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Bamgbose G, Johnson S, Tulin A. Cooperative targeting of PARP-1 domains to regulate metabolic and developmental genes. Front Endocrinol (Lausanne) 2023; 14:1152570. [PMID: 37347109 PMCID: PMC10281051 DOI: 10.3389/fendo.2023.1152570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023] Open
Abstract
PARP-1, also known as poly(ADP-ribose) polymerase 1, is a multifunctional nuclear enzyme that plays a critical role in transcriptional regulation through its three functional domains: the N-terminal DNA-binding domain (DBD) containing two zinc fingers for DNA binding and a third zinc finger for maintaining interdomain contacts, the auto modification domain (AD), and the C-terminal domain, which includes the protein-interacting WGR domain and the catalytic domain. Despite the critical role that PARP-1 plays in regulating gene expression, the mechanisms by which it is targeted to chromatin are not well understood. In this study, we aimed to understand the targeting of PARP-1 to chromatin using ChIP-seq of YFP-tagged deletional isoforms of PARP-1 (ZnI, ZnII, AD-WGR) and a construct that lacks only ZnI (ΔZnI). Our results indicate that other PARP-1 domains are sufficient to target PARP-1 to active genes in the absence of ZnI. Furthermore, we found that PARP-1 represses metabolic gene pathways and activates developmental gene pathways. The results of ChIP-seq analysis showed that PARP-1 and ΔZnI were preferentially bound to the gene bodies of PARP-1-regulated metabolic genes compared to developmental genes. PARP-1 domains (ZnI, ZnII and AD-WGR) also preferentially occupied the gene bodies of PARP-1-regulated metabolic genes, however, they were more enriched at the TSS of PARP-1-regulated developmental genes compared to metabolic genes. Thus, we propose that PARP-1 domains cooperatively target PARP-1 to PARP-1-regulated genes to coordinate metabolic and developmental gene expression programs.
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Affiliation(s)
| | | | - Alexei Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, , United States
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2
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Grochau-Wright ZI, Nedelcu AM, Michod RE. The Genetics of Fitness Reorganization during the Transition to Multicellularity: The Volvocine regA-like Family as a Model. Genes (Basel) 2023; 14:genes14040941. [PMID: 37107699 PMCID: PMC10137558 DOI: 10.3390/genes14040941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The evolutionary transition from single-celled to multicellular individuality requires organismal fitness to shift from the cell level to a cell group. This reorganization of fitness occurs by re-allocating the two components of fitness, survival and reproduction, between two specialized cell types in the multicellular group: soma and germ, respectively. How does the genetic basis for such fitness reorganization evolve? One possible mechanism is the co-option of life history genes present in the unicellular ancestors of a multicellular lineage. For instance, single-celled organisms must regulate their investment in survival and reproduction in response to environmental changes, particularly decreasing reproduction to ensure survival under stress. Such stress response life history genes can provide the genetic basis for the evolution of cellular differentiation in multicellular lineages. The regA-like gene family in the volvocine green algal lineage provides an excellent model system to study how this co-option can occur. We discuss the origin and evolution of the volvocine regA-like gene family, including regA-the gene that controls somatic cell development in the model organism Volvox carteri. We hypothesize that the co-option of life history trade-off genes is a general mechanism involved in the transition to multicellular individuality, making volvocine algae and the regA-like family a useful template for similar investigations in other lineages.
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Affiliation(s)
| | - Aurora M Nedelcu
- Biology Department, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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3
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Wu L, Huang J, Trivedi P, Sun X, Yu H, He Z, Zhang X. Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis. Discov Oncol 2022; 13:139. [PMID: 36520265 PMCID: PMC9755447 DOI: 10.1007/s12672-022-00597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Morphogenesis and organogenesis in the low organisms have been found to be modulated by a number of proteins, and one of such factor, deformed epidermal auto-regulatory factor-1 (DEAF-1) has been initially identified in Drosophila. The mammalian homologue of DEAF-1 and structurally related proteins have been identified, and they formed a family with over 20 members. The factors regulate gene expression through association with co-repressors, recognition of genomic marker, to exert histone modification by catalyze addition of some chemical groups to certain amino acid residues on histone and non-histone proteins, and degradation host proteins, so as to regulate cell cycle progression and execution of cell death. The formation of fused genes during chromosomal translocation, exemplified with myeloid transforming gene on chromosome 8 (MTG8)/eight-to-twenty one translocation (ETO) /ZMYND2, MTG receptor 1 (MTGR1)/ZMYND3, MTG on chromosome 16/MTGR2/ZMYND4 and BS69/ZMYND11 contributes to malignant transformation. Other anomaly like copy number variation (CNV) of BS69/ZMYND11 and promoter hyper methylation of BLU/ZMYND10 has been noted in malignancies. It has been reported that when fusing with Runt-related transcription factor 1 (RUNX1), the binding of MTG8/ZMYND2 with co-repressors is disturbed, and silencing of BLU/ZMYND10 abrogates its ability to inhibition of cell cycle and promotion of apoptotic death. Further characterization of the implication of ZMYND proteins in carcinogenesis would enhance understanding of the mechanisms of occurrence and early diagnosis of tumors, and effective antitumor efficacy.
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Affiliation(s)
- Longji Wu
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
- Institute of Modern Biology, Nanjing University, Nanjing, Jiangsu, China
| | - Jing Huang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Pankaj Trivedi
- Department of Experimental Medicine, La Sapienza University, Rome, Italy
| | - Xuerong Sun
- Institute of Aging, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Hongbing Yu
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Zhiwei He
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Xiangning Zhang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China.
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China.
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4
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Waters CT, Gisselbrecht SS, Sytnikova YA, Cafarelli TM, Hill DE, Bulyk ML. Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue. Genome Biol 2021; 22:348. [PMID: 34930411 PMCID: PMC8686523 DOI: 10.1186/s13059-021-02574-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers. We measure quantitative changes in enhancer activity and discover a range of epistatic interactions among the motifs, both synergistic and alleviating. We find that understanding the regulatory consequences of TF binding motifs requires that they be investigated in combination across enhancer contexts.
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Affiliation(s)
- Colin T Waters
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yuliya A Sytnikova
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Tiziana M Cafarelli
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - David E Hill
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, 02138, USA.
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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5
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Graca FA, Sheffield N, Puppa M, Finkelstein D, Hunt LC, Demontis F. A large-scale transgenic RNAi screen identifies transcription factors that modulate myofiber size in Drosophila. PLoS Genet 2021; 17:e1009926. [PMID: 34780463 PMCID: PMC8629395 DOI: 10.1371/journal.pgen.1009926] [Citation(s) in RCA: 10] [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: 05/04/2021] [Revised: 11/29/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
Myofiber atrophy occurs with aging and in many diseases but the underlying mechanisms are incompletely understood. Here, we have used >1,100 muscle-targeted RNAi interventions to comprehensively assess the function of 447 transcription factors in the developmental growth of body wall skeletal muscles in Drosophila. This screen identifies new regulators of myofiber atrophy and hypertrophy, including the transcription factor Deaf1. Deaf1 RNAi increases myofiber size whereas Deaf1 overexpression induces atrophy. Consistent with its annotation as a Gsk3 phosphorylation substrate, Deaf1 and Gsk3 induce largely overlapping transcriptional changes that are opposed by Deaf1 RNAi. The top category of Deaf1-regulated genes consists of glycolytic enzymes, which are suppressed by Deaf1 and Gsk3 but are upregulated by Deaf1 RNAi. Similar to Deaf1 and Gsk3 overexpression, RNAi for glycolytic enzymes reduces myofiber growth. Altogether, this study defines the repertoire of transcription factors that regulate developmental myofiber growth and the role of Gsk3/Deaf1/glycolysis in this process.
