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Zhang L, Wu C, Liu T, Tian Y, Wang D, Wang B, Yin Y. Propofol Protects the Blood-Brain Barrier After Traumatic Brain Injury by Stabilizing the Extracellular Matrix via Prrx1: From Neuroglioma to Neurotrauma. Neurochem Res 2024; 49:2743-2762. [PMID: 38951281 DOI: 10.1007/s11064-024-04202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
The purpose of this study is to explore the shared molecular pathogenesis of traumatic brain injury (TBI) and high-grade glioma and investigate the mechanism of propofol (PF) as a potential protective agent. By analyzing the Chinese glioma genome atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases, we compared the transcriptomic data of high-grade glioma and TBI patients to identify common pathological mechanisms. Through bioinformatics analysis, in vitro experiments and in vivo TBI model, we investigated the regulatory effect of PF on extracellular matrix (ECM)-related genes through Prrx1 under oxidative stress. The impact of PF on BBB integrity under oxidative stress was investigated using a dual-layer BBB model, and we explored the protective effect of PF on tight junction proteins and ECM-related genes in mice after TBI. The study found that high-grade glioma and TBI share ECM instability as an important molecular pathological mechanism. PF stabilizes the ECM and protects the BBB by directly binding to Prrx1 or indirectly regulating Prrx1 through miRNAs. In addition, PF reduces intracellular calcium ions and ROS levels under oxidative stress, thereby preserving BBB integrity. In a TBI mouse model, PF protected BBB integrity through up-regulated tight junction proteins and stabilized the expression of ECM-related genes. Our study reveals the shared molecular pathogenesis between TBI and glioblastoma and demonstrate the potential of PF as a protective agent of BBB. This provides new targets and approaches for the development of novel neurotrauma therapeutic drugs.
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Affiliation(s)
- Lan Zhang
- Department of Anesthesiology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Chenrui Wu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Tao Liu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu Tian
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Dong Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Wang
- Department of Neurosurgery, Tianjin University Huanhu Hospital, Tianjin, China.
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, China.
| | - Yiqing Yin
- Department of Anesthesiology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
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2
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Wang F, Ma W, Fan D, Hu J, An X, Wang Z. The biochemistry of melanogenesis: an insight into the function and mechanism of melanogenesis-related proteins. Front Mol Biosci 2024; 11:1440187. [PMID: 39228912 PMCID: PMC11368874 DOI: 10.3389/fmolb.2024.1440187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/22/2024] [Indexed: 09/05/2024] Open
Abstract
Melanin is an amino acid derivative produced by melanocyte through a series of enzymatic reactions using tyrosinase as substrate. Human skin and hair color is also closely related to melanin, so understanding the mechanisms and proteins that produce melanin is very important. There are many proteins involved in the process of melanin expression, For example, proteins involved in melanin formation such as p53, HNF-1α (Hepatocyte nuclear factor 1α), SOX10 (Sry-related HMg-Box gene 10) and pax3 (paired box gene 3), MC1R(Melanocortin 1 Receptor), MITF (Microphthalmia-associated transcription factor), TYR (tyrosinase), TYRP1 (tyrosinase-related protein-1), TYRP2 (tyrosinase-related protein-2), and can be regulated by changing their content to control the production rate of melanin. Others, such as OA1 (ocular albinism type 1), Par-2 (protease-activated receptor 2) and Mlph (Melanophilin), have been found to control the transfer rate of melanosomes from melanocytes to keratinocytes, and regulate the amount of human epidermal melanin to control the depth of human skin color. In addition to the above proteins, there are other protein families also involved in the process of melanin expression, such as BLOC, Rab and Rho. This article reviews the origin of melanocytes, the related proteins affecting melanin and the basic causes of related gene mutations. In addition, we also summarized the active ingredients of 5 popular whitening cosmetics and their mechanisms of action.
