, UCSF Diabetes Center, University of California San Francisco, San Francisco, CA 94143-0534, USA
| | - Kelly K D Vonk
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Jun Wang
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China and
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr Sami Ulus Maternity and Children's Research and Educational Hospital, Ankara 06080, Turkey
| | | | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands,
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22
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Zhou Y, Wang L, Vaseghi HR, Liu Z, Lu R, Alimohamadi S, Yin C, Fu JD, Wang GG, Liu J, Qian L. Bmi1 Is a Key Epigenetic Barrier to Direct Cardiac Reprogramming. Cell Stem Cell 2016; 18:382-95. [PMID: 26942853 PMCID: PMC4779178 DOI: 10.1016/j.stem.2016.02.003] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/01/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023]
Abstract
Direct reprogramming of induced cardiomyocytes (iCMs) suffers from low efficiency and requires extensive epigenetic repatterning, although the underlying mechanisms are largely unknown. To address these issues, we screened for epigenetic regulators of iCM reprogramming and found that reducing levels of the polycomb complex gene Bmi1 significantly enhanced induction of beating iCMs from neonatal and adult mouse fibroblasts. The inhibitory role of Bmi1 in iCM reprogramming is mediated through direct interactions with regulatory regions of cardiogenic genes, rather than regulation of cell proliferation. Reduced Bmi1 expression corresponded with increased levels of the active histone mark H3K4me3 and reduced levels of repressive H2AK119ub at cardiogenic loci, and de-repression of cardiogenic gene expression during iCM conversion. Furthermore, Bmi1 deletion could substitute for Gata4 during iCM reprogramming. Thus, Bmi1 acts as a critical epigenetic barrier to iCM production. Bypassing this barrier simplifies iCM generation and increases yield, potentially streamlining iCM production for therapeutic purposes.
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Affiliation(s)
- Yang Zhou
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haley Ruth Vaseghi
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ziqing Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sahar Alimohamadi
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chaoying Yin
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ji-Dong Fu
- Department of Medicine, Heart and Vascular Research Center, MetroHealth Campus, Case Western Reserve University, Cleveland, OH 44109, USA
| | - Greg G Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA.
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23
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Basenko EY, Kamei M, Ji L, Schmitz RJ, Lewis ZA. The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa. PLoS Genet 2016; 12:e1005790. [PMID: 26771905 PMCID: PMC4714748 DOI: 10.1371/journal.pgen.1005790] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023] Open
Abstract
LSH/DDM1 enzymes are required for DNA methylation in higher eukaryotes and have poorly defined roles in genome maintenance in yeast, plants, and animals. The filamentous fungus Neurospora crassa is a tractable system that encodes a single LSH/DDM1 homolog (NCU06306). We report that the Neurospora LSH/DDM1 enzyme is encoded by mutagen sensitive-30 (mus-30), a locus identified in a genetic screen over 25 years ago. We show that MUS-30-deficient cells have normal DNA methylation, but are hypersensitive to DNA damaging agents. MUS-30 is a nuclear protein, consistent with its predicted role as a chromatin remodeling enzyme, and levels of MUS-30 are increased following DNA damage. MUS-30 co-purifies with Neurospora WDR76, a homolog of yeast Changed Mutation Rate-1 and mammalian WD40 repeat domain 76. Deletion of wdr76 rescued DNA damage-hypersensitivity of Δmus-30 strains, demonstrating that the MUS-30-WDR76 interaction is functionally important. DNA damage-sensitivity of Δmus-30 is partially suppressed by deletion of methyl adenine glycosylase-1, a component of the base excision repair machinery (BER); however, the rate of BER is not affected in Δmus-30 strains. We found that MUS-30-deficient cells are not defective for DSB repair, and we observed a negative genetic interaction between Δmus-30 and Δmei-3, the Neurospora RAD51 homolog required for homologous recombination. Together, our findings suggest that MUS-30, an LSH/DDM1 homolog, is required to prevent DNA damage arising from toxic base excision repair intermediates. Overall, our study provides important new information about the functions of the LSH/DDM1 family of enzymes.
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Affiliation(s)
- Evelina Y. Basenko
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Masayuki Kamei
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Zachary A. Lewis
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
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Lsh Is Essential for Maintaining Global DNA Methylation Levels in Amphibia and Fish and Interacts Directly with Dnmt1. BIOMED RESEARCH INTERNATIONAL 2015; 2015:740637. [PMID: 26491684 PMCID: PMC4600896 DOI: 10.1155/2015/740637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/28/2015] [Accepted: 09/03/2015] [Indexed: 12/15/2022]
Abstract
Eukaryotic genomes are methylated at cytosine bases in the context of CpG dinucleotides, a pattern which is maintained through cell division by the DNA methyltransferase Dnmt1. Dramatic methylation losses are observed in plant and mouse cells lacking Lsh (lymphoid specific helicase), predominantly at repetitive sequences and gene promoters. However, the mechanism by which Lsh contributes to the maintenance of DNA methylation is unknown. Here we show that DNA methylation is lost in Lsh depleted frog and fish embryos, both of which exhibit developmental delay. Additionally, we show that both Lsh and Dnmt1 are associated with chromatin and that Lsh knockdown leads to a decreased Dnmt1-chromatin association. Coimmunoprecipitation experiments reveal that Lsh and Dnmt1 are found in the same protein complex, and pulldowns show this interaction is direct. Our data indicate that Lsh is usually diffuse in the nucleus but can be recruited to heterochromatin in a HP1α-dependent manner. These data together (a) show that the role of Lsh in DNA methylation is conserved in plants, amphibian, fish, and mice and (b) support a model in which Lsh contributes to Dnmt1 binding to chromatin, explaining how its loss can potentially lead to perturbations in DNA methylation maintenance.