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Affiliation(s)
- Flavia A. Graca
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Natalie Sheffield
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Melissa Puppa
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Liam C. Hunt
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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6
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Chen S, Deng X, Xiong J, He F, Yang L, Chen B, Chen C, Zhang C, Yang L, Peng J, Yin F. De novo variants of DEAF1 cause intellectual disability in six Chinese patients. Clin Chim Acta 2021; 518:17-21. [PMID: 33705764 DOI: 10.1016/j.cca.2021.02.026] [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: 02/03/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND It has been reported that de novo heterozygous variants of DEAF1 can cause DEAF1-associated neurodevelopmental disorder. The purpose of this article is to explore the clinical and genetic characteristics of Chinese patients harboring de novo DEAF1 variants. METHODS We assembled a cohort of six unrelated patients with de novo variants in DEAF1. Clinical and genetic features of these patients were summarized. RESULTS Each child showed intellectual disability (ID)/ global developmental delay (GDD). Severe language impairment was prominent. Behavior problems, seizures, sleep disturbance, and a high pain threshold were common features. DEAF1-related seizures were reported to be difficult to treat or intractable. Seizures in our cohort were almost all treatable. Valproic acid was the most commonly used drug. Five heterozygous missense mutations of DEAF1 gene were identified, three of which (p.W234C, p.L203P, p.H275Q) were not published in literature before. CONCLUSION Mutations of DEAF1 gene should be considered in ID/GDD patients with a nonspecific phenotype, comprising intellectual disability, prominent speech delay, abnormal behaviors, especially autism. In our study, DEAF1-related epilepsy is completely treatable in Eastern-Asian individuals when compared to patients in other regions, and valproic acid can be used as a first choice. The knowledge of DEAF1-related neurodevelopmental disorder and the de novo variant database of DEAF1 were expanded.
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Affiliation(s)
- Shimeng Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ciliu Zhang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Li Yang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China.
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7
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Ornelas-Ayala D, Garay-Arroyo A, García-Ponce B, R. Álvarez-Buylla E, Sanchez MDLP. The Epigenetic Faces of ULTRAPETALA1. FRONTIERS IN PLANT SCIENCE 2021; 12:637244. [PMID: 33719312 PMCID: PMC7947857 DOI: 10.3389/fpls.2021.637244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 05/27/2023]
Abstract
ULTRAPETALA1 (ULT1) is a versatile plant-exclusive protein, initially described as a trithorax group (TrxG) factor that regulates transcriptional activation and counteracts polycomb group (PcG) repressor function. As part of TrxG, ULT1 interacts with ARABIDOPSIS TRITHORAX1 (ATX1) to regulate H3K4me3 activation mark deposition. However, our recent studies indicate that ULT1 can also act independently of ATX1. Moreover, the ULT1 ability to interact with transcription factors (TFs) and PcG proteins indicates that it is a versatile protein with other roles. Therefore, in this work we revised recent information about the function of Arabidopsis ULT1 to understand the roles of ULT1 in plant development. Furthermore, we discuss the molecular mechanisms of ULT1, highlighting its epigenetic role, in which ULT1 seems to have characteristics of an epigenetic molecular switch that regulates repression and activation processes via TrxG and PcG complexes.
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Affiliation(s)
- Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
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8
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Lim S, Shparberg RA, Coorssen JR, O’Connor MD. Application of the RBBP9 Serine Hydrolase Inhibitor, ML114, Decouples Human Pluripotent Stem Cell Proliferation and Differentiation. Int J Mol Sci 2020; 21:ijms21238983. [PMID: 33256189 PMCID: PMC7730578 DOI: 10.3390/ijms21238983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Retinoblastoma binding protein 9 (RBBP9) is required for maintaining the expression of both pluripotency and cell cycle genes in human pluripotent stem cells (hPSCs). An siRNA-based study from our group showed it does so by influencing cell cycle progression through the RB/E2F pathway. In non-pluripotent cells, RBBP9 is also known to have serine hydrolase (SH) activity, acting on currently undefined target proteins. The role of RBBP9 SH activity in hPSCs, and during normal development, is currently unknown. To begin assessing whether RBBP9 SH activity might contribute to hPSC maintenance, hPSCs were treated with ML114—a selective chemical inhibitor of RBBP9 SH activity. Stem cells treated with ML114 showed significantly reduced population growth rate, colony size and progression through the cell cycle, with no observable change in cell morphology or decrease in pluripotency antigen expression—suggesting no initiation of hPSC differentiation. Consistent with this, hPSCs treated with ML114 retained the capacity for tri-lineage differentiation, as seen through teratoma formation. Subsequent microarray and Western blot analyses of ML114-treated hPSCs suggest the nuclear transcription factor Y subunit A (NFYA) may be a candidate effector of RBBP9 SH activity in hPSCs. These data support a role for RBBP9 in regulating hPSC proliferation independent of differentiation, whereby inhibition of RBBP9 SH activity de-couples decreased hPSC proliferation from initiation of differentiation.
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Affiliation(s)
- Seakcheng Lim
- School of Medicine, Western Sydney University, Campbelltown NSW 2560, Australia; (S.L.); (R.A.S.)
| | - Rachel A. Shparberg
- School of Medicine, Western Sydney University, Campbelltown NSW 2560, Australia; (S.L.); (R.A.S.)
| | - Jens R. Coorssen
- Departments of Health Sciences and Biological Sciences, Faculties of Applied Health Sciences and Mathematics & Science, Brock University, St. Catharines, ON L2S 3A1, Canada;
| | - Michael D. O’Connor
- School of Medicine, Western Sydney University, Campbelltown NSW 2560, Australia; (S.L.); (R.A.S.)
- Molecular Medicine Research Group, Western Sydney University, Campbelltown NSW 2560, Australia
- Correspondence:
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9
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Casanova EL, Konkel MK. The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements. Bioessays 2020; 42:e1900173. [PMID: 31943266 PMCID: PMC7029956 DOI: 10.1002/bies.201900173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil record and 2) the accumulation of regulatory elements and recombination within these same genes-often derived from transposable elements-drives punctuated bursts of morphological divergence and speciation across metazoa. This two-part hypothesis helps to explain the features that characterize PE, providing a theoretical genetic basis for the once-controversial theory. Also see the video abstract here https://youtu.be/C-fu-ks5yDs.
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Affiliation(s)
- Emily L. Casanova
- Department of Biomedical Sciences, University of South Carolina School of Medicine at Greenville, Greenville, South Carolina, USA
| | - Miriam K. Konkel
- Department of Genetics and Biochemistry, Clemson Center for Human Genetics, Biomedical Data Science and Informatics Program, Clemson University, Clemson, South Carolina, USA
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10
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A novel autosomal recessive DEAF1 nonsense variant: expanding the clinical phenotype. Clin Dysmorphol 2019; 29:114-117. [PMID: 31688097 DOI: 10.1097/mcd.0000000000000306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Nabais Sá MJ, Jensik PJ, McGee SR, Parker MJ, Lahiri N, McNeil EP, Kroes HY, Hagerman RJ, Harrison RE, Montgomery T, Splitt M, Palmer EE, Sachdev RK, Mefford HC, Scott AA, Martinez-Agosto JA, Lorenz R, Orenstein N, Berg JN, Amiel J, Heron D, Keren B, Cobben JM, Menke LA, Marco EJ, Graham JM, Pierson TM, Karimiani EG, Maroofian R, Manzini MC, Cauley ES, Colombo R, Odent S, Dubourg C, Phornphutkul C, de Brouwer APM, de Vries BBA, Vulto-vanSilfhout AT. De novo and biallelic DEAF1 variants cause a phenotypic spectrum. Genet Med 2019; 21:2059-2069. [PMID: 30923367 DOI: 10.1038/s41436-019-0473-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/15/2019] [Indexed: 01/24/2023] Open
Abstract
PURPOSE To investigate the effect of different DEAF1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and on DEAF1 activity in vitro. METHODS We assembled a cohort of 23 patients with de novo and biallelic DEAF1 variants, described the genotype-phenotype correlation, and investigated the differential effect of de novo and recessive variants on transcription assays using DEAF1 and Eif4g3 promoter luciferase constructs. RESULTS The proportion of the most prevalent phenotypic features, including intellectual disability, speech delay, motor delay, autism, sleep disturbances, and a high pain threshold, were not significantly different in patients with biallelic and pathogenic de novo DEAF1 variants. However, microcephaly was exclusively observed in patients with recessive variants (p < 0.0001). CONCLUSION We propose that different variants in the DEAF1 gene result in a phenotypic spectrum centered around neurodevelopmental delay. While a pathogenic de novo dominant variant would also incapacitate the product of the wild-type allele and result in a dominant-negative effect, a combination of two recessive variants would result in a partial loss of function. Because the clinical picture can be nonspecific, detailed phenotype information, segregation, and functional analysis are fundamental to determine the pathogenicity of novel variants and to improve the care of these patients.
