1
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Crain AT, Nevil M, Leatham-Jensen MP, Reeves KB, Matera AG, McKay DJ, Duronio RJ. Redesigning the Drosophila histone gene cluster: an improved genetic platform for spatiotemporal manipulation of histone function. Genetics 2024; 228:iyae117. [PMID: 39039029 PMCID: PMC11373521 DOI: 10.1093/genetics/iyae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024] Open
Abstract
Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoans is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult. Drosophila melanogaster provides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms were developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available to Drosophila researchers. Here we describe the development of a newly engineered platform that rectifies many of these weaknesses. We used CRISPR to precisely delete the RD histone gene array (HisC), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. We designed this cassette with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. We also present a method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate the generation of histone mutant cells in various tissues at different stages of Drosophila development and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599USA
| | - Markus Nevil
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599USA
- Seeding Postdoctoral Innovators in Research & Education, University of North Carolina, Chapel Hill, NC 27599USA
| | - Mary P Leatham-Jensen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599USA
| | - Katherine B Reeves
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599USA
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2
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Jamali M, Barar E, Shi J. Unveiling the Molecular Landscape of Pancreatic Ductal Adenocarcinoma: Insights into the Role of the COMPASS-like Complex. Int J Mol Sci 2024; 25:5069. [PMID: 38791111 PMCID: PMC11121229 DOI: 10.3390/ijms25105069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is poised to become the second leading cause of cancer-related death by 2030, necessitating innovative therapeutic strategies. Genetic and epigenetic alterations, including those involving the COMPASS-like complex genes, have emerged as critical drivers of PDAC progression. This review explores the genetic and epigenetic landscape of PDAC, focusing on the role of the COMPASS-like complex in regulating chromatin accessibility and gene expression. Specifically, we delve into the functions of key components such as KDM6A, KMT2D, KMT2C, KMT2A, and KMT2B, highlighting their significance as potential therapeutic targets. Furthermore, we discuss the implications of these findings for developing novel treatment modalities for PDAC.
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Affiliation(s)
- Marzieh Jamali
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erfaneh Barar
- Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Jiaqi Shi
- Department of Pathology & Clinical Labs, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Crain AT, Nevil M, Leatham-Jensen MP, Reeves KB, Matera AG, McKay DJ, Duronio RJ. Redesigning the Drosophila histone gene cluster: An improved genetic platform for spatiotemporal manipulation of histone function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591202. [PMID: 38712307 PMCID: PMC11071459 DOI: 10.1101/2024.04.25.591202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoan models is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such RD histone gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult. Drosophila melanogaster provides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms have been developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available to Drosophila researchers. Here we describe the development of a newly engineered platform that rectifies many of these weaknesses. We used CRISPR to precisely delete the RD histone gene array ( HisC ), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. We designed this cassette with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. We also present a method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate generation of histone mutant cells in various tissues at different stages of Drosophila development and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation.
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4
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Golden CS, Williams S, Serrano MA. Molecular insights of KMT2D and clinical aspects of Kabuki syndrome type 1. Birth Defects Res 2023; 115:1809-1824. [PMID: 37158694 PMCID: PMC10845236 DOI: 10.1002/bdr2.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Kabuki syndrome type 1 (KS1), a rare multisystem congenital disorder, presents with characteristic facial features, intellectual disability, persistent fetal fingertip pads, skeletal abnormalities, and postnatal growth delays. KS1 results from pathogenic variants in the KMT2D gene, which encodes a histone methyltransferase protein involved in chromatin remodeling, promoter and enhancer regulation, and scaffold formation during early development. KMT2D also mediates cell signaling pathways, responding to external stimuli and organizing effector protein assembly. Research on KMT2D's molecular mechanisms in KS1 has primarily focused on its histone methyltransferase activity, leaving a gap in understanding the methyltransferase-independent roles in KS1 clinical manifestations. METHODS This scoping review examines KMT2D's role in gene expression regulation across various species, cell types, and contexts. We analyzed human pathogenic KMT2D variants using publicly available databases and compared them to research organism models of KS1. We also conducted a systematic search of healthcare and governmental databases for clinical trials, studies, and therapeutic approaches. RESULTS Our review highlights KMT2D's critical roles beyond methyltransferase activity in diverse cellular contexts and conditions. We identified six distinct groups of KMT2D as a cell signaling mediator, including evidence of methyltransferase-dependent and -independent activity. A comprehensive search of the literature, clinical databases, and public registries emphasizes the need for basic research on KMT2D's functional complexity and longitudinal studies of KS1 patients to establish objective outcome measurements for therapeutic development. CONCLUSION We discuss how KMT2D's role in translating external cellular communication can partly explain the clinical heterogeneity observed in KS1 patients. Additionally, we summarize the current molecular diagnostic approaches and clinical trials targeting KS1. This review is a resource for patient advocacy groups, researchers, and physicians to support KS1 diagnosis and therapeutic development.
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Affiliation(s)
- Carly S Golden
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Saylor Williams
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
| | - Maria A Serrano
- Center for Regenerative Medicine, Section of Vascular Biology, Department of Medicine, Boston University, Boston, Massachusetts, USA
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5
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Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness. Cell Rep 2022; 41:111832. [PMID: 36516782 PMCID: PMC9764455 DOI: 10.1016/j.celrep.2022.111832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
How histone modifications affect animal development remains difficult to ascertain. Despite the prevalence of histone 3 lysine 4 monomethylation (H3K4me1) on enhancers, hypomethylation appears to have minor effects on phenotype and viability. Here, we genetically reduce H3K4me1 deposition in Drosophila melanogaster and find that hypomethylation reduces transcription factor enrichment in nuclear microenvironments, disrupts gene expression, and reduces phenotypic robustness. Using a developmental phenomics approach, we find changes in morphology, metabolism, behavior, and offspring production. However, many phenotypic changes are only detected when hypomethylated flies develop outside of standard laboratory environments or with specific genetic backgrounds. Therefore, quantitative phenomics measurements can unravel how pleiotropic modulators of gene expression affect developmental robustness under conditions resembling the natural environments of a species.