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25
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Lungu C, Muegge K, Jeltsch A, Jurkowska RZ. An ATPase-deficient variant of the SNF2 family member HELLS shows altered dynamics at pericentromeric heterochromatin. J Mol Biol 2015; 427:1903-15. [PMID: 25823553 PMCID: PMC7722765 DOI: 10.1016/j.jmb.2015.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/04/2015] [Accepted: 03/20/2015] [Indexed: 11/15/2022]
Abstract
The HELLS (helicase, lymphoid specific, also known as lymphoid-specific helicase) protein is related to the SNF2 (sucrose non-fermentable 2) family of chromatin remodeling ATPases. It is required for efficient DNA methylation in mammals, particularly at heterochromatin-located repetitive sequences. In this study, we investigated the interaction of HELLS with chromatin and used an ATPase-deficient HELLS variant to address the role of ATP hydrolysis in this process. Chromatin fractionation experiments demonstrated that, in the absence of the ATPase activity, HELLS is retained at the nuclear matrix compartment, defined in part by lamin B1. Microscopy studies revealed a stronger association of the ATPase-deficient mutant with heterochromatin. These results were further supported by fluorescence recovery after photobleaching measurements, which showed that, at heterochromatic sites, wild-type HELLS is very dynamic, with a recovery half-time of 0.8s and a mobile protein fraction of 61%. In contrast, the ATPase-deficient mutant displayed 4.5-s recovery half-time and a reduction in the mobile fraction to 30%. We also present evidence suggesting that, in addition to the ATPase activity, a functional H3K9me3 signaling pathway contributes to an efficient release of HELLS from pericentromeric chromatin. Overall, our results show that a functional ATPase activity is not required for the recruitment of HELLS to heterochromatin, but it is important for the release of the enzyme from these sites.
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Affiliation(s)
- Cristiana Lungu
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Basic Science Program, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
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26
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Ren J, Briones V, Barbour S, Yu W, Han Y, Terashima M, Muegge K. The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences. Nucleic Acids Res 2015; 43:1444-55. [PMID: 25578963 PMCID: PMC4330352 DOI: 10.1093/nar/gku1371] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/16/2014] [Accepted: 12/21/2014] [Indexed: 12/19/2022] Open
Abstract
Lsh, a chromatin remodeling protein of the SNF2 family, is critical for normal heterochromatin structure. In particular, DNA methylation at repeat elements, a hallmark of heterochromatin, is greatly reduced in Lsh(-/-) (KO) cells. Here, we examined the presumed nucleosome remodeling activity of Lsh on chromatin in the context of DNA methylation. We found that dynamic CG methylation was dependent on Lsh in embryonic stem cells. Moreover, we demonstrate that ATP function is critical for de novo methylation at repeat sequences. The ATP binding site of Lsh is in part required to promote stable association of the DNA methyltransferase 3b with the repeat locus. By performing nucleosome occupancy assays, we found distinct nucleosome occupancy in KO ES cells compared to WT ES cells after differentiation. Nucleosome density was restored to wild-type level by re-expressing wild-type Lsh but not the ATP mutant in KO ES cells. Our results suggest that ATP-dependent nucleosome remodeling is the primary molecular function of Lsh, which may promote de novo methylation in differentiating ES cells.
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Affiliation(s)
- Jianke Ren
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Victorino Briones
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Samantha Barbour
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Weishi Yu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Minoru Terashima
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA Basic Science Program, Leidos Biomedical Research, Inc., Mouse Cancer Genetics Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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27
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Dnmt3b Prefers Germ Line Genes and Centromeric Regions: Lessons from the ICF Syndrome and Cancer and Implications for Diseases. BIOLOGY 2014; 3:578-605. [PMID: 25198254 PMCID: PMC4192629 DOI: 10.3390/biology3030578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/18/2014] [Accepted: 08/21/2014] [Indexed: 01/06/2023]
Abstract
The correct establishment and maintenance of DNA methylation patterns are critical for mammalian development and the control of normal cell growth and differentiation. DNA methylation has profound effects on the mammalian genome, including transcriptional repression, modulation of chromatin structure, X chromosome inactivation, genomic imprinting, and the suppression of the detrimental effects of repetitive and parasitic DNA sequences on genome integrity. Consistent with its essential role in normal cells and predominance at repetitive genomic regions, aberrant changes of DNA methylation patterns are a common feature of diseases with chromosomal and genomic instabilities. In this context, the functions of DNA methyltransferases (DNMTs) can be affected by mutations or alterations of their expression. DNMT3B, which is involved in de novo methylation, is of particular interest not only because of its important role in development, but also because of its dysfunction in human diseases. Expression of catalytically inactive isoforms has been associated with cancer risk and germ line hypomorphic mutations with the ICF syndrome (Immunodeficiency Centromeric instability Facial anomalies). In these diseases, global genomic hypomethylation affects repeated sequences around centromeric regions, which make up large blocks of heterochromatin, and is associated with chromosome instability, impaired chromosome segregation and perturbed nuclear architecture. The review will focus on recent data about the function of DNMT3B, and the consequences of its deregulated activity on pathological DNA hypomethylation, including the illicit activation of germ line-specific genes and accumulation of transcripts originating from repeated satellite sequences, which may represent novel physiopathological biomarkers for human diseases. Notably, we focus on cancer and the ICF syndrome, pathological contexts in which hypomethylation has been extensively characterized. We also discuss the potential contribution of these deregulated protein-coding and non-coding transcription programs to the perturbation of cellular phenotypes.
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28
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Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K. Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Res 2014; 24:1613-23. [PMID: 25170028 PMCID: PMC4199375 DOI: 10.1101/gr.172015.114] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cytosine methylation is critical in mammalian development and plays a role in diverse biologic processes such as genomic imprinting, X chromosome inactivation, and silencing of repeat elements. Several factors regulate DNA methylation in early embryogenesis, but their precise role in the establishment of DNA methylation at a given site remains unclear. We have generated a comprehensive methylation map in fibroblasts derived from the murine DNA methylation mutant Hells−/− (helicase, lymphoid specific, also known as LSH). It has been previously shown that HELLS can influence de novo methylation of retroviral sequences and endogenous genes. Here, we describe that HELLS controls cytosine methylation in a nuclear compartment that is in part defined by lamin B1 attachment regions. Despite widespread loss of cytosine methylation at regulatory sequences, including promoter regions of protein-coding genes and noncoding RNA genes, overall relative transcript abundance levels in the absence of HELLS are similar to those in wild-type cells. A subset of promoter regions shows increases of the histone modification H3K27me3, suggesting redundancy of epigenetic silencing mechanisms. Furthermore, HELLS modulates CG methylation at all classes of repeat elements and is critical for repression of a subset of repeat elements. Overall, we provide a detailed analysis of gene expression changes in relation to DNA methylation alterations, which contributes to our understanding of the biological role of cytosine methylation.