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Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, OPD2 Northern General Hospital, Sheffield, UK
| | - Nayana Lahiri
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust & St George's, University of London, London, UK
| | - Evan P McNeil
- Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Randi J Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis School of Medicine, Sacramento, Sacramento, CA, USA.,Department of Pediatrics, University of California Davis Medical Center, Sacramento, Sacramento, CA, USA
| | - Rachel E Harrison
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tara Montgomery
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington-Seattle, Seattle, WA, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan N Berg
- Department of Clinical Genetics, Ninewells Hospital and Medical School, Dundee, Angus, UK.,Clinical Genetics, University of Dundee, Dundee, Angus, UK
| | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Delphine Heron
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Jan-Maarten Cobben
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,North West Thames Genetics NHS, Northwick Park Hospital, London, UK
| | - Leonie A Menke
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Elysa J Marco
- Department of Child Neurology, Cortica Healthcare, San Rafael, CA, USA
| | - John M Graham
- Division of Clinical Genetics and Dysmorphology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tyler Mark Pierson
- Department of Pediatrics, Department of Neurology, and the Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - M Chiara Manzini
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Edmund S Cauley
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Roberto Colombo
- Faculty of Medicine"Agostino Gemelli"Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, CLAD-Ouest CHU Rennes, Univ Rennes, CNRS 6290 Institut de Génétique et Développement de Rennes (IGDR), Rennes, France
| | | | - Chanika Phornphutkul
- Division of Human Genetics, Department of Pediatrics, Hasbro Children's Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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12
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Independent evolution of complex development in animals and plants: deep homology and lateral gene transfer. Dev Genes Evol 2019; 229:25-34. [PMID: 30685797 DOI: 10.1007/s00427-019-00626-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/10/2019] [Indexed: 01/25/2023]
Abstract
The evolution of multicellularity is a premier example of phenotypic convergence: simple multicellularity evolved independently many times, and complex multicellular phenotypes are found in several distant groups. Furthermore, both animal and plant lineages have independently reached extreme levels of morphological, functional, and developmental complexity. This study explores the genetic basis for the parallel evolution of complex multicellularity and development in the animal and green plant (i.e., green algae and land plants) lineages. Specifically, the study (i) identifies the SAND domain-a DNA-binding domain with important roles in the regulation of cell proliferation and differentiation, as unique to animals, green algae, and land plants; and (ii) suggests that the parallel deployment of this ancestral domain in similar regulatory roles could have contributed to the independent evolution of complex development in these distant groups. Given the deep animal-green plant divergence, the limited distribution of the SAND domain is best explained by invoking a lateral gene transfer (LGT) event from a green alga to an early metazoan. The presence of a sequence motif specifically shared by a family of SAND-containing transcription factors involved in the evolution of complex multicellularity in volvocine algae and two types of SAND proteins that emerged early in the evolution of animals is consistent with this scenario. Overall, these findings imply that (i) in addition to be involved in the evolution of similar phenotypes, deep homologous sequences can also contribute to shaping parallel evolutionary trajectories in distant lineages, and (ii) LGT could provide an additional source of latent homologous sequences that can be deployed in analogous roles and affect the evolutionary potentials of distantly related groups.
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13
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Expanding the phenotype in autosomal dominant mental retardation-24: a novel variation in DEAF1 gene. Clin Dysmorphol 2018; 28:94-97. [PMID: 30451703 DOI: 10.1097/mcd.0000000000000252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Xu G, Zhang J, Lyu H, Song Q, Feng Q, Xiang H, Zheng S. DNA methylation mediates BmDeaf1-regulated tissue- and stage-specific expression of BmCHSA-2b in the silkworm, Bombyx mori. Epigenetics Chromatin 2018; 11:32. [PMID: 29903048 PMCID: PMC6001065 DOI: 10.1186/s13072-018-0202-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accurate regulation of tissue- and stage-specific expression of genes is prerequisite for normal development in organisms. DNA methylation plays an important role in modulating gene expression in mammals and plants. However, there is no direct evidence showing how DNA methylation regulates gene transcription in insects. RESULTS During the development of Bombyx mori wing, the expression level of DNA methyltransferase 1 (BmDnmt1) gradually declined and became stationary at pupal stage, resulting in a lower methylation rate of the intragenic promoter of the mid-pupal wing-specific gene BmCHSA-2b, an epidermal chitin synthase controlling mid-pupal wing development in B. mori. The higher methylation rate of the promoter in the pupal epidermis was decreased and BmCHSA-2b transcription was significantly increased by the treatment with the DNA methylation inhibitor, 5-azacytidine-2'-deoxycytidine, suggesting that DNA methylation regulates the tissue-specific expression of BmCHSA-2b. Pupa-specific transcription factor BmDEAF1 bound to the unmethylated intragenic promoter and activated the BmCHSA-2b transcription in the mid-pupal wing. BmDnmt1 and BmDeaf1 influenced the BmCHSA-2b transcription by binding competitively to the CpG island in the promoter. CONCLUSIONS All the data together demonstrate that the cooperation between the down-regulation of BmDnmt1 and increased stage-specific expression of BmDeaf1 enhances BmCHSA-2b tissue- and stage-specific transcription to ensure mid-wing development in B. mori. This study highlights an elaborate regulation mechanism how tissue- and stage-specific gene expression is regulated through promoter methylation in insect development.
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Affiliation(s)
- Guanfeng Xu
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jie Zhang
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hao Lyu
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65211, USA
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hui Xiang
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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15
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Li SJ, Yu SS, Luo HY, Li X, Rao B, Wang Y, Li ZZ, Liu G, Zou LP, Zhang JS, Feng C, Liu J, Liu JW, Hu N, Chen XQ, Yu SY, Li K, He MW, Yu XG, Wang J, Guo SL, Chen ZY, Zhang L, Ma L. Two de novo variations identified by massively parallel sequencing in 13 Chinese families with children diagnosed with autism spectrum disorder. Clin Chim Acta 2018; 479:144-147. [PMID: 29366832 DOI: 10.1016/j.cca.2018.01.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 01/09/2023]
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous neurodevelopmental disorder characterized by impairments in social interaction and communication, and by restricted and repetitive behaviors. The genetic architecture of ASD has been elucidated, including chromosomal rearrangements, de novo or inherited rare variants, and copy number variants. However, the genetic mechanism of Chinese families with ASD children is explored rarely. To identify genetic pathogenesis, we performed massively parallel sequencing on 13 Chinese ASD trio families, and found two de novo variations. The novel de novo splice alteration c.664 + 2T > G in the DEAF1 gene and the novel de novo missense mutation c.95 C > T in the AADAT gene associated with ASD may be important clues for exploring the etiology of this disorder.