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6
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Wang Y, Lee H, Fear JM, Berger I, Oliver B, Przytycka TM. NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks. Commun Biol 2022; 5:1282. [PMID: 36418514 PMCID: PMC9684490 DOI: 10.1038/s42003-022-04226-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
The inference of Gene Regulatory Networks (GRNs) is one of the key challenges in systems biology. Leading algorithms utilize, in addition to gene expression, prior knowledge such as Transcription Factor (TF) DNA binding motifs or results of TF binding experiments. However, such prior knowledge is typically incomplete, therefore, integrating it with gene expression to infer GRNs remains difficult. To address this challenge, we introduce NetREX-CF-Regulatory Network Reconstruction using EXpression and Collaborative Filtering-a GRN reconstruction approach that brings together Collaborative Filtering to address the incompleteness of the prior knowledge and a biologically justified model of gene expression (sparse Network Component Analysis based model). We validated the NetREX-CF using Yeast data and then used it to construct the GRN for Drosophila Schneider 2 (S2) cells. To corroborate the GRN, we performed a large-scale RNA-Seq analysis followed by a high-throughput RNAi treatment against all 465 expressed TFs in the cell line. Our knockdown result has not only extensively validated the GRN we built, but also provides a benchmark that our community can use for evaluating GRNs. Finally, we demonstrate that NetREX-CF can infer GRNs using single-cell RNA-Seq, and outperforms other methods, by using previously published human data.
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Affiliation(s)
- Yijie Wang
- Computer Science Department, Indiana University, Bloomington, IN, 47408, USA.
| | - Hangnoh Lee
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD, 20892, USA
| | - Justin M Fear
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD, 20892, USA
| | - Isabelle Berger
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD, 20892, USA
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD, 20892, USA.
| | - Teresa M Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA.
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7
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Huang W, Zhu JY, Fu Y, van de Leemput J, Han Z. Lpt, trr, and Hcf regulate histone mono- and dimethylation that are essential for Drosophila heart development. Dev Biol 2022; 490:53-65. [PMID: 35853502 PMCID: PMC10728806 DOI: 10.1016/j.ydbio.2022.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022]
Abstract
Mammalian KMT2C, KMT2D, and HCFC1 are expressed during heart development and have been associated with congenital heart disease, but their roles in heart development remain elusive. We found that the Drosophila Lpt and trr genes encode the N-terminal and C-terminal homologs, respectively, of mammalian KMT2C or KMT2D. Lpt and trr mutant embryos showed reduced cardiac progenitor cells. Silencing of Lpt, trr, or both simultaneously in the heart led to similar abnormal cardiac morphology, tissue fibrosis, and cardiac functional defects. Like KMT2D, Lpt and trr were found to modulate histone H3K4 mono- and dimethylation, but not trimethylation. Investigation of downstream genes regulated by mouse KMT2D in the heart showed that their fly homologs are similarly regulated by Lpt or trr in the fly heart, suggesting that Lpt and trr regulate an evolutionarily conserved transcriptional network for heart development. Moreover, we showed that cardiac silencing of Hcf, the fly homolog of mammalian HCFC1, leads to heart defects similar to those observed in Lpt and trr silencing, as well as reduced H3K4 monomethylation. Our findings suggest that Lpt and trr function together to execute the conserved function of mammalian KMT2C and KMT2D in histone H3 lysine K4 mono- and dimethylation required for heart development. Possibly aided by Hcf, which we show plays a related role in H3K4 methylation during fly heart development.
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Affiliation(s)
- Wen Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jun-Yi Zhu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yulong Fu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Genomic Diagnostics and Bioinformatics, Department of Pathology, The University of Alabama at Birmingham, Alabama, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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8
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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9
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Schwenty-Lara J, Pauli S, Borchers A. Using Xenopus to analyze neurocristopathies like Kabuki syndrome. Genesis 2020; 59:e23404. [PMID: 33351273 DOI: 10.1002/dvg.23404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/08/2022]
Abstract
Neurocristopathies are human congenital syndromes that arise from defects in neural crest (NC) development and are typically associated with malformations of the craniofacial skeleton. Genetic analyses have been very successful in identifying pathogenic mutations, however, model organisms are required to characterize how these mutations affect embryonic development thereby leading to complex clinical conditions. The African clawed frog Xenopus laevis provides a broad range of in vivo and in vitro tools allowing for a detailed characterization of NC development. Due to the conserved nature of craniofacial morphogenesis in vertebrates, Xenopus is an efficient and versatile system to dissect the morphological and cellular phenotypes as well as the signaling events leading to NC defects. Here, we review a set of techniques and resources how Xenopus can be used as a disease model to investigate the pathogenesis of Kabuki syndrome and neurocristopathies in a wider sense.