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Affiliation(s)
- Weishi Yu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Carl McIntosh
- BCGC, Bioinformatics, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Ryan Lister
- Howard Hughes Medical Institute and Genome Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Iris Zhu
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland 20894, USA
| | - Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Jianke Ren
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland 20894, USA
| | - Eunice Lee
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Victorino Briones
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Minoru Terashima
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Robert Leighty
- Data Management Services, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Joseph R Ecker
- Howard Hughes Medical Institute and Genome Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA; Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, Maryland 21702, USA
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29
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CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity. Proc Natl Acad Sci U S A 2014; 111:5890-5. [PMID: 24711395 DOI: 10.1073/pnas.1320945111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNA methylation patterns are established in early embryogenesis and are critical for cellular differentiation. To investigate the role of CG methylation in potential enhancer formation, we assessed H3K4me1 modification in murine embryonic fibroblasts (MEFs) derived from the DNA methylation mutant Lsh(-/-) mice. We report here de novo formation of putative enhancer elements at CG hypomethylated sites that can be dynamically altered. We found a subset of differentially enriched H3K4me1 regions clustered at neuronal lineage genes and overlapping with known cis-regulatory elements present in brain tissue. Reprogramming of Lsh(-/-) MEFs into induced pluripotent stem (iPS) cells leads to increased neuronal lineage gene expression of premarked genes and enhanced differentiation potential of Lsh(-/-) iPS cells toward the neuronal lineage pathway compared with WT iPS cells in vitro and in vivo. The state of CG hypomethylation and H3K4me1 enrichment is partially maintained in Lsh(-/-) iPS cells. The acquisition of H3K27ac and activity of subcloned fragments in an enhancer reporter assay indicate functional activity of several of de novo H3K4me1-marked sequences. Our results suggest a functional link of H3K4me1 enrichment at CG hypomethylated sites, enhancer formation, and cellular plasticity.
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30
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Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol 2013; 14:R146. [PMID: 24367978 PMCID: PMC4054100 DOI: 10.1186/gb-2013-14-12-r146] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 12/24/2013] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND DNA methylation contributes to genomic integrity by suppressing repeat-associated transposition. In addition to the canonical DNA methyltransferases, several auxiliary chromatin factors are required to maintain DNA methylation at intergenic and satellite repeats. The interaction between Lsh, a chromatin helicase, and the de novo methyltransferase Dnmt3b facilitates deposition of DNA methylation at stem cell genes, which are hypomethylated in Lsh-/- embryos. We wished to determine if a similar targeting mechanism operates to maintain DNA methylation at repetitive sequences. RESULTS We mapped genome-wide DNA methylation patterns in Lsh-/- and Dnmt3b-/- somatic cells. DNA methylation is predominantly lost from specific genomic repeats in Lsh-/- cells: LTR -retrotransposons, LINE-1 repeats and mouse satellites. RNA-seq experiments demonstrate that specific IAP LTRs and satellites, but not LINE-1 elements, are aberrantly transcribed in Lsh-/- cells. LTR hypomethylation in Dnmt3b-/- cells is moderate, whereas IAP, LINE-1 and satellite elements are hypomethylated but silent. Repressed LINE-1 elements in Lsh-/- cells gain H3K4me3, but H3K9me3 levels are unaltered, indicating that DNA hypomethylation alone is not permissive for their transcriptional activation. Mis-expressed IAPs and satellites lose H3K9me3 and gain H3K4me3 in Lsh-/- cells. CONCLUSIONS Our study emphasizes that regulation of repetitive elements by Lsh and DNA methylation is selective and context dependent. Silencing of repeats in somatic cells appears not to be critically dependent on Dnmt3b function. We propose a model where Lsh is specifically required at a precise developmental window to target de novo methylation to repeat sequences, which is subsequently maintained by Dnmt1 to enforce selective repeat silencing.
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Affiliation(s)
- Donncha S Dunican
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Hazel A Cruickshanks
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Masako Suzuki
- Departments of Genetics (Computational Genetics) and Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, USA
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Tracey Davey
- Newcastle Medical School, Framlington Place, Newcastle University, Newcastle Upon Tyne NE2 4HH, England
| | - Robert J Arceci
- Room 2 M51 Cancer Research Building, Pediatrics and Oncology, Cellular and Molecular Medicine, Johns Hopkins, Baltimore, MD, USA
| | - John Greally
- Departments of Genetics (Computational Genetics) and Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, USA
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Richard R Meehan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
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Meiosis arrest female 1 (MARF1) has nuage-like function in mammalian oocytes. Proc Natl Acad Sci U S A 2012; 109:18653-60. [PMID: 23090997 DOI: 10.1073/pnas.1216904109] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Orderly regulation of meiosis and protection of germline genomic integrity from transposable elements are essential for male and female gamete development. In the male germline, these processes are ensured by proteins associated with cytoplasmic nuage, but morphologically similar germ granules or nuage have not been identified in mammalian female germ cells. Indeed, many mutations affecting nuage-associated proteins such as PIWI and tudor domain containing proteins 5 and 7 (TDRD5/7) can result in failure of meiosis, up-regulation of retrotransposons, and infertility only in males and not in females. We recently identified MARF1 (meiosis arrest female 1) as a protein essential for controlling meiosis and retrotransposon surveillance in oocytes; and in contrast to PIWI-pathway mutations, Marf1 mutant females are infertile, whereas mutant males are fertile. Here we put forward the hypothesis that MARF1 in mouse oocytes is a functional counterpart of the nuage-associated components of spermatocytes. We describe the developmental pattern of Marf1 expression and its roles in retrotransposon silencing and protection from DNA double-strand breaks. Analysis of MARF1 protein domains compared with PIWI and TDRD5/7 revealed that these functional similarities are reflected in remarkable structural analogies. Thus, functions that in the male germline require protein interactions and cooperative scaffolding are combined in MARF1, allowing a single molecule to execute crucial activities of meiotic regulation and protection of germline genomic integrity.