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Affiliation(s)
- Shi-Jun Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China.
| | | | | | - Xin Li
- BGI-shenzhen, Shenzhen 518083, China
| | - Bin Rao
- BGI-shenzhen, Shenzhen 518083, China
| | - Yi Wang
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhen-Zhen Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China
| | - Gang Liu
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Ji-Shui Zhang
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Chen Feng
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian-Wei Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Nan Hu
- Department of Rehabilitation Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiao-Qiao Chen
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Sheng-Yuan Yu
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Ke Li
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Mian-Wang He
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xin-Guang Yu
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Jun Wang
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Sheng-Li Guo
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi-Ye Chen
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Lei Zhang
- Department of Medical Information, Chinese PLA General Hospital, Beijing 100853, China
| | - Lin Ma
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
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16
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Chen L, Jensik PJ, Alaimo JT, Walkiewicz M, Berger S, Roeder E, Faqeih EA, Bernstein JA, Smith ACM, Mullegama SV, Saffen DW, Elsea SH. Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype. Hum Mutat 2017; 38:1774-1785. [PMID: 28940898 PMCID: PMC5679464 DOI: 10.1002/humu.23339] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 11/06/2022]
Abstract
Deformed epidermal autoregulatory factor-1 (DEAF1), a transcription factor essential for central nervous system and early embryonic development, has recently been implicated in a series of intellectual disability-related neurodevelopmental anomalies termed, in this study, as DEAF1-associated neurodevelopmental disorder (DAND). We identified six potentially deleterious DEAF1 variants in a cohort of individuals with DAND via clinical exome sequencing (CES) and in silico analysis, including two novel de novo variants: missense variant c.634G > A p.Gly212Ser in the SAND domain and deletion variant c.913_915del p.Lys305del in the NLS domain, as well as c.676C > T p.Arg226Trp, c.700T > A p.Trp234Arg, c.737G > C p.Arg246Thr, and c.791A > C p.Gln264Pro. Luciferase reporter, immunofluorescence staining, and electrophoretic mobility shift assays revealed that these variants had decreased transcriptional repression activity at the DEAF1 promoter and reduced affinity to consensus DEAF1 DNA binding sequences. In addition, c.913_915del p.K305del localized primarily to the cytoplasm and interacted with wild-type DEAF1. Our results demonstrate that variants located within the SAND or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients. These findings illustrate the importance of experimental characterization of variants with uncertain significance identified by CES to assess their potential clinical significance and possible use in diagnosis.
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Affiliation(s)
- Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Joseph T. Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Seth Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Departments of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Eissa A. Faqeih
- Department of Pediatrics Subspecialty, Children’s Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ann C. M. Smith
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sureni V. Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - David W. Saffen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Institutes of Brain Science, Fudan University, Shanghai, China
- State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai, China
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
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17
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Gu B, Lambert JP, Cockburn K, Gingras AC, Rossant J. AIRE is a critical spindle-associated protein in embryonic stem cells. eLife 2017; 6:e28131. [PMID: 28742026 PMCID: PMC5560860 DOI: 10.7554/elife.28131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022] Open
Abstract
Embryonic stem (ES) cells go though embryo-like cell cycles regulated by specialized molecular mechanisms. However, it is not known whether there are ES cell-specific mechanisms regulating mitotic fidelity. Here we showed that Autoimmune Regulator (Aire), a transcription coordinator involved in immune tolerance processes, is a critical spindle-associated protein in mouse ES(mES) cells. BioID analysis showed that AIRE associates with spindle-associated proteins in mES cells. Loss of function analysis revealed that Aire was important for centrosome number regulation and spindle pole integrity specifically in mES cells. We also identified the c-terminal LESLL motif as a critical motif for AIRE's mitotic function. Combined maternal and zygotic knockout further revealed Aire's critical functions for spindle assembly in preimplantation embryos. These results uncovered a previously unappreciated function for Aire and provide new insights into the biology of stem cell proliferation and potential new angles to understand fertility defects in humans carrying Aire mutations.
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Affiliation(s)
- Bin Gu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Canada
| | | | - Katie Cockburn
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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18
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Field A, Xiang J, Anderson WR, Graham P, Pick L. Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers. PLoS One 2016; 11:e0163128. [PMID: 27723822 PMCID: PMC5056698 DOI: 10.1371/journal.pone.0163128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/03/2016] [Indexed: 12/11/2022] Open
Abstract
The orphan nuclear receptor Ftz-F1 is expressed in all somatic nuclei in Drosophila embryos, but mutations result in a pair-rule phenotype. This was explained by the interaction of Ftz-F1 with the homeodomain protein Ftz that is expressed in stripes in the primordia of segments missing in either ftz-f1 or ftz mutants. Ftz-F1 and Ftz were shown to physically interact and coordinately activate the expression of ftz itself and engrailed by synergistic binding to composite Ftz-F1/Ftz binding sites. However, attempts to identify additional target genes on the basis of Ftz-F1/ Ftz binding alone has met with only limited success. To discern rules for Ftz-F1 target site selection in vivo and to identify additional target genes, a microarray analysis was performed comparing wildtype and ftz-f1 mutant embryos. Ftz-F1-responsive genes most highly regulated included engrailed and nine additional genes expressed in patterns dependent on both ftz and ftz-f1. Candidate enhancers for these genes were identified by combining BDTNP Ftz ChIP-chip data with a computational search for Ftz-F1 binding sites. Of eight enhancer reporter genes tested in transgenic embryos, six generated expression patterns similar to the corresponding endogenous gene and expression was lost in ftz mutants. These studies identified a new set of Ftz-F1 targets, all of which are co-regulated by Ftz. Comparative analysis of enhancers containing Ftz/Ftz-F1 binding sites that were or were not bona fide targets in vivo suggested that GAF negatively regulates enhancers that contain Ftz/Ftz-F1 binding sites but are not actually utilized. These targets include other regulatory factors as well as genes involved directly in morphogenesis, providing insight into how pair-rule genes establish the body pattern.
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Affiliation(s)
- Amanda Field
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Jie Xiang
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - W. Ray Anderson
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Patricia Graham
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
- * E-mail:
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19
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Gund C, Powis Z, Alcaraz W, Desai S, Baranano K. Identification of a syndrome comprising microcephaly and intellectual disability but not white matter disease associated with a homozygous c.676C>T p.R226W DEAF1 mutation. Am J Med Genet A 2016; 170A:1330-2. [PMID: 26834045 DOI: 10.1002/ajmg.a.37580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 01/21/2016] [Indexed: 11/07/2022]
Abstract
We evaluated a 13-year-old East Pakistani male affected with microcephaly, apparent intellectual disability, hypotonia, and brisk reflexes without spasticity. His parents were first cousins. The patient also had a brother who was similarly affected and died at 10 years due to an accident. Previous SNP array testing showed a 1.63 Mb duplication at 16p13.11 of uncertain significance along with regions of homozygosity. Exome sequencing identified a known pathogenic homozygous alteration in DEAF1, c.676C>T (p.R226W), in this patient. The alteration had been reported in two individuals from a consanguineous Saudi Arabian family. Both individuals had microcephaly, intellectual disability, hypotonia, feeding difficulties, and poor growth. The patient reported here did not have evidence of white matter disease, as had been reported with prior patients. We conclude that this DEAF1 gene alteration caused this patient's symptoms and that white matter disease should not be considered a obligate feature of this syndrome.