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Affiliation(s)
- Janina Schwenty-Lara
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany.,DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-University Marburg, Marburg, Germany
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10
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [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: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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11
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Ford DJ, Zraly CB, Perez JH, Dingwall AK. The Drosophila MLR COMPASS-like complex regulates bantam miRNA expression differentially in the context of cell fate. Dev Biol 2020; 468:41-53. [PMID: 32946789 DOI: 10.1016/j.ydbio.2020.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
The conserved MLR COMPASS-like complexes are histone modifiers that are recruited by a variety of transcription factors to enhancer regions where they act as necessary epigenetic tools for enhancer establishment and function. A critical in vivo target of the Drosophila MLR complex is the bantam miRNA that regulates cell survival and functions in feedback regulation of cellular signaling pathways during development. We determine that loss of Drosophila MLR complex function in developing wing and eye imaginal discs results in growth and patterning defects that are sensitive to bantam levels. Consistent with an essential regulatory role in modulating bantam transcription, the MLR complex binds to tissue-specific bantam enhancers and contributes to fine-tuning expression levels during larval tissue development. In wing imaginal discs, the MLR complex attenuates bantam enhancer activity by negatively regulating expression; whereas, in differentiating eye discs, the complex exerts either positive or negative regulatory activity on bantam transcription depending on cell fate. Furthermore, while the MLR complex is not required to control bantam levels in undifferentiated eye cells anterior to the morphogenetic furrow, it serves to prepare critical enhancer control of bantam transcription for later regulation upon differentiation. Our investigation into the transcriptional regulation of a single target in a developmental context has provided novel insights as to how the MLR complex contributes to the precise timing of gene expression, and how the complex functions to help orchestrate the regulatory output of conserved signaling pathways during animal development.
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Affiliation(s)
- David J Ford
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA; Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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12
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Zraly CB, Zakkar A, Perez JH, Ng J, White KP, Slattery M, Dingwall AK. The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development. Nucleic Acids Res 2020; 48:3476-3495. [PMID: 32052053 PMCID: PMC7144903 DOI: 10.1093/nar/gkaa082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers depending on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.
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Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abdul Zakkar
- Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jeffrey Ng
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Slattery
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.,Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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13
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Park K, Kim JA, Kim J. Transcriptional regulation by the KMT2 histone H3K4 methyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194545. [DOI: 10.1016/j.bbagrm.2020.194545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/21/2020] [Accepted: 03/13/2020] [Indexed: 01/09/2023]
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14
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Crump NT, Milne TA. Why are so many MLL lysine methyltransferases required for normal mammalian development? Cell Mol Life Sci 2019; 76:2885-2898. [PMID: 31098676 PMCID: PMC6647185 DOI: 10.1007/s00018-019-03143-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022]
Abstract
The mixed lineage leukemia (MLL) family of proteins became known initially for the leukemia link of its founding member. Over the decades, the MLL family has been recognized as an important class of histone H3 lysine 4 (H3K4) methyltransferases that control key aspects of normal cell physiology and development. Here, we provide a brief history of the discovery and study of this family of proteins. We address two main questions: why are there so many H3K4 methyltransferases in mammals; and is H3K4 methylation their key function?
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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15
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Rickels R, Herz HM, Sze CC, Cao K, Morgan MA, Collings CK, Gause M, Takahashi YH, Wang L, Rendleman EJ, Marshall SA, Krueger A, Bartom ET, Piunti A, Smith ER, Abshiru NA, Kelleher NL, Dorsett D, Shilatifard A. Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability. Nat Genet 2017; 49:1647-1653. [PMID: 28967912 DOI: 10.1038/ng.3965] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022]
Abstract
Histone H3 lysine 4 monomethylation (H3K4me1) is an evolutionarily conserved feature of enhancer chromatin catalyzed by the COMPASS-like methyltransferase family, which includes Trr in Drosophila melanogaster and MLL3 (encoded by KMT2C) and MLL4 (encoded by KMT2D) in mammals. Here we demonstrate that Drosophila embryos expressing catalytically deficient Trr eclose and develop to productive adulthood. Parallel experiments with a trr allele that augments enzyme product specificity show that conversion of H3K4me1 at enhancers to H3K4me2 and H3K4me3 is also compatible with life and results in minimal changes in gene expression. Similarly, loss of the catalytic SET domains of MLL3 and MLL4 in mouse embryonic stem cells (mESCs) does not disrupt self-renewal. Drosophila embryos with trr alleles encoding catalytic mutants manifest subtle developmental abnormalities when subjected to temperature stress or altered cohesin levels. Collectively, our findings suggest that animal development can occur in the context of Trr or mammalian COMPASS-like proteins deficient in H3K4 monomethylation activity and point to a possible role for H3K4me1 on cis-regulatory elements in specific settings to fine-tune transcriptional regulation in response to environmental stress.
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Affiliation(s)
- Ryan Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hans-Martin Herz
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Christie C Sze
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kaixiang Cao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marc A Morgan
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Maria Gause
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Annika Krueger
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nebiyu A Abshiru
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Dale Dorsett
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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16
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Huang YC, Lin SJ, Shih HY, Chou CH, Chu HH, Chiu CC, Yuh CH, Yeh TH, Cheng YC. Epigenetic regulation of NOTCH1 and NOTCH3 by KMT2A inhibits glioma proliferation. Oncotarget 2017; 8:63110-63120. [PMID: 28968975 PMCID: PMC5609907 DOI: 10.18632/oncotarget.18668] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Glioblastomas are among the most fatal brain tumors; however, the molecular determinants of their tumorigenic behavior are not adequately defined. In this study, we analyzed the role of KMT2A in the glioblastoma cell line U-87 MG. KMT2A knockdown promoted cell proliferation. Moreover, it increased the DNA methylation of NOTCH1 and NOTCH3 and reduced the expression of NOTCH1 and NOTCH3. NOTCH1 or NOTCH3 activation inhibited U-87 MG cell proliferation, whereas NOTCH1 and NOTCH3 inhibition by shRNAs induced cell proliferation, thus demonstrating the tumor-suppressive ability of NOTCH1 and NOTCH3 in U-87 MG cells. The induced cell proliferation caused by KMT2A knockdown could be nullified by using either constitutively active NOTCH1 or constitutively active NOTCH3. This result demonstrates that KMT2A positively regulates NOTCH1 and NOTCH3 and that this mechanism is essential for inhibiting the U-87 MG cell proliferation. The role of KMT2A knockdown in promoting tumor growth was further confirmed in vivo by transplanting U-87 MG cells into the brains of zebrafish larvae. In conclusion, we identified KMT2A-NOTCH as a negative regulatory cascade for glioblastoma cell proliferation, and this result provides important information for KMT2A- or NOTCH-targeted therapeutic strategies for brain tumors.