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Abstract
Mobile DNAs have had a central role in shaping our genome. More than half of our DNA is comprised of interspersed repeats resulting from replicative copy and paste events of retrotransposons. Although most are fixed, incapable of templating new copies, there are important exceptions to retrotransposon quiescence. De novo insertions cause genetic diseases and cancers, though reliably detecting these occurrences has been difficult. New technologies aimed at uncovering polymorphic insertions reveal that mobile DNAs provide a substantial and dynamic source of structural variation. Key questions going forward include how and how much new transposition events affect human health and disease.
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Affiliation(s)
- Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Briones V, Muegge K. The ghosts in the machine: DNA methylation and the mystery of differentiation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:757-62. [PMID: 22381140 PMCID: PMC7477944 DOI: 10.1016/j.bbagrm.2012.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/01/2012] [Accepted: 02/09/2012] [Indexed: 01/29/2023]
Abstract
Methylation regulates DNA by altering chromatin and limiting accessibility of transcription factors and RNA polymerase. In this way, DNA methylation controls gene expression and plays a role in ES cell regulation, tissue differentiation and the development of the organism. In abnormal circumstances methylation can also induce diseases and promote cancer progression. Chromatin remodeling proteins such as the SNF2 family member Lsh regulates genome-wide cytosine methylation patterns during mammalian development. Lsh promotes methylation by targeting and repressing repeat sequences that are imbedded in heterochromatin. Lsh also regulates cytosine methylation at unique loci. Alterations in histone modifications (such as H3K4me3, histone acetylation, H3K27me3 and H2Aub) can be associated with DNA methylation changes making Lsh-mediated cytosine methylation part of a larger epigenetic network defining gene expression and cellular differentiation during development. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Victorino Briones
- Laboratory of Cancer Prevention, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD, USA
| | - Kathrin Muegge
- Laboratory of Cancer Prevention, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD, USA
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Zeng W, Baumann C, Schmidtmann A, Honaramooz A, Tang L, Bondareva A, Dores C, Fan T, Xi S, Geiman T, Rathi R, de Rooij D, De La Fuente R, Muegge K, Dobrinski I. Lymphoid-specific helicase (HELLS) is essential for meiotic progression in mouse spermatocytes. Biol Reprod 2011; 84:1235-41. [PMID: 21349825 PMCID: PMC3099587 DOI: 10.1095/biolreprod.110.085720] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/28/2010] [Accepted: 02/03/2011] [Indexed: 01/15/2023] Open
Abstract
Lymphoid-specific helicase (HELLS; also known as LSH) is a member of the SNF2 family of chromatin remodeling proteins. Because Hells-null mice die at birth, a phenotype in male meiosis cannot be studied in these animals. Allografting of testis tissue from Hells(-/-) to wild-type mice was employed to study postnatal germ cell differentiation. Testes harvested at Day 18.5 of gestation from Hells(-/-), Hells(+/-), and Hells(+/+) mice were grafted ectopically to immunodeficient mice. Bromodeoxyuridine incorporation at 1 wk postgrafting revealed fewer dividing germ cells in grafts from Hells(-/-) than from Hells(+/+) mice. Whereas spermatogenesis proceeded through meiosis with round spermatids in grafts from Hells heterozygote and wild-type donor testes, spermatogenesis arrested at stage IV, and midpachytene spermatocytes were the most advanced germ cell type in grafts from Hells(-/-) mice at 4, 6, and 8 wk after grafting. Analysis of meiotic configurations at 22 days posttransplantation revealed an increase in Hells(-/-) spermatocytes with abnormal chromosome synapsis. These results indicate that in the absence of HELLS, proliferation of spermatogonia is reduced and germ cell differentiation arrested at the midpachytene stage, implicating an essential role for HELLS during male meiosis. This study highlights the utility of testis tissue grafting to study spermatogenesis in animal models that cannot reach sexual maturity.
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Affiliation(s)
- Wenxian Zeng
- Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
| | - Claudia Baumann
- Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia
| | - Anja Schmidtmann
- Laboratory of Cancer Prevention, SAIC-FCRDC, National Cancer Institute, Frederick, Maryland
| | - Ali Honaramooz
- Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lin Tang
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Alla Bondareva
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Camila Dores
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tao Fan
- Laboratory of Cancer Prevention, SAIC-FCRDC, National Cancer Institute, Frederick, Maryland
| | - Sichuan Xi
- Laboratory of Cancer Prevention, SAIC-FCRDC, National Cancer Institute, Frederick, Maryland
| | - Theresa Geiman
- Laboratory of Cancer Prevention, SAIC-FCRDC, National Cancer Institute, Frederick, Maryland
| | - Rahul Rathi
- Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
| | - Dirk de Rooij
- Center for Reproductive Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Rabindranath De La Fuente
- Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia
| | - Kathrin Muegge
- Laboratory of Cancer Prevention, SAIC-FCRDC, National Cancer Institute, Frederick, Maryland
| | - Ina Dobrinski
- Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
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35
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ΔNp63α is an oncogene that targets chromatin remodeler Lsh to drive skin stem cell proliferation and tumorigenesis. Cell Stem Cell 2011; 8:164-76. [PMID: 21295273 DOI: 10.1016/j.stem.2010.12.009] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 10/21/2010] [Accepted: 11/15/2010] [Indexed: 12/17/2022]
Abstract
The p53 homolog p63 is essential for development, yet its role in cancer is not clear. We discovered that p63 deficiency evokes the tumor-suppressive mechanism of cellular senescence, causing a striking absence of stratified epithelia such as the skin. Here we identify the predominant p63 isoform, ΔNp63α, as a protein that bypasses oncogene-induced senescence to drive tumorigenesis in vivo. Interestingly, bypass of senescence promotes stem-like proliferation and maintains survival of the keratin 15-positive stem cell population. Furthermore, we identify the chromatin-remodeling protein Lsh as a new target of ΔNp63α that is an essential mediator of senescence bypass. These findings indicate that ΔNp63α is an oncogene that cooperates with Ras to promote tumor-initiating stem-like proliferation and suggest that Lsh-mediated chromatin-remodeling events are critical to this process.