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Affiliation(s)
- Feifei Wang
- Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
- Yunnan Botanee Bio-Technology Group Co., Ltd., Kunming, China
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- Shanghai Jiyan Bio-Pharmaceutical Co., Ltd., Shanghai, China
| | - Wenjing Ma
- Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
- Shanghai Jiyan Bio-Pharmaceutical Co., Ltd., Shanghai, China
| | - Dongjie Fan
- Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
- Shanghai Jiyan Bio-Pharmaceutical Co., Ltd., Shanghai, China
| | - Jing Hu
- Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
- Shanghai Jiyan Bio-Pharmaceutical Co., Ltd., Shanghai, China
| | - Xiaohong An
- Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
- Yunnan Botanee Bio-Technology Group Co., Ltd., Kunming, China
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- Shanghai Jiyan Bio-Pharmaceutical Co., Ltd., Shanghai, China
| | - Zuding Wang
- Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
- Yunnan Botanee Bio-Technology Group Co., Ltd., Kunming, China
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Jiang Y, Yi Z, Zheng Y, Ouyang J, Guo D, Li S, Xiao X, Wang P, Sun W, Zhang Q. The Systemic Genotype-Phenotype Characterization of PAX6-Related Eye Disease in 164 Chinese Families. Invest Ophthalmol Vis Sci 2024; 65:46. [PMID: 39212610 PMCID: PMC11364179 DOI: 10.1167/iovs.65.10.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose This study aims to evaluate the genetic and phenotypic characteristics and elucidate the genotype-phenotype correlations of a large Chinese cohort with PAX6-related disorders. Methods Variants detected with exome sequencing were filtered through multistep bioinformatic and co-segregation analyses, and validated by Sanger sequencing. The related clinical data were collected, and cluster analysis and statistical analysis of the PAX6-related phenotypes across different variant groups were carried out. Parental mosaicism was investigated using cloning analysis and Droplet digital PCR. Results A total of 119 pathogenic or likely pathogenic PAX6 variants, including 74 truncation, 31 missense, and 14 others, were identified in 228 patients from 164 unrelated families. The most common phenotypes were foveal hypoplasia (97.8%), nystagmus (92.6%), aniridia (76.7%), cataract (36.8%), and iris hypoplasia (22.4%). Mosaicism ranging from 13.9% to 18.8% was identified in 3 unrelated patients' parents with relatively mild phenotypes. Missense variants in the linker region of the paired domain were associated with high myopia, whereas truncation variants in the homeodomain and proline-serine-threonine-rich domain were associated with hyperopia. Similarly, the degree of iris defects, visual acuity, and associated ocular comorbidity varied among the different types and locations of PAX6 variants. Conclusions Our data indicate that foveal hypoplasia but not aniridia is the most common sign of PAX6-related disorders, contributing to subtle iris changes that might easily be overlooked in clinical practice. Recognition of mosaicism in atypical cases or parents with very mild phenotypes is important in genetic counseling as their offspring are at increased risk of typical aniridia. Recognition of the genotype-phenotype relationship emphasizes involvement of PAX6 regulation in shaping complex ocular phenotypes.
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Affiliation(s)
- Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yuxi Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dongwei Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky A, Schoch E, Gagliani E, Herr A, Gebelein B, Kovall R. Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface. Nucleic Acids Res 2024; 52:7987-8002. [PMID: 38874471 PMCID: PMC11260452 DOI: 10.1093/nar/gkae522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the following question: How do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely 7 bp apart. However, the mechanistic basis for Gsx-DNA binding and cooperativity is poorly understood. Here, we used biochemical, biophysical, structural and modeling approaches to (i) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation, (ii) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions, (iii) solve a high-resolution monomer/DNA structure that reveals that Gsx2 induces a 20° bend in DNA, (iv) identify a Gsx2 protein-protein interface required for cooperative DNA binding and (v) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors.