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Affiliation(s)
- Yin-Cheng Huang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
| | - Sheng-Jia Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Hung-Yu Shih
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Chung-Han Chou
- School of Medicine, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Hsiao-Han Chu
- School of Medicine, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Ching-Chi Chiu
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
| | - Chiou-Hwa Yuh
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Tu-Hsueh Yeh
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan.,Department of Neurology, Taipei Medical University Hospital, Taipei, Taiwan.,School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Chuan Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, Taoyuan, Taiwan.,Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou Medical Center, Taoyuan, Taiwan
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17
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Abstract
In this review, Hu and Shilatifard summarize recent advances in our understanding of the role of chromatin modifiers in normal hematopoiesis and their contributions in hematopoietic transformation. Hematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms in which normal hematopoiesis has gone awry and together account for ∼10% of all new cancer cases diagnosed in the United States in 2016. Recent intensive genomic sequencing of hematopoietic malignancies has identified recurrent mutations in genes that encode regulators of chromatin structure and function, highlighting the central role that aberrant epigenetic regulation plays in the pathogenesis of these neoplasms. Deciphering the molecular mechanisms for how alterations in epigenetic modifiers, specifically histone and DNA methylases and demethylases, drive hematopoietic cancer could provide new avenues for developing novel targeted epigenetic therapies for treating hematological malignancies. Just as past studies of blood cancers led to pioneering discoveries relevant to other cancers, determining the contribution of epigenetic modifiers in hematologic cancers could also have a broader impact on our understanding of the pathogenesis of solid tumors in which these factors are mutated.
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Affiliation(s)
- Deqing Hu
- Department of Biochemistry and Molecular Genetics
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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18
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Le Gallo M, Rudd ML, Urick ME, Hansen NF, Zhang S, Lozy F, Sgroi DC, Vidal Bel A, Matias-Guiu X, Broaddus RR, Lu KH, Levine DA, Mutch DG, Goodfellow PJ, Salvesen HB, Mullikin JC, Bell DW. Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing. Cancer 2017; 123:3261-3268. [PMID: 28485815 DOI: 10.1002/cncr.30745] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND The molecular pathogenesis of clear cell endometrial cancer (CCEC), a tumor type with a relatively unfavorable prognosis, is not well defined. We searched exome-wide for novel somatically mutated genes in CCEC and assessed the mutational spectrum of known and candidate driver genes in a large cohort of cases. METHODS We conducted whole exome sequencing of paired tumor-normal DNAs from 16 cases of CCEC (12 CCECs and the CCEC components of 4 mixed histology tumors). Twenty-two genes-of-interest were Sanger-sequenced from another 47 cases of CCEC. Microsatellite instability (MSI) and microsatellite stability (MSS) were determined by genotyping 5 mononucleotide repeats. RESULTS Two tumor exomes had relatively high mutational loads and MSI. The other 14 tumor exomes were MSS and had 236 validated nonsynonymous or splice junction somatic mutations among 222 protein-encoding genes. Among the 63 cases of CCEC in this study, we identified frequent somatic mutations in TP53 (39.7%), PIK3CA (23.8%), PIK3R1 (15.9%), ARID1A (15.9%), PPP2R1A (15.9%), SPOP (14.3%), and TAF1 (9.5%), as well as MSI (11.3%). Five of 8 mutations in TAF1, a gene with no known role in CCEC, localized to the putative histone acetyltransferase domain and included 2 recurrently mutated residues. Based on patterns of MSI and mutations in 7 genes, CCEC subsets molecularly resembled serous endometrial cancer (SEC) or endometrioid endometrial cancer (EEC). CONCLUSION Our findings demonstrate molecular similarities between CCEC and SEC and EEC and implicate TAF1 as a novel candidate CCEC driver gene. Cancer 2017;123:3261-8. © 2017 American Cancer Society.