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36
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Tao Y, Xi S, Shan J, Maunakea A, Che A, Briones V, Lee EY, Geiman T, Huang J, Stephens R, Leighty RM, Zhao K, Muegge K. Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences. Proc Natl Acad Sci U S A 2011; 108:5626-31. [PMID: 21427231 PMCID: PMC3078362 DOI: 10.1073/pnas.1017000108] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is critical for normal development and plays important roles in genome organization and transcriptional regulation. Although DNA methyltransferases have been identified, the factors that establish and contribute to genome-wide methylation patterns remain elusive. Here, we report a high-resolution cytosine methylation map of the murine genome modulated by Lsh, a chromatin remodeling family member that has previously been shown to regulate CpG methylation at repetitive sequences. We provide evidence that Lsh also controls genome-wide cytosine methylation at nonrepeat sequences and relate those changes to alterations in H4K4me3 modification and gene expression. Deletion of Lsh alters the allocation of cytosine methylation in chromosomal regions of 50 kb to 2 Mb and, in addition, leads to changes in the methylation profile at the 5' end of genes. Furthermore, we demonstrate that loss of Lsh promotes--as well as prevents--cytosine methylation. Our data indicate that Lsh is an epigenetic modulator that is critical for normal distribution of cytosine methylation throughout the murine genome.
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Affiliation(s)
- Yongguang Tao
- Basic Science Program, Laboratory of Cancer Prevention
| | - Sichuan Xi
- Basic Science Program, Laboratory of Cancer Prevention
| | - Jigui Shan
- Advanced Biomedical Computing Center, and
| | - Alika Maunakea
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20817
| | - Anney Che
- Advanced Biomedical Computing Center, and
| | | | - Eunice Y. Lee
- Basic Science Program, Laboratory of Cancer Prevention
| | | | | | | | - Robert M. Leighty
- Data Management Services, Science Applications International Corporation Frederick, Inc., National Cancer Institute Frederick, Frederick, MD 21702; and
| | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20817
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37
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Niu J, Chen T, Han L, Wang P, Li N, Tong T. Transcriptional activation of the senescence regulator Lsh by E2F1. Mech Ageing Dev 2011; 132:180-6. [PMID: 21453717 DOI: 10.1016/j.mad.2011.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 02/28/2011] [Accepted: 03/11/2011] [Indexed: 12/22/2022]
Abstract
Lsh, a protein related to the SNF2 family of chromatin-remodeling ATPases, is a major epigenetic regulator that is essential for DNA methylation and histone acetylation at repetitive elements. Lsh represses endogenous p16(INK4a) expression by recruiting HDAC to the p16(INK4a) promoter, which in turn delays cell senescence. However, the molecular mechanisms that govern loss of Lsh expression during cellular senescence have yet to be elucidated. Here we investigate the transcriptional regulation of the human Lsh promoter. We find that the minimal Lsh promoter is located between positions -216 and -119 relative to the transcription start site, and contains two putative E2F binding sites. Ectopic E2F1 increases expression of Lsh at both transcriptional and translational levels. E2F1 physically interacts with the Lsh promoter by binding to each of the two putative binding sites and transactivates the Lsh promoter. E2F1 also induces Lsh protein expression and transactivates the Lsh promoter in 2BS cells. At the same time, E2F1-induced Lsh promoter activity is reduced in senescent cells compared to young cells. These results indicate that E2F1 plays a crucial role in transcriptional control of the human Lsh gene and the decrease of Lsh expression in senescent cells is related to the repression of E2F1.
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Affiliation(s)
- Jing Niu
- Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, PR China
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38
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Hargreaves DC, Crabtree GR. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res 2011; 21:396-420. [PMID: 21358755 DOI: 10.1038/cr.2011.32] [Citation(s) in RCA: 614] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macromolecular assemblies that regulate chromatin structure using the energy of ATP hydrolysis have critical roles in development, cancer, and stem cell biology. The ATPases of this family are encoded by 27 human genes and are usually associated with several other proteins that are stable, non-exchangeable subunits. One fundamental mechanism used by these complexes is thought to be the movement or exchange of nucleosomes to regulate transcription. However, recent genetic studies indicate that chromatin remodelers may also be involved in regulating other aspects of chromatin structure during many cellular processes. The SWI/SNF family in particular appears to have undergone a substantial change in subunit composition and mechanism coincident with the evolutionary advent of multicellularity and the appearance of linking histones. The differential usage of this greater diversity of mammalian BAF subunits is essential for the development of specific cell fates, including the progression from pluripotency to multipotency to committed neurons. Recent human genetic screens have revealed that BRG1, ARID1A, BAF155, and hSNF5 are frequently mutated in tumors, indicating that BAF complexes also play a critical role in the initiation or progression of cancer. The mechanistic bases underlying the genetic requirements for BAF and other chromatin remodelers in development and cancer are relatively unexplored and will be a focus of this review.