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Affiliation(s)
| | - Zöe Powis
- Ambry Genetics, 15 Argonaut, Aliso Viejo, California
| | - Wendy Alcaraz
- Ambry Genetics, 15 Argonaut, Aliso Viejo, California
| | - Sonal Desai
- Kennedy Krieger Institute, Baltimore, Maryland
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20
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Residual expression of SMYD2 and SMYD3 is associated with the acquisition of complex karyotype in chronic lymphocytic leukemia. Tumour Biol 2016; 37:9473-81. [PMID: 26790435 DOI: 10.1007/s13277-016-4846-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/13/2016] [Indexed: 12/17/2022] Open
Abstract
SET and MYND domain containing 2 (SMYD2) and the SET and MYND domain containing 3 (SMYD3) are the most studied and well-characterized members of SMYD family. It has been demonstrated that their altered expression is associated with the progression of several solid tumors. Nevertheless, whether these methyltransferases exert any impact in chronic lymphocytic leukemia (CLL) remains unknown. Here, we investigated the gene expression profile of SMYD2 and SMYD3 in 59 samples of CLL and 10 normal B cells. The obtained results were associated with white blood cells (WBC) and platelet counts, ZAP-70 protein expression, and cytogenetic analysis. We found that SMYD2 and SMYD3 are overexpressed in CLL patients and, interestingly, patients with residual expression of both genes presented a high WBC count and complex karyotype. Furthermore, a strong correlation between SMYD2 and SMYD3 gene expression was unveiled. Our data demonstrate the association of a residual expression of SMYD2 and SMYD3 with CLL progression indicators and suggests both genes are regulated by a common transcriptional control in this type of cancer. These results may provide the basis for the development of new therapeutic strategies to prevent CLL progression.
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21
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Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain. Sci Rep 2016; 6:19010. [PMID: 26743651 PMCID: PMC4705554 DOI: 10.1038/srep19010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/02/2015] [Indexed: 12/12/2022] Open
Abstract
RAI1 (retinoic acid induced-1) is a dosage-sensitive gene that causes Smith-Magenis syndrome (SMS) when mutated or deleted and Potocki-Lupski Syndrome (PTLS) when duplicated, with psychiatric features commonly observed in both syndromes. How common genetic variants regulate this gene, however, is unknown. In this study, we found that RAI1 mRNA expression in Chinese prefrontal and temporal cortex correlate with genotypes of common single nucleotide polymorphisms (SNPs) located in the RAI1 5′-upstream region. Using genotype imputation, “R2-Δ2” analysis, and data from the RegulomeDB database, we identified SNPs rs4925102 and rs9907986 as possible regulatory variants, accounting for approximately 30–40% of the variance in RAI1 mRNA expression in both brain regions. Specifically, rs4925102 and rs9907986 are predicted to disrupt the binding of retinoic acid RXR-RAR receptors and the transcription factor DEAF1 (Deformed epidermal autoregulatory factor-1), respectively. Consistent with these predictions, we observed binding of RXRα and RARα to the predicted RAI1 target in chromatin immunoprecipitation assays. Retinoic acid is crucial for early development of the central neural system, and DEAF1 is associated with intellectual disability. The observation that a significant portion of RAI1 mRNA expression is genetically controlled raises the possibility that common RAI1 5′-region regulatory variants contribute more generally to psychiatric disorders.
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22
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Role of the Red Ginseng in Defense against the Environmental Heat Stress in Sprague Dawley Rats. Molecules 2015; 20:20240-53. [PMID: 26569207 PMCID: PMC6331845 DOI: 10.3390/molecules201119692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 01/21/2023] Open
Abstract
Global temperature change causes heat stress related disorders in humans. A constituent of red ginseng has been known the beneficial effect on the resistance to many diseases. However, the mechanism of red ginseng (RG) against heat stress still remains unclear. To determine the effect of RG on heat stress, we examined the effect of the RG on the gene expression profiles in rats subjected to environmental heat stress. We evaluated the transcripts associated with hepatic lipid accumulation and oxidative stress in rats subjected to heat stress. We also analyzed the reactive oxygen species (ROS) contents. Our results suggested RG inhibited heat stress mediated altering mRNA expressions include HSPA1, DEAF1, HMGCR, and FMO1. We also determined RG attenuated fat accumulation in the liver by altering C/EBPβ expression. RG promoted to repress the heat stress mediated hepatic cell death by inhibiting of Bcl-2 expression in rats subjected to heat stress. Moreover, RG administered group during heat stress dramatically decreased the malondialdehyde (MDA) contents and ROS associated genes compared with the control group. Thus, we suggest that RG might influence inhibitory effect on environmental heat stress induced abnormal conditions in humans.
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23
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Brown MA, Foreman K, Harriss J, Das C, Zhu L, Edwards M, Shaaban S, Tucker H. C-terminal domain of SMYD3 serves as a unique HSP90-regulated motif in oncogenesis. Oncotarget 2015; 6:4005-19. [PMID: 25738358 PMCID: PMC4414169 DOI: 10.18632/oncotarget.2970] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/16/2014] [Indexed: 01/25/2023] Open
Abstract
The SMYD3 histone methyl transferase (HMTase) and the nuclear chaperone, HSP90, have been independently implicated as proto-oncogenes in several human malignancies. We show that a degenerate tetratricopeptide repeat (TPR)-like domain encoded in the SMYD3 C-terminal domain (CTD) mediates physical interaction with HSP90. We further demonstrate that the CTD of SMYD3 is essential for its basal HMTase activity and that the TPR-like structure is required for HSP90-enhanced enzyme activity. Loss of SMYD3-HSP90 interaction leads to SMYD3 mislocalization within the nucleus, thereby losing its chromatin association. This results in reduction of SMYD3-mediated cell proliferation and, potentially, impairment of SMYD3's oncogenic activity. These results suggest a novel approach for blocking HSP90-driven malignancy in SMYD3-overexpressing cells with a reduced toxicity profile over current HSP90 inhibitors.
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Affiliation(s)
- Mark A. Brown
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | | | - June Harriss
- University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, TX 78712, USA
| | - Chhaya Das
- University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, TX 78712, USA
| | - Li Zhu
- University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, TX 78712, USA
| | - Melissa Edwards
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, TX 78712, USA
| | | | - Haley Tucker
- University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, TX 78712, USA
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Jensik PJ, Vargas JD, Reardon SN, Rajamanickam S, Huggenvik JI, Collard MW. DEAF1 binds unmethylated and variably spaced CpG dinucleotide motifs. PLoS One 2014; 9:e115908. [PMID: 25531106 PMCID: PMC4274154 DOI: 10.1371/journal.pone.0115908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 11/19/2022] Open
Abstract
DEAF1 is a transcriptional regulator associated with autoimmune and neurological disorders and is known to bind TTCG motifs. To further ascertain preferred DEAF1 DNA ligands, we screened a random oligonucleotide library containing an "anchored" CpG motif. We identified a binding consensus that generally conformed to a repeated TTCGGG motif, with the two invariant CpG dinucleotides separated by 6-11 nucleotides. Alteration of the consensus surrounding the dual CpG dinucleotides, or cytosine methylation of a single CpG half-site, eliminated DEAF1 binding. A sequence within the Htr1a promoter that resembles the binding consensus but contains a single CpG motif was confirmed to have low affinity binding with DEAF1. A DEAF1 binding consensus was identified in the EIF4G3 promoter and ChIP assay showed endogenous DEAF1 was bound to the region. We conclude that DEAF1 preferentially binds variably spaced and unmethylated CpG-containing half-sites when they occur within an appropriate consensus.
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Affiliation(s)
- Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
- * E-mail:
| | - Jesse D. Vargas
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Sara N. Reardon
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Jodi I. Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Michael W. Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
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25
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Joseph S, Kwan AH, Stokes PH, Mackay JP, Cubeddu L, Matthews JM. The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4. PLoS One 2014; 9:e109108. [PMID: 25310299 PMCID: PMC4195752 DOI: 10.1371/journal.pone.0109108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/27/2014] [Indexed: 12/23/2022] Open
Abstract
LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.