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Affiliation(s)
- Matthieu Le Gallo
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Meghan L Rudd
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Mary Ellen Urick
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Suiyuan Zhang
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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- National Institutes of Health Intramural Sequencing Center, National Institutes of Health, Bethesda, Maryland
| | - Fred Lozy
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Dennis C Sgroi
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - August Vidal Bel
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain.,Department of Pathology, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari de Bellvitge, Barcelona, Spain.,Department of Pathology and Molecular Genetics/Oncological Pathology Group, Hospital Universitari Arnau de Vilanova, Universitat de Lleida, IRB Lleida, Lleida, Spain
| | - Russell R Broaddus
- Division of Surgery, Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Karen H Lu
- Division of Surgery, Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Douglas A Levine
- Gynecologic Oncology, Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York
| | - David G Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri
| | - Paul J Goodfellow
- Department of Obstetrics and Gynecology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Helga B Salvesen
- Department of Clinical Science, Center for Cancer Biomarkers, University of Bergen, Bergen, Norway.,Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,National Institutes of Health Intramural Sequencing Center, National Institutes of Health, Bethesda, Maryland
| | - Daphne W Bell
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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19
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Sze CC, Shilatifard A. MLL3/MLL4/COMPASS Family on Epigenetic Regulation of Enhancer Function and Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026427. [PMID: 27638352 DOI: 10.1101/cshperspect.a026427] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
During development, precise spatiotemporal patterns of gene expression are coordinately controlled by cis-regulatory modules known as enhancers. Their crucial role in development helped spur numerous studies aiming to elucidate the functional properties of enhancers within their physiological and disease contexts. In recent years, the role of enhancer malfunction in tissue-specific tumorigenesis is increasingly investigated. Here, we direct our focus to two primary players in enhancer regulation and their role in cancer pathogenesis: MLL3 and MLL4, members of the COMPASS family of histone H3 lysine 4 (H3K4) methyltransferases, and their complex-specific subunit UTX, a histone H3 lysine 27 (H3K27) demethylase. We review the most recent evidence on the underlying roles of MLL3/MLL4 and UTX in cancer and highlight key outstanding questions to help drive future research and contribute to our fundamental understanding of cancer and facilitate identification of therapeutic opportunities.
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Affiliation(s)
- Christie C Sze
- Department of Biochemistry and Molecular Genetics and Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics and Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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20
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Abstract
Mutations in enhancer-associated chromatin-modifying components and genomic alterations in non-coding regions of the genome occur frequently in cancer, and other diseases pointing to the importance of enhancer fidelity to ensure proper tissue homeostasis. In this review, I will use specific examples to discuss how mutations in chromatin-modifying factors might affect enhancer activity of disease-relevant genes. I will then consider direct evidence from single nucleotide polymorphisms, small insertions, or deletions but also larger genomic rearrangements such as duplications, deletions, translocations, and inversions of specific enhancers to demonstrate how they have the ability to impact enhancer activity of disease genes including oncogenes and tumor suppressor genes. Considering that the scientific community only fairly recently has begun to focus its attention on "enhancer malfunction" in disease, I propose that multiple new enhancer-regulated and disease-relevant processes will be uncovered in the near future that will constitute the mechanistic basis for novel therapeutic avenues.
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Affiliation(s)
- Hans-Martin Herz
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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21
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Dawkins JBN, Wang J, Maniati E, Heward JA, Koniali L, Kocher HM, Martin SA, Chelala C, Balkwill FR, Fitzgibbon J, Grose RP. Reduced Expression of Histone Methyltransferases KMT2C and KMT2D Correlates with Improved Outcome in Pancreatic Ductal Adenocarcinoma. Cancer Res 2016; 76:4861-71. [PMID: 27280393 PMCID: PMC5321534 DOI: 10.1158/0008-5472.can-16-0481] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/30/2016] [Indexed: 12/21/2022]
Abstract
Genes encoding the histone H3 lysine 4 methyltransferases KMT2C and KMT2D are subject to deletion and mutation in pancreatic ductal adenocarcinoma (PDAC), where these lesions identify a group of patients with a more favorable prognosis. In this study, we demonstrate that low KMT2C and KMT2D expression in biopsies also defines better outcome groups, with median survivals of 15.9 versus 9.2 months (P = 0.029) and 19.9 versus 11.8 months (P = 0.001), respectively. Experiments with eight human pancreatic cell lines showed attenuated cell proliferation when these methyltransferases were depleted, suggesting that this improved outcome may reflect a cell-cycle block with diminished progression from G0-G1 RNA-seq analysis of PDAC cell lines following KMT2C or KMT2D knockdown identified 31 and 124 differentially expressed genes, respectively, with 19 genes in common. Gene-set enrichment analysis revealed significant downregulation of genes related to cell-cycle and growth. These data were corroborated independently by examining KMT2C/D signatures extracted from the International Cancer Genome Consortium and The Cancer Genome Atlas datasets. Furthermore, these experiments highlighted a potential role for NCAPD3, a condensin II complex subunit, as an outcome predictor in PDAC using existing gene expression series. Kmt2d depletion in KC/KPC cell lines also led to an increased response to the nucleoside analogue 5-fluorouracil, suggesting that lower levels of this methyltransferase may mediate the sensitivity of PDAC to particular treatments. Therefore, it may also be therapeutically beneficial to target these methyltransferases in PDAC, especially in those patients demonstrating higher KTM2C/D expression. Cancer Res; 76(16); 4861-71. ©2016 AACR.
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Affiliation(s)
- Joshua B N Dawkins
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - James A Heward
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Lola Koniali
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Hemant M Kocher
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Sarah A Martin
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Claude Chelala
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Frances R Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Richard P Grose
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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22
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Skinner A, Khan SJ, Smith-Bolton RK. Trithorax regulates systemic signaling during Drosophila imaginal disc regeneration. Development 2016; 142:3500-11. [PMID: 26487779 DOI: 10.1242/dev.122564] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although tissue regeneration has been studied in a variety of organisms, from Hydra to humans, many of the genes that regulate the ability of each animal to regenerate remain unknown. The larval imaginal discs of the genetically tractable model organism Drosophila melanogaster have complex patterning, well-characterized development and a high regenerative capacity, and are thus an excellent model system for studying mechanisms that regulate regeneration. To identify genes that are important for wound healing and tissue repair, we have carried out a genetic screen for mutations that impair regeneration in the wing imaginal disc. Through this screen we identified the chromatin-modification gene trithorax as a key regeneration gene. Here we show that animals heterozygous for trithorax are unable to maintain activation of a developmental checkpoint that allows regeneration to occur. This defect is likely to be caused by abnormally high expression of puckered, a negative regulator of Jun N-terminal kinase (JNK) signaling, at the wound site. Insufficient JNK signaling leads to insufficient expression of an insulin-like peptide, dILP8, which is required for the developmental checkpoint. Thus, trithorax regulates regeneration signaling and capacity.