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Affiliation(s)
- Diana C Hargreaves
- Howard Hughes Medical Institute, Beckman Center B211, 279 Campus Drive, Mailcode 5323, Stanford University School of Medicine, Stanford, CA 94305-5323, USA
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39
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Myant K, Termanis A, Sundaram AYM, Boe T, Li C, Merusi C, Burrage J, de Las Heras JI, Stancheva I. LSH and G9a/GLP complex are required for developmentally programmed DNA methylation. Genome Res 2010; 21:83-94. [PMID: 21149390 DOI: 10.1101/gr.108498.110] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
LSH, a member of the SNF2 family of chromatin remodeling ATPases encoded by the Hells gene, is essential for normal levels of DNA methylation in the mammalian genome. While the role of LSH in the methylation of repetitive DNA sequences is well characterized, its contribution to the regulation of DNA methylation and the expression of protein-coding genes has not been studied in detail. In this report we investigate genome-wide patterns of DNA methylation at gene promoters in Hells(-/-) mouse embryonic fibroblasts (MEFs). We find that in the absence of LSH, DNA methylation is lost or significantly reduced at ∼20% of all normally methylated promoter sequences. As a consequence, a large number of genes are misexpressed in Hells(-/-) MEFs. Comparison of Hells(-/-) MEFs with wild-type MEFs and embryonic stem (ES) cells suggests that LSH is important for de novo DNA methylation events that accompany the establishment and differentiation of embryonic lineage cells. We further show that the generation of normal DNA methylation patterns and stable gene silencing at specific promoters require cooperation between LSH and the G9a/GLP complex of histone methylases. At such loci, G9a recruitment is compromised when LSH is absent or greatly reduced. Taken together, our data suggest a mechanism whereby LSH promotes binding of DNA methyltransferases and the G9a/GLP complex to specific loci and facilitates developmentally programmed DNA methylation and stable gene silencing during lineage commitment and differentiation.
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Affiliation(s)
- Kevin Myant
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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40
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Hermo L, Pelletier RM, Cyr DG, Smith CE. Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 5: intercellular junctions and contacts between germs cells and Sertoli cells and their regulatory interactions, testicular cholesterol, and genes/proteins associated with more than one germ cell generation. Microsc Res Tech 2010; 73:409-94. [PMID: 19941291 DOI: 10.1002/jemt.20786] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the testis, cell adhesion and junctional molecules permit specific interactions and intracellular communication between germ and Sertoli cells and apposed Sertoli cells. Among the many adhesion family of proteins, NCAM, nectin and nectin-like, catenins, and cadherens will be discussed, along with gap junctions between germ and Sertoli cells and the many members of the connexin family. The blood-testis barrier separates the haploid spermatids from blood borne elements. In the barrier, the intercellular junctions consist of many proteins such as occludin, tricellulin, and claudins. Changes in the expression of cell adhesion molecules are also an essential part of the mechanism that allows germ cells to move from the basal compartment of the seminiferous tubule to the adluminal compartment thus crossing the blood-testis barrier and well-defined proteins have been shown to assist in this process. Several structural components show interactions between germ cells to Sertoli cells such as the ectoplasmic specialization which are more closely related to Sertoli cells and tubulobulbar complexes that are processes of elongating spermatids embedded into Sertoli cells. Germ cells also modify several Sertoli functions and this also appears to be the case for residual bodies. Cholesterol plays a significant role during spermatogenesis and is essential for germ cell development. Lastly, we list genes/proteins that are expressed not only in any one specific generation of germ cells but across more than one generation.
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Affiliation(s)
- Louis Hermo
- Faculty of Medicine, Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 2B2.
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41
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Waseem A, Ali M, Odell EW, Fortune F, Teh MT. Downstream targets of FOXM1: CEP55 and HELLS are cancer progression markers of head and neck squamous cell carcinoma. Oral Oncol 2010; 46:536-42. [PMID: 20400365 DOI: 10.1016/j.oraloncology.2010.03.022] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 03/18/2010] [Accepted: 03/18/2010] [Indexed: 12/17/2022]
Abstract
We recently showed that upregulation of a key oncogene FOXM1 precedes head and neck squamous cell carcinoma (HNSCC) malignancy. Furthermore, we also identified a centrosomal protein CEP55 and a DNA helicase/putative stem cell marker HELLS, which are both downstream targets of FOXM1. In this study, we have investigated the expression profiles of CEP55 and HELLS using immunohistochemistry and quantified by digital densitometry in a tissue panel (20 samples) consisting of normal oral mucosa, dysplasias, HNSCC and lymph node metastasis (LnMet) samples. Furthermore, we corroborated our findings using absolute real-time PCR (qPCR) on a panel of 12 primary normal human oral keratinocytes, five dysplasia and 10 HNSCC cell lines. Finally, we validated our study using bioinformatics microarray analysis on an independent HNSCC patient cohort (four normal and 16 tumours). In normal oral mucosa, CEP55 protein was detected at very low level within the upper differentiated layers. In contrast, CEP55 was highly expressed in oral dysplasia whereas only moderate expression was detected in HNSCC and LnMet. Low level of HELLS expression was detected in the basal cell layer of the normal oral mucosa, moderate level was seen in dysplasia and high levels in both HNSCC and LnMet. These expression patterns were consistent with both qPCR data from the cell line panel and microarray data analysis of TNM-stage defined HNSCC samples confirming the progressive expression pattern of CEP55 and HELLS. To our knowledge, this is the first pilot study demonstrating that both CEP55 and HELLS mRNA and protein expression positively correlate with pre-malignancy and HNSCC progression. This study provides strong evidence that CEP55 and HELLS may be used in conjunction with FOXM1 as a biomarker set for early cancer detection and indicators of malignant conversion and progression.
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Affiliation(s)
- Ahmad Waseem
- Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London E1 2AD, England, United Kingdom
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42
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Abstract
Development from separate parental germ cells through fertilization and proceeding to a fully functioning adult animal occurs through an intricate program of transcriptional and chromatin changes. Epigenetic alterations such as DNA methylation are an important part of this process. This review looks at the role of DNA methylation in early embryonic development, as well as how this epigenetic mark affects stem cell differentiation and tissue-specific gene expression in somatic cells.
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Affiliation(s)
- Theresa M Geiman
- Laboratory of Cancer Prevention, National Cancer Institute-Frederick, SAIC-Frederick, MD 21702, USA.