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Affiliation(s)
- Jordan A Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Srivastava D, Gowribidanur-Chinnaswamy P, Gaur P, Spies M, Swaroop A, Artemyev NO. Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element. Structure 2024:S0969-2126(24)00242-9. [PMID: 39084215 DOI: 10.1016/j.str.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/03/2024] [Accepted: 07/04/2024] [Indexed: 08/02/2024]
Abstract
Two retinal transcription factors, cone-rod homeobox (CRX) and neural retina leucine zipper (NRL), cooperate functionally and physically to control photoreceptor development and homeostasis. Mutations in CRX and NRL cause severe retinal diseases. Despite the roles of NRL and CRX, insight into their functions at the molecular level is lacking. Here, we have solved the crystal structure of the CRX homeodomain in complex with its cognate response element (Ret4) from the rhodopsin proximal promoter region. The structure reveals an unexpected 2:1 stoichiometry of CRX/Ret4 and unique orientation of CRX molecules on DNA, and it explains the mechanisms of pathogenic mutations in CRX. Mutations R41Q and E42K disrupt the CRX protein-protein contacts based on the structure and reduce the CRX/Ret4 binding stoichiometry, suggesting a novel disease mechanism. Furthermore, we show that NRL alters the stoichiometry and increases affinity of CRX binding at the rhodopsin promoter, which may enhance transcription of rod-specific genes and suppress transcription of cone-specific genes.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | | | - Paras Gaur
- Department of Biochemistry and Molecular Biology, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585809. [PMID: 38585983 PMCID: PMC10996540 DOI: 10.1101/2024.03.21.585809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Jie Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zara Shariff
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Stephen P. Plassmeyer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (BETHESDA, MD.) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [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: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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9
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky AE, Schoch E, Gagliani EK, Herr AB, Gebelein B, Kovall RA. Cooperative Gsx2-DNA Binding Requires DNA Bending and a Novel Gsx2 Homeodomain Interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570805. [PMID: 38106145 PMCID: PMC10723402 DOI: 10.1101/2023.12.08.570805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the question - how do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely seven base pairs apart. However, the mechanistic basis for Gsx DNA binding and cooperativity are poorly understood. Here, we used biochemical, biophysical, structural, and modeling approaches to (1) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation; (2) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions; (3) solve a high-resolution monomer/DNA structure that reveals Gsx2 induces a 20° bend in DNA; (4) identify a Gsx2 protein-protein interface required for cooperative DNA binding; and (5) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors, thereby providing a deeper understanding of HD specificity.
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Affiliation(s)
- Jordan A. Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K. Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A. Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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10
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Gruenbacher S, Jaritz M, Hill L, Schäfer M, Busslinger M. Essential role of the Pax5 C-terminal domain in controlling B cell commitment and development. J Exp Med 2023; 220:e20230260. [PMID: 37725138 PMCID: PMC10509461 DOI: 10.1084/jem.20230260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/28/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
The B cell regulator Pax5 consists of multiple domains whose function we analyzed in vivo by deletion in Pax5. While B lymphopoiesis was minimally affected in mice with homozygous deletion of the octapeptide or partial homeodomain, both sequences were required for optimal B cell development. Deletion of the C-terminal regulatory domain 1 (CRD1) interfered with B cell development, while elimination of CRD2 modestly affected B-lymphopoiesis. Deletion of CRD1 and CRD2 arrested B cell development at an uncommitted pro-B cell stage. Most Pax5-regulated genes required CRD1 or both CRD1 and CRD2 for their activation or repression as these domains induced or eliminated open chromatin at Pax5-activated or Pax5-repressed genes, respectively. Co-immunoprecipitation experiments demonstrated that the activating function of CRD1 is mediated through interaction with the chromatin-remodeling BAF, H3K4-methylating Set1A-COMPASS, and H4K16-acetylating NSL complexes, while its repressing function depends on recruitment of the Sin3-HDAC and MiDAC complexes. These data provide novel molecular insight into how different Pax5 domains regulate gene expression to promote B cell commitment and development.