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Affiliation(s)
- Andrea Skinner
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61853, USA
| | - Sumbul Jawed Khan
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61853, USA
| | - Rachel K Smith-Bolton
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61853, USA
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23
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Kimura S, Loppin B. Two bromodomain proteins functionally interact to recapitulate an essential BRDT-like function in Drosophila spermatocytes. Open Biol 2015; 5:140145. [PMID: 25652540 PMCID: PMC4345279 DOI: 10.1098/rsob.140145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In mammals, the testis-specific bromodomain and extra terminal (BET) protein BRDT is essential for spermatogenesis. In Drosophila, it was recently reported that the tBRD-1 protein is similarly required for male fertility. Interestingly, however, tBRD-1 has two conserved bromodomains in its N-terminus but it lacks an extra terminal (ET) domain characteristic of BET proteins. Here, using proteomics approaches to search for tBRD-1 interactors, we identified tBRD-2 as a novel testis-specific bromodomain protein. In contrast to tBRD-1, tBRD-2 contains a single bromodomain, but which is associated with an ET domain in its C-terminus. Strikingly, we show that tbrd-2 knock-out males are sterile and display aberrant meiosis in a way highly similar to tbrd-1 mutants. Furthermore, these two factors co-localize and are interdependent in spermatocytes. We propose that Drosophila tBRD-1 and tBRD-2 associate into a functional BET complex in spermatocytes, which recapitulates the activity of the single mammalian BRDT-like protein.
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Affiliation(s)
- Shuhei Kimura
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, 69622 Villeurbanne cedex, France
| | - Benjamin Loppin
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, 69622 Villeurbanne cedex, France
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24
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Abstract
Histone-lysine N-methyltransferase 2 (KMT2) family proteins methylate lysine 4 on the histone H3 tail at important regulatory regions in the genome and thereby impart crucial functions through modulating chromatin structures and DNA accessibility. Although the human KMT2 family was initially named the mixed-lineage leukaemia (MLL) family, owing to the role of the first-found member KMT2A in this disease, recent exome-sequencing studies revealed KMT2 genes to be among the most frequently mutated genes in many types of human cancers. Efforts to integrate the molecular mechanisms of KMT2 with its roles in tumorigenesis have led to the development of first-generation inhibitors of KMT2 function, which could become novel cancer therapies.
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Affiliation(s)
- Rajesh C. Rao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI 48109
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
- Correspondence: , Tel: (734) 6151315, Fax: (734) 7636476
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25
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Sinkovics JG. The cell survival pathways of the primordial RNA-DNA complex remain conserved in the extant genomes and may function as proto-oncogenes. Eur J Microbiol Immunol (Bp) 2015; 5:25-43. [PMID: 25883792 PMCID: PMC4397846 DOI: 10.1556/eujmi-d-14-00034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/22/2014] [Indexed: 01/09/2023] Open
Abstract
Malignantly transformed (cancer) cells of multicellular hosts, including human cells, operate activated biochemical pathways that recognizably derived from unicellular ancestors. The descendant heat shock proteins of thermophile archaea now chaperon oncoproteins. The ABC cassettes of toxin-producer zooxantella Symbiodinia algae pump out the cytoplasmic toxin molecules; malignantly transformed cells utilize the derivatives of these cassettes to get rid of chemotherapeuticals. High mobility group helix-loop-helix proteins, protein arginine methyltransferases, proliferating cell nuclear antigens, and Ki-67 nuclear proteins, that protect and repair DNA in unicellular life forms, support oncogenes in transformed cells. The cell survival pathways of Wnt-β-catenin, Hedgehog, PI3K, MAPK-ERK, STAT, Ets, JAK, Pak, Myb, achaete scute, circadian rhythms, Bruton kinase and others, which are physiological in uni- and early multicellular eukaryotic life forms, are constitutively encoded in complex oncogenic pathways in selected single cells of advanced multicellular eukaryotic hosts. Oncogenes and oncoproteins in advanced multicellular hosts recreate selected independently living and immortalized unicellular life forms, which are similar to extinct and extant protists. These unicellular life forms are recognized at the clinics as autologous "cancer cells".
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Affiliation(s)
- J G Sinkovics
- St. Joseph's Hospital Cancer Institute Affiliated with the H. L. Moffitt Comprehensive Cancer Center, Morsani College of Medicine, Department of Molecular Medicine, The University of South Florida Tampa, FL USA
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26
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The cancer COMPASS: navigating the functions of MLL complexes in cancer. Cancer Genet 2015; 208:178-91. [PMID: 25794446 DOI: 10.1016/j.cancergen.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/13/2022]
Abstract
The mixed-lineage leukemia family of histone methyltransferases (MLL1-4, or KMT2A-D) were previously linked to cancer through the founding member, MLL1/KMT2A, which is often involved in translocation-associated gene fusion events in childhood leukemias. However, in recent years, a multitude of tumor exome sequencing studies have revealed that orthologues MLL3/KMT2C and MLL2/KMT2D are mutated in a significant percentage of a large variety of malignancies, particularly solid tumors. These unexpected findings necessitate a deeper inspection into the activities and functional differences between the MLL/KMT2 family members. This review provides an overview of this protein family and its relation to cancers, focusing on the recent links between MLL3/KMT2C and MLL2/4/KMT2D and their potential roles as tumor suppressors in an assortment of cell types.