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Affiliation(s)
- Soumya Joseph
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Ann H. Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Philippa H. Stokes
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Liza Cubeddu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
- School of Science and Health, University of Western Sydney, Campbelltown, NSW Australia
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26
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Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, Vergult S, de Rocker N, Newhall KJ, Raghavan R, Reardon SN, Jarrett K, McIntyre T, Bulinski J, Ownby SL, Huggenvik JI, McKnight GS, Rose GM, Cai X, Willaert A, Zweier C, Endele S, de Ligt J, van Bon BWM, Lugtenberg D, de Vries PF, Veltman JA, van Bokhoven H, Brunner HG, Rauch A, de Brouwer APM, Carvill GL, Hoischen A, Mefford HC, Eichler EE, Vissers LELM, Menten B, Collard MW, de Vries BBA. Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems. Am J Hum Genet 2014; 94:649-61. [PMID: 24726472 DOI: 10.1016/j.ajhg.2014.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 11/29/2022] Open
Abstract
Recently, we identified in two individuals with intellectual disability (ID) different de novo mutations in DEAF1, which encodes a transcription factor with an important role in embryonic development. To ascertain whether these mutations in DEAF1 are causative for the ID phenotype, we performed targeted resequencing of DEAF1 in an additional cohort of over 2,300 individuals with unexplained ID and identified two additional individuals with de novo mutations in this gene. All four individuals had severe ID with severely affected speech development, and three showed severe behavioral problems. DEAF1 is highly expressed in the CNS, especially during early embryonic development. All four mutations were missense mutations affecting the SAND domain of DEAF1. Altered DEAF1 harboring any of the four amino acid changes showed impaired transcriptional regulation of the DEAF1 promoter. Moreover, behavioral studies in mice with a conditional knockout of Deaf1 in the brain showed memory deficits and increased anxiety-like behavior. Our results demonstrate that mutations in DEAF1 cause ID and behavioral problems, most likely as a result of impaired transcriptional regulation by DEAF1.
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Affiliation(s)
| | - Shivakumar Rajamanickam
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Philip J Jensik
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Nina de Rocker
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Kathryn J Newhall
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ramya Raghavan
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sara N Reardon
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Kelsey Jarrett
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Tara McIntyre
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Joseph Bulinski
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Stacy L Ownby
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Jodi I Huggenvik
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - G Stanley McKnight
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Gregory M Rose
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Anatomy, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Xiang Cai
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Andy Willaert
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Joep de Ligt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Petra F de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland; Zurich Center of Integrative Human Physiology, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Michael W Collard
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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27
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Faqeih EA, Al-Owain M, Colak D, Kenana R, Al-Yafee Y, Al-Dosary M, Al-Saman A, Albalawi F, Al-Sarar D, Domiaty D, Daghestani M, Kaya N. Novel homozygous DEAF1 variant suspected in causing white matter disease, intellectual disability, and microcephaly. Am J Med Genet A 2014; 164A:1565-70. [PMID: 24668509 DOI: 10.1002/ajmg.a.36482] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/12/2014] [Indexed: 11/11/2022]
Abstract
DEAF1 encodes a transcriptional binding factor and is a regulator of serotonin receptor 1A. Its protein has a significant expression in the neurons of different brain regions and is involved in early embryonic development. In addition, its role in neural tube development is evident from the knockout mouse as many homozygotes have exencephaly. Heterozygous mutations of this gene have been linked to intellectual disability in addition to the gene's involvement in major depression, suicidal tendencies, and panic disorder. In this clinical report, we describe two children from a consanguineous family with intellectual disability, microcephaly, and hypotonia. The brain MRI of both patients showed bilateral and symmetrical white matter abnormalities, and one of the patients had a seizure disorder. Using whole exome sequencing combined with homozygosity mapping, a homozygous p.R226W (c.676C>T) mutation in DEAF1 was found in both patients. Furthermore, sequencing analysis confirmed complete segregation in tested family members and absence of the mutation in control cohort (n = 650). The mutation is located in a highly conserved structural domain that mediates DNA binding and therefore regulates transcriptional activity of its target molecules. This study indicates, for the first time to our knowledge, a hereditary role of DEAF1 in white matter abnormalities, microcephaly and syndromic intellectual disability.
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Affiliation(s)
- Eissa A Faqeih
- Section of Medical Genetic, Pediatric Department, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
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28
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Kateb F, Perrin H, Tripsianes K, Zou P, Spadaccini R, Bottomley M, Franzmann TM, Buchner J, Ansieau S, Sattler M. Structural and functional analysis of the DEAF-1 and BS69 MYND domains. PLoS One 2013; 8:e54715. [PMID: 23372760 PMCID: PMC3555993 DOI: 10.1371/journal.pone.0054715] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
DEAF-1 is an important transcriptional regulator that is required for embryonic development and is linked to clinical depression and suicidal behavior in humans. It comprises various structural domains, including a SAND domain that mediates DNA binding and a MYND domain, a cysteine-rich module organized in a Cys(4)-Cys(2)-His-Cys (C4-C2HC) tandem zinc binding motif. DEAF-1 transcription regulation activity is mediated through interactions with cofactors such as NCoR and SMRT. Despite the important biological role of the DEAF-1 protein, little is known regarding the structure and binding properties of its MYND domain.Here, we report the solution structure, dynamics and ligand binding of the human DEAF-1 MYND domain encompassing residues 501-544 determined by NMR spectroscopy. The structure adopts a ββα fold that exhibits tandem zinc-binding sites with a cross-brace topology, similar to the MYND domains in AML1/ETO and other proteins. We show that the DEAF-1 MYND domain binds to peptides derived from SMRT and NCoR corepressors. The binding surface mapped by NMR titrations is similar to the one previously reported for AML1/ETO. The ligand binding and molecular functions of the related BS69 MYND domain were studied based on a homology model and mutational analysis. Interestingly, the interaction between BS69 and its binding partners (viral and cellular proteins) seems to require distinct charged residues flanking the predicted MYND domain fold, suggesting a different binding mode. Our findings demonstrate that the MYND domain is a conserved zinc binding fold that plays important roles in transcriptional regulation by mediating distinct molecular interactions with viral and cellular proteins.
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Affiliation(s)
- Fatiha Kateb
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Helene Perrin
- Institut National de la Santé Et de la Recherche Médicale U590, Centre Léon Bérard, Université Claude Bernard Lyon I, Lyon, France
| | - Konstantinos Tripsianes
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Peijian Zou
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Roberta Spadaccini
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | | | - Titus M. Franzmann
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Stephane Ansieau
- Institut National de la Santé Et de la Recherche Médicale U590, Centre Léon Bérard, Université Claude Bernard Lyon I, Lyon, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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29
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Foreman KW, Brown M, Park F, Emtage S, Harriss J, Das C, Zhu L, Crew A, Arnold L, Shaaban S, Tucker P. Structural and functional profiling of the human histone methyltransferase SMYD3. PLoS One 2011; 6:e22290. [PMID: 21779408 PMCID: PMC3136521 DOI: 10.1371/journal.pone.0022290] [Citation(s) in RCA: 83] [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: 02/25/2011] [Accepted: 06/21/2011] [Indexed: 12/13/2022] Open
Abstract
The SET and MYND Domain (SMYD) proteins comprise a unique family of multi-domain SET histone methyltransferases that are implicated in human cancer progression. Here we report an analysis of the crystal structure of the full length human SMYD3 in a complex with an analog of the S-adenosyl methionine (SAM) methyl donor cofactor. The structure revealed an overall compact architecture in which the "split-SET" domain adopts a canonical SET domain fold and closely assembles with a Zn-binding MYND domain and a C-terminal superhelical 9 α-helical bundle similar to that observed for the mouse SMYD1 structure. Together, these structurally interlocked domains impose a highly confined binding pocket for histone substrates, suggesting a regulated mechanism for its enzymatic activity. Our mutational and biochemical analyses confirm regulatory roles of the unique structural elements both inside and outside the core SET domain and establish a previously undetected preference for trimethylation of H4K20.