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Affiliation(s)
- Sarah Gruenbacher
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Louisa Hill
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Markus Schäfer
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
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11
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Zheng Y, Sun C, Zhang X, Ruzycki PA, Chen S. Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms. eLife 2023; 12:RP87147. [PMID: 37963072 PMCID: PMC10645426 DOI: 10.7554/elife.87147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here, we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Chi Sun
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
| | - Philip A Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Genetics, Washington University in St LouisSaint LouisUnited States
| | - Shiming Chen
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Ophthalmology and Visual Sciences, Washington University in St LouisSaint LouisUnited States
- Department of Developmental Biology, Washington University in St LouisSaint LouisUnited States
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12
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Vasilyeva TA, Sukhanova NV, Marakhonov AV, Kuzina NY, Shilova NV, Kadyshev VV, Kutsev SI, Zinchenko RA. Co-Occurrence of Congenital Aniridia Due to Nonsense PAX6 Variant p.(Cys94*) and Chromosome 21 Trisomy in the Same Patient. Int J Mol Sci 2023; 24:15527. [PMID: 37958513 PMCID: PMC10650867 DOI: 10.3390/ijms242115527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
This study aims to present a clinical case involving the unique co-occurrence of congenital aniridia and Down syndrome in a young girl and to analyze the combined impact of these conditions on the patient's phenotype. The investigation involved comprehensive pediatric and ophthalmological examinations alongside karyotyping and Sanger sequencing of the PAX6 gene. The patient exhibited distinctive features associated with both congenital aniridia and Down syndrome, suggesting a potential exacerbation of their effects. Cytogenetic and molecular genetic analysis revealed the presence of trisomy 21 and a known pathogenic nonsense variant in exon 6 of the PAX6 gene (c.282C>A, p.(Cys94*)) corresponding to the paired domain of the protein. The observation of these two hereditary anomalies offers valuable insights into the molecular pathogenetic mechanisms underlying each condition. Additionally, it provides a basis for a more nuanced prognosis of the complex disease course in this patient. This case underscores the importance of considering interactions between different genetic disorders in clinical assessments and treatment planning.
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Affiliation(s)
| | | | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.A.V.); (N.V.S.); (N.Y.K.); (N.V.S.); (V.V.K.); (S.I.K.); (R.A.Z.)
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13
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Cain B, Webb J, Yuan Z, Cheung D, Lim HW, Kovall R, Weirauch MT, Gebelein B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Res 2023; 51:6055-6072. [PMID: 37114997 PMCID: PMC10325903 DOI: 10.1093/nar/gkad318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
Homeodomain proteins constitute one of the largest families of metazoan transcription factors. Genetic studies have demonstrated that homeodomain proteins regulate many developmental processes. Yet, biochemical data reveal that most bind highly similar DNA sequences. Defining how homeodomain proteins achieve DNA binding specificity has therefore been a long-standing goal. Here, we developed a novel computational approach to predict cooperative dimeric binding of homeodomain proteins using High-Throughput (HT) SELEX data. Importantly, we found that 15 of 88 homeodomain factors form cooperative homodimer complexes on DNA sites with precise spacing requirements. Approximately one third of the paired-like homeodomain proteins cooperatively bind palindromic sequences spaced 3 bp apart, whereas other homeodomain proteins cooperatively bind sites with distinct orientation and spacing requirements. Combining structural models of a paired-like factor with our cooperativity predictions identified key amino acid differences that help differentiate between cooperative and non-cooperative factors. Finally, we confirmed predicted cooperative dimer sites in vivo using available genomic data for a subset of factors. These findings demonstrate how HT-SELEX data can be computationally mined to predict cooperativity. In addition, the binding site spacing requirements of select homeodomain proteins provide a mechanism by which seemingly similar AT-rich DNA sequences can preferentially recruit specific homeodomain factors.