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27
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Agha Z, Iqbal Z, Azam M, Ayub H, Vissers LELM, Gilissen C, Ali SHB, Riaz M, Veltman JA, Pfundt R, van Bokhoven H, Qamar R. Exome sequencing identifies three novel candidate genes implicated in intellectual disability. PLoS One 2014; 9:e112687. [PMID: 25405613 PMCID: PMC4236113 DOI: 10.1371/journal.pone.0112687] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/10/2014] [Indexed: 01/07/2023] Open
Abstract
Intellectual disability (ID) is a major health problem mostly with an unknown etiology. Recently exome sequencing of individuals with ID identified novel genes implicated in the disease. Therefore the purpose of the present study was to identify the genetic cause of ID in one syndromic and two non-syndromic Pakistani families. Whole exome of three ID probands was sequenced. Missense variations in two plausible novel genes implicated in autosomal recessive ID were identified: lysine (K)-specific methyltransferase 2B (KMT2B), zinc finger protein 589 (ZNF589), as well as hedgehog acyltransferase (HHAT) with a de novo mutation with autosomal dominant mode of inheritance. The KMT2B recessive variant is the first report of recessive Kleefstra syndrome-like phenotype. Identification of plausible causative mutations for two recessive and a dominant type of ID, in genes not previously implicated in disease, underscores the large genetic heterogeneity of ID. These results also support the viewpoint that large number of ID genes converge on limited number of common networks i.e. ZNF589 belongs to KRAB-domain zinc-finger proteins previously implicated in ID, HHAT is predicted to affect sonic hedgehog, which is involved in several disorders with ID, KMT2B associated with syndromic ID fits the epigenetic module underlying the Kleefstra syndromic spectrum. The association of these novel genes in three different Pakistani ID families highlights the importance of screening these genes in more families with similar phenotypes from different populations to confirm the involvement of these genes in pathogenesis of ID.
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Affiliation(s)
- Zehra Agha
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Zafar Iqbal
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Humaira Ayub
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Syeda Hafiza Benish Ali
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Moeen Riaz
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Joris A. Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- * E-mail: (HvB); (RQ)
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
- Department of Biochemistry, Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
- * E-mail: (HvB); (RQ)
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Qing Y, Yin F, Wang W, Zheng Y, Guo P, Schozer F, Deng H, Pan D. The Hippo effector Yorkie activates transcription by interacting with a histone methyltransferase complex through Ncoa6. eLife 2014; 3. [PMID: 25027438 PMCID: PMC4118621 DOI: 10.7554/elife.02564] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/11/2014] [Indexed: 01/05/2023] Open
Abstract
The Hippo signaling pathway regulates tissue growth in Drosophila through the transcriptional coactivator Yorkie (Yki). How Yki activates target gene transcription is poorly understood. Here, we identify Nuclear receptor coactivator 6 (Ncoa6), a subunit of the Trithorax-related (Trr) histone H3 lysine 4 (H3K4) methyltransferase complex, as a Yki-binding protein. Like Yki, Ncoa6 and Trr are functionally required for Hippo-mediated growth control and target gene expression. Strikingly, artificial tethering of Ncoa6 to Sd is sufficient to promote tissue growth and Yki target expression even in the absence of Yki, underscoring the importance of Yki-mediated recruitment of Ncoa6 in transcriptional activation. Consistent with the established role for the Trr complex in histone methylation, we show that Yki, Ncoa6, and Trr are required for normal H3K4 methylation at Hippo target genes. These findings shed light on Yki-mediated transcriptional regulation and uncover a potential link between chromatin modification and tissue growth.
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Affiliation(s)
- Yun Qing
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Feng Yin
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Wei Wang
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Yonggang Zheng
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Pengfei Guo
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Frederick Schozer
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Hua Deng
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Duojia Pan
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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29
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Oh H, Slattery M, Ma L, White KP, Mann RS, Irvine KD. Yorkie promotes transcription by recruiting a histone methyltransferase complex. Cell Rep 2014; 8:449-59. [PMID: 25017066 DOI: 10.1016/j.celrep.2014.06.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 04/28/2014] [Accepted: 06/11/2014] [Indexed: 12/19/2022] Open
Abstract
Hippo signaling limits organ growth by inhibiting the transcriptional coactivator Yorkie. Despite the key role of Yorkie in both normal and oncogenic growth, the mechanism by which it activates transcription has not been defined. We report that Yorkie binding to chromatin correlates with histone H3K4 methylation and is sufficient to locally increase it. We show that Yorkie can recruit a histone methyltransferase complex through binding between WW domains of Yorkie and PPxY sequence motifs of NcoA6, a subunit of the Trithorax-related (Trr) methyltransferase complex. Cell culture and in vivo assays establish that this recruitment of NcoA6 contributes to Yorkie's ability to activate transcription. Mammalian NcoA6, a subunit of Trr-homologous methyltransferase complexes, can similarly interact with Yorkie's mammalian homolog YAP. Our results implicate direct recruitment of a histone methyltransferase complex as central to transcriptional activation by Yorkie, linking the control of cell proliferation by Hippo signaling to chromatin modification.