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Affiliation(s)
- Kenneth W Foreman
- OSI Pharmaceuticals, Inc., Farmingdale, New York, United States of America.
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30
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SET/MYND Lysine Methyltransferases Regulate Gene Transcription and Protein Activity. Genes (Basel) 2011; 2:210-8. [PMID: 24710145 PMCID: PMC3924839 DOI: 10.3390/genes2010210] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/25/2011] [Accepted: 02/07/2011] [Indexed: 12/20/2022] Open
Abstract
The SET and MYND (SMYD) family of lysine methyltransferases is defined by a SET domain that is split into two segments by a MYND domain, followed by a cysteine-rich post-SET domain. While members of the SMYD family are important in the SET-mediated regulation of gene transcription, pathological consequences have also been associated with aberrant expression of SMYD proteins. The last decade has witnessed a rapid increase in the studies and corresponding understanding of these highly impactful enzymes. Herein, we review the current body of knowledge related to the SMYD family of lysine methyltransferases and their role in transcriptional regulation, epigenetics, and tumorigenesis.
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31
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A de novo paradigm for mental retardation. Nat Genet 2010; 42:1109-12. [PMID: 21076407 DOI: 10.1038/ng.712] [Citation(s) in RCA: 595] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 10/18/2010] [Indexed: 12/15/2022]
Abstract
The per-generation mutation rate in humans is high. De novo mutations may compensate for allele loss due to severely reduced fecundity in common neurodevelopmental and psychiatric diseases, explaining a major paradox in evolutionary genetic theory. Here we used a family based exome sequencing approach to test this de novo mutation hypothesis in ten individuals with unexplained mental retardation. We identified and validated unique non-synonymous de novo mutations in nine genes. Six of these, identified in six different individuals, are likely to be pathogenic based on gene function, evolutionary conservation and mutation impact. Our findings provide strong experimental support for a de novo paradigm for mental retardation. Together with de novo copy number variation, de novo point mutations of large effect could explain the majority of all mental retardation cases in the population.
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Mourikis P, Lake RJ, Firnhaber CB, DeDecker BS. Modifiers of notch transcriptional activity identified by genome-wide RNAi. BMC DEVELOPMENTAL BIOLOGY 2010; 10:107. [PMID: 20959007 PMCID: PMC2976970 DOI: 10.1186/1471-213x-10-107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 10/19/2010] [Indexed: 11/30/2022]
Abstract
Background The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. Results Employing complementary data analyses, we found 399 putative modifiers: 189 promoting and 210 antagonizing Notch activated transcription. These modifiers included several known Notch interactors, validating the robustness of the assay. Many novel modifiers were also identified, covering a range of cellular localizations from the extracellular matrix to the nucleus, as well as a large number of proteins with unknown function. Chromatin-modifying proteins represent a major class of genes identified, including histone deacetylase and demethylase complex components and other chromatin modifying, remodeling and replacement factors. A protein-protein interaction map of the Notch-dependent transcription modifiers revealed that a large number of the identified proteins interact physically with these core chromatin components. Conclusions The genome-wide RNAi screen identified many genes that can modulate Notch transcriptional output. A protein interaction map of the identified genes highlighted a network of chromatin-modifying enzymes and remodelers that regulate Notch transcription. Our results open new avenues to explore the mechanisms of Notch signal regulation and the integration of this pathway into diverse cellular processes.
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Affiliation(s)
- Philippos Mourikis
- Stem Cells & Development, Department of Developmental Biology, Pasteur Institute, CNRS URA 2578, Paris, France
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33
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Cooper MT, Conant AW, Kennison JA. Molecular genetic analysis of Chd3 and polytene chromosome region 76B-D in Drosophila melanogaster. Genetics 2010; 185:811-22. [PMID: 20439780 PMCID: PMC2907203 DOI: 10.1534/genetics.110.115121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/20/2010] [Indexed: 01/08/2023] Open
Abstract
The Drosophila melanogaster Chd3 gene encodes a member of the CHD group of SNF2/RAD54 ATPases. CHD proteins are conserved from yeast to man and many are subunits of chromatin-remodeling complexes that facilitate transcription. Drosophila CHD3 proteins are not found in protein complexes, but as monomers that remodel chromatin in vitro. CHD3 colocalize with elongating RNA polymerase II on salivary gland polytene chromosomes. Since the role of Chd3 in development was unknown, we isolated and characterized the essential genes within the 640-kb region of the third chromosome (polytene chromosome region 76B-D) that includes Chd3. We recovered mutations in 24 genes that are essential for zygotic viability. We found that transposon-insertion mutants for 46% of the essential genes are included in the Drosophila Gene Disruption Project collection. None of the essential genes that we identified are in a 200-kb region that includes Chd3. We generated a deletion of Chd3 by targeted gene replacement. This deletion had no effect on either viability or fertility.
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Affiliation(s)
| | | | - James A. Kennison
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland 20892-2785
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34
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Sehadova H, Glaser FT, Gentile C, Simoni A, Giesecke A, Albert JT, Stanewsky R. Temperature entrainment of Drosophila's circadian clock involves the gene nocte and signaling from peripheral sensory tissues to the brain. Neuron 2009; 64:251-66. [PMID: 19874792 DOI: 10.1016/j.neuron.2009.08.026] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 08/20/2009] [Accepted: 08/19/2009] [Indexed: 11/30/2022]
Abstract
Circadian clocks are synchronized by the natural day/night and temperature cycles. Our previous work demonstrated that synchronization by temperature is a tissue autonomous process, similar to synchronization by light. We show here that this is indeed the case, with the important exception of the brain. Using luciferase imaging we demonstrate that brain clock neurons depend on signals from peripheral tissues in order to be synchronized by temperature. Reducing the function of the gene nocte in chordotonal organs changes their structure and function and dramatically interferes with temperature synchronization of behavioral activity. Other mutants known to affect the function of these sensory organs also interfere with temperature synchronization, demonstrating the importance of nocte in this process and identifying the chordotonal organs as relevant sensory structures. Our work reveals surprising and important mechanistic differences between light- and temperature-synchronization and advances our understanding of how clock resetting is accomplished in nature.
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Affiliation(s)
- Hana Sehadova
- School of Biological and Chemical Sciences, Queen Mary College, University of London, London, UK
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Abstract
While promiscuous expression of tissue-specific antigens (TSAs) in the thymus is essential for self-tolerance, immunologically relevant TSA expression may also occur in the secondary lymphoid organs. A new study links the transcriptional regulator Deaf1 with altered TSA expression in the secondary lymphoid organs and autoimmune diabetes.
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Barker HE, Smyth GK, Wettenhall J, Ward TA, Bath ML, Lindeman GJ, Visvader JE. Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland. BMC DEVELOPMENTAL BIOLOGY 2008; 8:94. [PMID: 18826651 PMCID: PMC2570686 DOI: 10.1186/1471-213x-8-94] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2008] [Accepted: 10/01/2008] [Indexed: 12/14/2022]
Abstract
Background The transcription factor DEAF-1 has been identified as a high affinity binding partner of the LIM-only protein LMO4 that plays important roles in mammary gland development and breast cancer. Here we investigated the influence of DEAF-1 on human and mouse mammary epithelial cells both in vitro and in vivo and identified a potential target gene. Results Overexpression of DEAF-1 in human breast epithelial MCF10A cells enhanced cell proliferation in the mammary acini that develop in 3D cultures. To investigate the effects of Deaf-1 on mammary gland development and oncogenesis, we generated MMTV-Deaf-1 transgenic mice. Increased ductal side-branching was observed in young virgin mammary glands, accompanied by augmented cell proliferation. In addition, the ratio of the progesterone receptor isoforms PRA and PRB, previously implicated in regulating ductal side-branching, was altered. Affymetrix gene profiling studies revealed Rac3 as a potential target gene and quantitative RT-PCR analysis confirmed that Rac3 was upregulated by Deaf-1 in immortalized mouse mammary epithelial cells. Furthermore, MMTV-Deaf-1 transgenic mammary glands were found to have elevated levels of Rac3 mRNA, suggesting that it is a bona fide target. Conclusion We have demonstrated that overexpression of Deaf-1 enhances the proliferation of human breast epithelial cells in vitro and mouse epithelial cells in vivo. Transgenic mammary glands overexpressing Deaf-1 exhibited a modest side-branching phenotype, accompanied by an increase in the number of BrdU-positive cells and a decrease in the proportion of PRA-expressing cells. Although proliferation was enhanced in Deaf-1 transgenic mice, overexpression of this gene was not sufficient to induce the formation of mammary tumors. In addition, our studies identified Rac3, encoding a small Rho-like GTPase, as a potential target of Deaf-1 in mouse mammary epithelial cells.