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Affiliation(s)
- Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Jordan Webb
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David Cheung
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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14
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Zheng Y, Sun C, Zhang X, Ruzycki PA, Chen S. Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526652. [PMID: 36778408 PMCID: PMC9915647 DOI: 10.1101/2023.02.01.526652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases CRX-mediated transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinder photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, USA
| | - Shiming Chen
- Molecular Genetic and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, USA
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15
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Smirnov VM, Robert MP, Condroyer C, Navarro J, Antonio A, Rozet JM, Sahel JA, Perrault I, Audo I, Zeitz C. Association of Missense Variants in VSX2 With a Peculiar Form of Congenital Stationary Night Blindness Affecting All Bipolar Cells. JAMA Ophthalmol 2022; 140:1163-1173. [PMID: 36264558 PMCID: PMC9585472 DOI: 10.1001/jamaophthalmol.2022.4146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023]
Abstract
Importance Congenital stationary night blindness (CSNB) is an inherited stationary retinal disorder that is clinically and genetically heterogeneous. To date, the genetic association between some cases with CSNB and an unusual complex clinical picture is unclear. Objective To describe an unreported CSNB phenotype and the associated gene defect in 3 patients from 2 unrelated families. Design, Setting, and Participants This retrospective case series was conducted in 2021 and 2022 at a national referral center for rare ocular diseases. Data for 3 patients from a cohort of 140 genetically unsolved CSNB cases were analyzed clinically and genetically. Exposures Complete ocular examination including full-field electroretinography and multimodal fundus imaging (spectral-domain optical coherence tomography, color, infrared reflectance, and short-wavelength autofluorescence photographs) were performed. The gene defect was identified by exome sequencing and confirmed by Sanger sequencing and co-segregation analysis in 1 family. Screening was performed for genetically unsolved CSNB cases for VSX2 variants by direct Sanger sequencing. Main Outcomes and Measures Ocular and molecular biology findings. Results The series included 3 patients whose clinical investigations occurred at ages in the early 30s, younger than 12 years, and in the mid 40s. They had nystagmus, low stable visual acuity, and myopia from birth and experienced night blindness. Two older patients had bilateral lens luxation and underwent lens extraction. Full-field electroretinography revealed an electronegative Schubert-Bornschein appearance, combining characteristics of incomplete and complete CSNB, affecting the function of rod and cone ON- and OFF-bipolar cells. Exome sequencing and co-segregation analysis in a consanguineous family with 2 affected members identified a homozygous variant in VSX2. Subsequently, screening of the CSNB cohort identified another unrelated patient harboring a distinct VSX2 variant. Conclusions and Relevance This case series revealed a peculiar pan-bipolar cell retinopathy with lens luxation associated with variants in VSX2. Clinicians should be aware of this association and VSX2 added to CSNB diagnostic gene panels.
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Affiliation(s)
- Vasily M. Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Université de Lille, Faculté de Médecine, Lille, France
- Exploration de la Vision et Neuro-Ophtalmologie, CHU de Lille, Lille, France
| | - Matthieu P. Robert
- Ophthalmology Department, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Borelli Centre, UMR 9010, CNRS-SSA-ENS Paris Saclay-Paris University, Gif-sur-Yvette, France
| | | | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR 1163, Institute of Genetic Diseases, Imagine Institute, and Paris University, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR 1163, Institute of Genetic Diseases, Imagine Institute, and Paris University, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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16
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Clanor PB, Buchholz CN, Hayes JE, Friedman MA, White AM, Enke RA, Berndsen CE. Structural and functional analysis of the human cone‐rod homeobox transcription factor. Proteins 2022; 90:1584-1593. [PMID: 35255174 PMCID: PMC9271546 DOI: 10.1002/prot.26332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.