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Affiliation(s)
- Hyangyee Oh
- Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Slattery
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, HHSC 1104, New York, NY 10032, USA; Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, 900 East 57th Street, KCBD 10115, Chicago, IL 60637, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, 900 East 57th Street, KCBD 10115, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, 900 East 57th Street, KCBD 10115, Chicago, IL 60637, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, HHSC 1104, New York, NY 10032, USA
| | - Kenneth D Irvine
- Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.
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30
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Abstract
Why certain point mutations in a general transcription factor are associated with specific forms of cancer has been a major question in cancer biology. Enhancers are DNA regulatory elements that are key regulators of tissue-specific gene expression. Recent studies suggest that enhancer malfunction through point mutations in either regulatory elements or factors modulating enhancer-promoter communication could be the cause of tissue-specific cancer development. In this Perspective, we will discuss recent findings in the identification of cancer-related enhancer mutations and the role of Drosophila Trr and its human homologs, the MLL3 and MLL4/COMPASS-like complexes, as enhancer histone H3 lysine 4 (H3K4) monomethyltransferases functioning in enhancer-promoter communication. Recent genome-wide studies in the cataloging of somatic mutations in cancer have identified mutations in intergenic sequences encoding regulatory elements-and in MLL3 and MLL4 in both hematological malignancies and solid tumors. We propose that cancer-associated mutations in MLL3 and MLL4 exert their properties through the malfunction of Trr/MLL3/MLL4-dependent enhancers.
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Enhancer biology and enhanceropathies. Nat Struct Mol Biol 2014; 21:210-9. [DOI: 10.1038/nsmb.2784] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/06/2014] [Indexed: 12/18/2022]
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32
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Van der Meulen J, Speleman F, Van Vlierberghe P. The H3K27me3 demethylase UTX in normal development and disease. Epigenetics 2014; 9:658-68. [PMID: 24561908 PMCID: PMC4063824 DOI: 10.4161/epi.28298] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In 2007, the Ubiquitously Transcribed Tetratricopeptide Repeat on chromosome X (UTX) was identified as a histone demethylase that specifically targets di- and tri-methyl groups on lysine 27 of histone H3 (H3K27me2/3). Since then, UTX has been proven essential during normal development, as it is critically required for correct reprogramming, embryonic development and tissue-specific differentiation. UTX is a member of the MLL2 H3K4 methyltransferase complex and its catalytic activity has been linked to regulation of HOX and RB transcriptional networks. In addition, an H3K27me2/3 demethylase independent function for UTX was uncovered in promoting general chromatin remodeling in concert with the BRG1-containing SWI/SNF remodeling complex. Constitutional inactivation of UTX causes a specific hereditary disorder called the Kabuki syndrome, whereas somatic loss of UTX has been reported in a variety of human cancers. Here, we compile the breakthrough discoveries made from the first disclosure of UTX as a histone demethylase till the identification of disease-related UTX mutations and specific UTX inhibitors.
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Affiliation(s)
| | - Frank Speleman
- Center for Medical Genetics; Ghent University; Ghent, Belgium
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Abstract
PURPOSE OF REVIEW Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease featuring heterogeneous genetic, phenotypic, and clinical characteristics. Understanding the basis for this heterogeneity represents a critical step toward further progress in the management of this disease, which remains a clinical challenge in approximately one-third of patients. This review summarizes current knowledge about the molecular pathogenesis of DLBCL, and describes how recent advances in the genomic characterization of this cancer have provided new insights into its biology, revealing several potential targets for improved diagnosis and therapy. RECENT FINDINGS In the past few years, the development of high-resolution technologies has provided significant help in identifying genetic lesions and/or disrupted signaling pathways that are required for DLBCL initiation and progression. These studies uncovered the involvement of cellular programs that had not been previously appreciated, including histone/chromatin remodeling and immune recognition. Alterations in these pathways could favor epigenetic reprogramming and escape from cellular immunity. SUMMARY The identification of genetic alterations that contribute to the malignant transformation of a B cell into a DLBCL is helping to better understand the biology of this disease and to identify critical nodes driving tumor progression or resistance to therapy. The rapid pace at which these discoveries are taking place is poised to have significant impact for patient stratification based on molecular predictors and for the development of rational targeted therapies.
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Gu B, Lee MG. Histone H3 lysine 4 methyltransferases and demethylases in self-renewal and differentiation of stem cells. Cell Biosci 2013; 3:39. [PMID: 24172249 PMCID: PMC3953348 DOI: 10.1186/2045-3701-3-39] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 07/27/2013] [Indexed: 12/22/2022] Open
Abstract
Epigenetic mechanisms are fundamental to understanding the regulatory networks of
gene expression that govern stem cell maintenance and differentiation.
Methylated histone H3 lysine 4 (H3K4) has emerged as a key epigenetic signal for
gene transcription; it is dynamically modulated by several specific H3K4
methyltransferases and demethylases. Recent studies have described new
epigenetic mechanisms by which H3K4 methylation modifiers control self-renewal
and lineage commitments of stem cells. Such advances in stem cell biology would
have a high impact on the research fields of cancer stem cell and regenerative
medicine. In this review, we discuss the recent progress in understanding the
roles of H3K4 methylation modifiers in regulating embryonic and adult stem
cells’ fates.
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35
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The Drosophila COMPASS-like Cmi-Trr coactivator complex regulates dpp/BMP signaling in pattern formation. Dev Biol 2013; 380:185-98. [DOI: 10.1016/j.ydbio.2013.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 01/01/2023]
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36
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Drosophila SETs its sights on cancer: Trr/MLL3/4 COMPASS-like complexes in development and disease. Mol Cell Biol 2013; 33:1698-701. [PMID: 23459940 DOI: 10.1128/mcb.00203-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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