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Affiliation(s)
- Holly E Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3050, Australia.
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Abstract
Immunity genes are activated in the Drosophila fat body by Rel and GATA transcription factors. Here, we present evidence that an additional regulatory factor, deformed epidermal autoregulatory factor-1 (DEAF-1), also contributes to the immune response and is specifically important for the induction of two genes encoding antimicrobial peptides, Metchnikowin (Mtk) and Drosomycin (Drs). The systematic mutagenesis of a minimal Mtk 5' enhancer identified a sequence motif essential for both a response to LPS preparations in S2 cells and activation in the larval fat body in response to bacterial infection. Using affinity chromatography coupled to multidimensional protein identification technology (MudPIT), we identified DEAF-1 as a candidate regulator. DEAF-1 activates the expression of Mtk and Drs promoter-luciferase fusion genes in S2 cells. SELEX assays and footprinting data indicate that DEAF-1 binds to and activates Mtk and Drs regulatory DNAs via a TTCGGBT motif. The insertion of this motif into the Diptericin (Dpt) regulatory region confers DEAF-1 responsiveness to this normally DEAF-1-independent enhancer. The coexpression of DEAF-1 with Dorsal, Dif, and Relish results in the synergistic activation of transcription. We propose that DEAF-1 is a regulator of Drosophila immunity.
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Brown MA, Sims RJ, Gottlieb PD, Tucker PW. Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex. Mol Cancer 2006; 5:26. [PMID: 16805913 PMCID: PMC1524980 DOI: 10.1186/1476-4598-5-26] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 06/28/2006] [Indexed: 12/31/2022] Open
Abstract
Background Disrupting the balance of histone lysine methylation alters the expression of genes involved in tumorigenesis including proto-oncogenes and cell cycle regulators. Methylation of lysine residues is commonly catalyzed by a family of proteins that contain the SET domain. Here, we report the identification and characterization of the SET domain-containing protein, Smyd2. Results Smyd2 mRNA is most highly expressed in heart and brain tissue, as demonstrated by northern analysis and in situ hybridization. Over-expressed Smyd2 localizes to the cytoplasm and the nucleus in 293T cells. Although accumulating evidence suggests that methylation of histone 3, lysine 36 (H3K36) is associated with actively transcribed genes, we show that the SET domain of Smyd2 mediates H3K36 dimethylation and that Smyd2 represses transcription from an SV40-luciferase reporter. Smyd2 associates specifically with the Sin3A histone deacetylase complex, which was recently linked to H3K36 methylation within the coding regions of active genes in yeast. Finally, we report that exogenous expression of Smyd2 suppresses cell proliferation. Conclusion We propose that Sin3A-mediated deacetylation within the coding regions of active genes is directly linked to the histone methyltransferase activity of Smyd2. Moreover, Smyd2 appears to restrain cell proliferation, likely through direct modulation of chromatin structure.
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Affiliation(s)
- Mark A Brown
- Section of Molecular Genetics and Microbiology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Robert J Sims
- Section of Molecular Genetics and Microbiology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
- Present address: Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Paul D Gottlieb
- Section of Molecular Genetics and Microbiology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Philip W Tucker
- Section of Molecular Genetics and Microbiology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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Jensik PJ, Huggenvik JI, Collard MW. Identification of a nuclear export signal and protein interaction domains in deformed epidermal autoregulatory factor-1 (DEAF-1). J Biol Chem 2004; 279:32692-9. [PMID: 15161925 DOI: 10.1074/jbc.m400946200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deformed epidermal autoregulatory factor-1 (DEAF-1) is a DNA-binding protein required for embryonic development and linked to clinical depression and suicidal behavior in humans. Although primarily nuclear, cytoplasmic localization of DEAF-1 has been observed, and this suggests the presence of a nuclear export signal (NES). Using a series of fluorescent fusion proteins, an NES with a novel spacing of leucines (LXLX(6)LLX(5)LX(2)L) was identified near the COOH-terminal MYND domain at amino acids 454-476. The NES was leptomycin B-sensitive and mutation of the leucine residues decreased or eliminated nuclear export activity. In vitro pull downs and an in vivo fluorescent protein interaction assay identified a DEAF-1/DEAF-1 protein interaction domain within the NES region. DNA binding had been previously mapped to a positively charged surface patch in the novel DNA binding fold called the "SAND" domain. A second protein-protein interaction domain was identified at amino acids 243-306 that contains the DNA-binding SAND domain and also an adjacent zinc binding motif and a monopartite nuclear localization signal (NLS). Deletion of these adjacent sequences or mutation of the conserved cysteines or histidine in the zinc binding motif not only inhibits protein interaction but also eliminates DNA binding, demonstrating that DEAF-1 protein-protein interaction is required for DNA recognition. The identification of an NES and NLS provides a basis for the control of DEAF-1 subcellular localization and function, whereas the requirement of protein-protein interaction by the SAND domain appears to be unique among this class of transcription factors.
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Affiliation(s)
- Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA
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Hahm K, Sum EYM, Fujiwara Y, Lindeman GJ, Visvader JE, Orkin SH. Defective neural tube closure and anteroposterior patterning in mice lacking the LIM protein LMO4 or its interacting partner Deaf-1. Mol Cell Biol 2004; 24:2074-82. [PMID: 14966286 PMCID: PMC350571 DOI: 10.1128/mcb.24.5.2074-2082.2004] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Accepted: 11/13/2003] [Indexed: 11/20/2022] Open
Abstract
LMO4 belongs to a family of transcriptional regulators that comprises two zinc-binding LIM domains. LIM-only (LMO) proteins appear to function as docking sites for other factors, leading to the assembly of multiprotein complexes. The transcription factor Deaf-1/NUDR has been identified as one partner protein of LMO4. We have disrupted the Lmo4 and Deaf-1 genes in mice to define their biological function in vivo. All Lmo4 mutants died shortly after birth and showed defects within the presphenoid bone, with 50% of mice also exhibiting exencephaly. Homeotic transformations were observed in Lmo4-null embryos and newborn mice, but with incomplete penetrance. These included skeletal defects in cervical vertebrae and the rib cage. Furthermore, fusions of cranial nerves IX and X and defects in cranial nerve V were apparent in some Lmo4(-/-) and Lmo4(+/-) mice. Remarkably, Deaf-1 mutants displayed phenotypic abnormalities similar to those observed in Lmo4 mutants. These included exencephaly, transformation of cervical segments, and rib cage abnormalities. In contrast to Lmo4 nullizygous mice, nonexencephalic Deaf-1 mutants remained healthy. No defects in the sphenoid bone or cranial nerves were apparent. Thus, Lmo4 and Deaf-1 mutant mice exhibit overlapping as well as distinct phenotypes. Our data indicate an important role for these two transcriptional regulators in pathways affecting neural tube closure and skeletal patterning, most likely reflecting their presence in a functional complex in vivo.
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Affiliation(s)
- Kyungmin Hahm
- Division of Hematology-Oncology, Department of Pediatrics, Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
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