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Affiliation(s)
| | - Christine N. Buchholz
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
| | - Jonathan E. Hayes
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
| | | | - Andrew M. White
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
| | - Ray A. Enke
- Department of Biology James Madison University Harrisonburg Virginia USA
- Center for Genome and Metagenome Studies James Madison University Harrisonburg Virginia USA
| | - Christopher E. Berndsen
- Department of Chemistry and Biochemistry James Madison University Harrisonburg Virginia USA
- Center for Genome and Metagenome Studies James Madison University Harrisonburg Virginia USA
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17
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Interaction of human CRX and NRL in live HEK293T cells measured using fluorescence resonance energy transfer (FRET). Sci Rep 2022; 12:6937. [PMID: 35484285 PMCID: PMC9050680 DOI: 10.1038/s41598-022-10689-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 12/04/2022] Open
Abstract
CRX and NRL are retina-specific transcription factors that control rod photoreceptor differentiation and synergistically activate rod phototransduction gene expression. Previous experiments showed they interact in vitro and in yeast two-hybrid assays. Here, we examined CRX-NRL interaction in live HEK293T cells using two fluorescence resonance energy transfer (FRET) approaches: confocal microscopy and flow cytometry (FC-FRET). FC-FRET can provide measurements from many cells having wide donor–acceptor expression ranges. FRET efficiencies were calibrated with a series of donor (EGFP)-acceptor (mCherry) fusion proteins separated with linkers between 6–45 amino acids. CRX and NRL were fused at either terminus with EGFP or mCherry to create fluorescent proteins, and all combinations were tested in transiently transfected cells. FRET signals between CRX or NRL homo-pairs were highest with both fluorophores fused to the DNA binding domains (DBD), lower with both fused to the activation domains (AD), and not significant when fused on opposite termini. NRL had stronger FRET signals than CRX. A significant FRET signal between CRX and NRL hetero-pairs was detected when donor was fused to the CRX DNA binding domain and the acceptor fused to the NRL activation domain. FRET signals increased with CRX or NRL expression levels at a rate much higher than expected for collisional FRET alone. Together, our results show the formation of CRX-NRL complexes in live HEK293T cells that are close enough for FRET.
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18
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Datta RR, Rister J. The power of the (imperfect) palindrome: Sequence-specific roles of palindromic motifs in gene regulation. Bioessays 2022; 44:e2100191. [PMID: 35195290 PMCID: PMC8957550 DOI: 10.1002/bies.202100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/22/2022]
Abstract
In human languages, a palindrome reads the same forward as backward (e.g., 'madam'). In regulatory DNA, a palindrome is an inverted sequence repeat that allows a transcription factor to bind as a homodimer or as a heterodimer with another type of transcription factor. Regulatory palindromes are typically imperfect, that is, the repeated sequences differ in at least one base pair, but the functional significance of this asymmetry remains poorly understood. Here, we review the use of imperfect palindromes in Drosophila photoreceptor differentiation and mammalian steroid receptor signaling. Moreover, we discuss mechanistic explanations for the predominance of imperfect palindromes over perfect palindromes in these two gene regulatory contexts. Lastly, we propose to elucidate whether specific imperfectly palindromic variants have specific regulatory functions in steroid receptor signaling and whether such variants can help predict transcriptional outcomes as well as the response of individual patients to drug treatments.