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43
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Xi S, Geiman TM, Briones V, Guang Tao Y, Xu H, Muegge K. Lsh participates in DNA methylation and silencing of stem cell genes. Stem Cells 2009; 27:2691-702. [PMID: 19650037 PMCID: PMC3327128 DOI: 10.1002/stem.183] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Transcriptional control of stem cell genes is a critical step in differentiation of embryonic stem cells and in reprogramming of somatic cells into stem cells. Here we report that Lsh, a regulator of repressive chromatin at retrotransposons, also plays an important role in silencing of stem cell-specific genes such as Oct4. We found that CpG methylation is gained during in vitro differentiation of several stem cell-specific genes (in 11 of 12 promoter regions) and thus appears to be a common epigenetic mark. Lsh depletion prevents complete silencing of stem cell gene expression and moreover promotes the maintenance of stem cell characteristics in culture. Lsh is required for establishment of DNA methylation patterns at stem cell genes during differentiation, in part by regulating access of Dnmt3b to its genomic targets. Our results indicate that Lsh is involved in the control of stem cell genes and suggest that Lsh is an important epigenetic modulator during early stem cell differentiation.
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Affiliation(s)
- Sichuan Xi
- Laboratory of Cancer Prevention, SAIC-Frederick, National Cancer Institute, Frederick, MD 21701, USA
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44
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Zhou R, Han L, Li G, Tong T. Senescence delay and repression of p16INK4a by Lsh via recruitment of histone deacetylases in human diploid fibroblasts. Nucleic Acids Res 2009; 37:5183-96. [PMID: 19561196 PMCID: PMC2731912 DOI: 10.1093/nar/gkp533] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Lymphoid specific helicase (Lsh) belongs to the family of SNF2/helicases. Disruption of Lsh leads to developmental growth retardation and premature aging in mice. However, the specific effect of Lsh on human cellular senescence remains unknown. Herein, we report that Lsh overexpression delays cell senescence by silencing p16INK4a in human fibroblasts. The patterns of p16INK4a and Lsh expression during cell senescence present the inverse correlation. We also find that Lsh requires histone deacetylase (HDAC) activity to repress p16INK4a and treatment with trichostatin A (TSA) is sufficient to block the repressor effect of Lsh. Moreover, overexpression of Lsh is correlated with deacetylation of histone H3 at the p16 promoter, and TSA treatment in Lsh-expressing cells reverses the acetylation status of histones. Additionally, we demonstrate an interaction between Lsh, histone deacetylase 1 (HDAC1) and HDAC2 in vivo. Furthermore, we demonstrate that Lsh interacts in vivo with the p16 promoter and recruits HDAC1. Our data suggest that Lsh represses endogenous p16INK4a expression by recruiting HDAC to establish a repressive chromatin structure at the p16INK4a promoter, which in turn delays cell senescence.
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Affiliation(s)
- Rui Zhou
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Research Center on Aging, Beijing 100191, People's Republic of China
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45
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Fan T, Schmidtmann A, Xi S, Briones V, Zhu H, Suh HC, Gooya J, Keller JR, Xu H, Roayaei J, Anver M, Ruscetti S, Muegge K. DNA hypomethylation caused by Lsh deletion promotes erythroleukemia development. Epigenetics 2008; 3:134-42. [PMID: 18487951 PMCID: PMC3113485 DOI: 10.4161/epi.3.3.6252] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Hematopoietic malignancies are frequently associated with DNA hypomethylation but the molecular mechanisms involved in tumor formation remain poorly understood. Here we report that mice lacking Lsh develop leukemia associated with DNA hypomethylation and oncogene activation. Lsh is a member of the SNF2 chromatin remodeling family and is required for de novo methylation of genomic DNA. Mice that received Lsh deficient hematopoietic progenitors showed severe impairment of hematopoiesis, suggesting that Lsh is necessary for normal hematopoiesis. A subset of mice developed erythroleukemia, a tumor that does not spontaneously occur in mice. Tumor tissues were CpG hypomethylated and showed a modest elevation of the transcription factor PU.1, an oncogene that is crucial for Friend virus induced erythroleukemia. Analysis of Lsh(-/-) hematopoietic progenitors revealed widespread DNA hypomethylation at repetitive sequences and hypomethylation at specific retroviral elements within the PU.1 gene. Wild type cells showed Lsh and Dnmt3b binding at the retroviral elements located within the PU.1 gene. On the other hand, Lsh deficient cells had no detectable Dnmt3b association suggesting that Lsh is necessary for recruitment of Dnmt3b to its target. Furthermore, Lsh(-/-) hematopoietic precursors showed impaired suppression of retroviral elements in the PU.1 gene, an increase of PU.1 transcripts and protein levels. Thus DNA hypomethylation caused by Lsh depletion is linked to transcriptional upregulation of retroviral elements and oncogenes such as PU.1 which in turn may promote the development of erythroleukemia in mice.
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Affiliation(s)
- Tao Fan
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Anja Schmidtmann
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Sichuan Xi
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Victorino Briones
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Heming Zhu
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Hyung Chan Suh
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - John Gooya
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Jonathan R. Keller
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Hong Xu
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Jean Roayaei
- Computer and Statistical Services; National Cancer Institute; Frederick, Maryland USA
| | - Miriam Anver
- Pathology/Histotechnology Laboratory; SAIC Frederick; National Cancer Institute; Frederick, Maryland USA
| | - Sandra Ruscetti
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
| | - Kathrin Muegge
- Laboratory of Cancer Prevention; SAIC-FCRDC; Basic Research Program; National Cancer Institute; Frederick, Maryland USA
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46
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Baumann C, Schmidtmann A, Muegge K, De La Fuente R. Association of ATRX with pericentric heterochromatin and the Y chromosome of neonatal mouse spermatogonia. BMC Mol Biol 2008; 9:29. [PMID: 18366812 PMCID: PMC2275742 DOI: 10.1186/1471-2199-9-29] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 03/13/2008] [Indexed: 11/10/2022] Open
Abstract
Background Establishment of chromosomal cytosine methylation and histone methylation patterns are critical epigenetic modifications required for heterochromatin formation in the mammalian genome. However, the nature of the primary signal(s) targeting DNA methylation at specific genomic regions is not clear. Notably, whether histone methylation and/or chromatin remodeling proteins play a role in the establishment of DNA methylation during gametogenesis is not known. The chromosomes of mouse neonatal spermatogonia display a unique pattern of 5-methyl cytosine staining whereby centromeric heterochromatin is hypo-methylated whereas chromatids are strongly methylated. Thus, in order to gain some insight into the relationship between global DNA and histone methylation in the germ line we have used neonatal spermatogonia as a model to determine whether these unique chromosomal DNA methylation patterns are also reflected by concomitant changes in histone methylation. Results Our results demonstrate that histone H3 tri-methylated at lysine 9 (H3K9me3), a hallmark of constitutive heterochromatin, as well as the chromatin remodeling protein ATRX remained associated with pericentric heterochromatin regions in spite of their extensive hypo-methylation. This suggests that in neonatal spermatogonia, chromosomal 5-methyl cytosine patterns are regulated independently of changes in histone methylation, potentially reflecting a crucial mechanism to maintain pericentric heterochromatin silencing. Furthermore, chromatin immunoprecipitation and fluorescence in situ hybridization, revealed that ATRX as well as H3K9me3 associate with Y chromosome-specific DNA sequences and decorate both arms of the Y chromosome, suggesting a possible role in heterochromatinization and the predominant transcriptional quiescence of this chromosome during spermatogenesis. Conclusion These results are consistent with a role for histone modifications and chromatin remodeling proteins such as ATRX in maintaining transcriptional repression at constitutive heterochromatin domains in the absence of 5-methyl cytosine and provide evidence suggesting that the establishment and/or maintenance of repressive histone and chromatin modifications at pericentric heterochromatin following genome-wide epigenetic reprogramming in the germ line may precede the establishment of chromosomal 5-methyl cytosine patterns as a genomic silencing strategy in neonatal spermatogonia.
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Affiliation(s)
- Claudia Baumann
- Female Germ Cell Biology Group, Department of Clinical Studies, Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square, PA 19348, USA.
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47
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Latham T, Gilbert N, Ramsahoye B. DNA methylation in mouse embryonic stem cells and development. Cell Tissue Res 2007; 331:31-55. [PMID: 18060563 DOI: 10.1007/s00441-007-0537-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 10/17/2007] [Indexed: 01/01/2023]
Abstract
Mammalian development is associated with considerable changes in global DNA methylation levels at times of genomic reprogramming. Normal DNA methylation is essential for development but, despite considerable advances in our understanding of the DNA methyltransferases, the reason that development fails when DNA methylation is deficient remains unclear. Furthermore, although much is known about the enzymes that cause DNA methylation, comparatively little is known about the mechanisms or significance of active demethylation in early development. In this review, we discuss the roles of the various DNA methyltransferases and their likely functions in development.
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Affiliation(s)
- Tom Latham
- Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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De La Fuente R, Baumann C, Fan T, Schmidtmann A, Dobrinski I, Muegge K. Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells. Nat Cell Biol 2006; 8:1448-54. [PMID: 17115026 DOI: 10.1038/ncb1513] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 09/05/2006] [Indexed: 11/08/2022]
Abstract
Lymphoid specific helicase (Lsh) is a major epigenetic regulator that is essential for DNA methylation and transcriptional silencing of parasitic elements in the mammalian genome. However, whether Lsh is involved in the regulation of chromatin-mediated processes during meiosis is not known. Here, we show that Lsh is essential for the completion of meiosis and transcriptional repression of repetitive elements in the female gonad. Oocytes from Lsh knockout mice exhibit demethylation of transposable elements and tandem repeats at pericentric heterochromatin, as well as incomplete chromosome synapsis associated with persistent RAD51 foci and gammaH2AX phosphorylation. Failure to load crossover-associated foci results in the generation of non-exchange chromosomes. The severe oocyte loss observed and lack of ovarian follicle formation, together with the patterns of Lsh nuclear compartmentalization in the germ line, demonstrate that Lsh has a critical and previously unidentified role in epigenetic gene silencing and maintenance of genomic stability during female meiosis.
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Affiliation(s)
- Rabindranath De La Fuente
- Female Germ Cell Biology Group, Department of Clinical Studies, Center for Animal Transgenesis and Germ Cell Research, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, PA 19348, USA.
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49
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Owen-Hughes T. The role of Snf2-related proteins in cancer. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2006:47-59. [PMID: 16568948 DOI: 10.1007/3-540-37633-x_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Several HDAC inhibitors that exhibit impressive anti-tumour activity are now in clinical trials. Proteins that function in the same pathways might also serve as valuable therapeutic targets. A subset of histone deacetylase activities are found to be physically associated with ATP-dependent remodelling enzymes and may assist their function. This raises the possibility that ATP-dependent remodelling enzymes should be considered as therapeutic targets. Here some of the links between ATP-dependent chromatin remodelling enzymes and cancer are reviewed.
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Affiliation(s)
- T Owen-Hughes
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Scotland, UK.
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50
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Ueda Y, Okano M, Williams C, Chen T, Georgopoulos K, Li E. Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 2006; 133:1183-92. [PMID: 16501171 DOI: 10.1242/dev.02293] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
ICF (Immunodeficiency, Centromeric instability and Facial anomalies) syndrome is a rare autosomal recessive disease caused by mutations in the DNA methyltransferase gene DNMT3B. To investigate the function of Dnmt3b in mouse development and to create animal models for ICF syndrome, we have generated three mutant alleles of Dnmt3b in mice: one carrying a deletion of the catalytic domain (null allele) and two carrying ICF-like missense mutations in the catalytic domain. The Dnmt3b null allele results in embryonic lethality from E14.5 to E16.5 with multiple tissue defects, including liver hypotrophy, ventricular septal defect and haemorrhage. By contrast, mice homozygous for the ICF mutations develop to term and some survive to adulthood. These mice show phenotypes that are reminiscent of ICF patients, including hypomethylation of repetitive sequences, low body weight, distinct cranial facial anomalies and T cell death by apoptosis. These results indicate that Dnmt3b plays an essential role at different stages of mouse development, and that ICF missense mutations cause partial loss of function. These mutant mice will be useful for further elucidation of the pathogenic and molecular mechanisms underlying ICF syndrome.
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Affiliation(s)
- Yoshihide Ueda
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
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