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Affiliation(s)
- Rhea R Datta
- Department of Biology, Hamilton College, Clinton, New York, USA
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
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19
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Ettensohn CA, Guerrero-Santoro J, Khor JM. Lessons from a transcription factor: Alx1 provides insights into gene regulatory networks, cellular reprogramming, and cell type evolution. Curr Top Dev Biol 2022; 146:113-148. [PMID: 35152981 DOI: 10.1016/bs.ctdb.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The skeleton-forming cells of sea urchins and other echinoderms have been studied by developmental biologists as models of cell specification and morphogenesis for many decades. The gene regulatory network (GRN) deployed in the embryonic skeletogenic cells of euechinoid sea urchins is one of the best understood in any developing animal. Recent comparative studies have leveraged the information contained in this GRN, bringing renewed attention to the diverse patterns of skeletogenesis within the phylum and the evolutionary basis for this diversity. The homeodomain-containing transcription factor, Alx1, was originally shown to be a core component of the skeletogenic GRN of the sea urchin embryo. Alx1 has since been found to be key regulator of skeletal cell identity throughout the phylum. As such, Alx1 is currently serving as a lens through which multiple developmental processes are being investigated. These include not only GRN organization and evolution, but also cell reprogramming, cell type evolution, and the gene regulatory control of morphogenesis. This review summarizes our current state of knowledge concerning Alx1 and highlights the insights it is yielding into these important developmental and evolutionary processes.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
| | | | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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20
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Racca JD, Chatterjee D, Chen YS, Rai RK, Yang Y, Georgiadis MM, Haas E, Weiss MA. Tenuous transcriptional threshold of human sex determination. II. SRY exploits water-mediated clamp at the edge of ambiguity. Front Endocrinol (Lausanne) 2022; 13:1029177. [PMID: 36568077 PMCID: PMC9771472 DOI: 10.3389/fendo.2022.1029177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Y-encoded transcription factor SRY initiates male differentiation in therian mammals. This factor contains a high-mobility-group (HMG) box, which mediates sequence-specific DNA binding with sharp DNA bending. A companion article in this issue described sex-reversal mutations at box position 72 (residue 127 in human SRY), invariant as Tyr among mammalian orthologs. Although not contacting DNA, the aromatic ring seals the domain's minor wing at a solvent-exposed junction with a basic tail. A seeming paradox was posed by the native-like biochemical properties of inherited Swyer variant Y72F: its near-native gene-regulatory activity is consistent with the father's male development, but at odds with the daughter's XY female somatic phenotype. Surprisingly, aromatic rings (Y72, F72 or W72) confer higher transcriptional activity than do basic or polar side chains generally observed at solvated DNA interfaces (Arg, Lys, His or Gln). Whereas biophysical studies (time-resolved fluorescence resonance energy transfer and heteronuclear NMR spectroscopy) uncovered only subtle perturbations, dissociation of the Y72F complex was markedly accelerated relative to wild-type. Studies of protein-DNA solvation by molecular-dynamics (MD) simulations of an homologous high-resolution crystal structure (SOX18) suggest that Y72 para-OH anchors a network of water molecules at the tail-DNA interface, perturbed in the variant in association with nonlocal conformational fluctuations. Loss of the Y72 anchor among SRY variants presumably "unclamps" its basic tail, leading to (a) rapid DNA dissociation despite native affinity and (b) attenuated transcriptional activity at the edge of sexual ambiguity. Conservation of Y72 suggests that this water-mediated clamp operates generally among SRY and metazoan SOX domains.
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Affiliation(s)
- Joseph D. Racca
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Joseph D. Racca, ; Michael A. Weiss,
| | - Deepak Chatterjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ratan K. Rai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elisha Haas
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Joseph D. Racca, ; Michael A. Weiss,
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21
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Profile of Claude Desplan. Proc Natl Acad Sci U S A 2021; 118:2110547118. [PMID: 34244438 DOI: 10.1073/pnas.2110547118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Lewin TD, Royall AH, Holland PWH. Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. J Mol Evol 2021; 89:396-414. [PMID: 34097121 PMCID: PMC8208926 DOI: 10.1007/s00239-021-10012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.
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Affiliation(s)
- Thomas D Lewin
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Amy H Royall
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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23
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Guerrero-Santoro J, Khor JM, Açıkbaş AH, Jaynes JB, Ettensohn CA. Analysis of the DNA-binding properties of Alx1, an evolutionarily conserved regulator of skeletogenesis in echinoderms. J Biol Chem 2021; 297:100901. [PMID: 34157281 PMCID: PMC8319359 DOI: 10.1016/j.jbc.2021.100901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
Alx1, a homeodomain-containing transcription factor, is a highly conserved regulator of skeletogenesis in echinoderms. In sea urchins, Alx1 plays a central role in the differentiation of embryonic primary mesenchyme cells (PMCs) and positively regulates the transcription of most biomineralization genes expressed by these cells. The alx1 gene arose via duplication and acquired a skeletogenic function distinct from its paralog (alx4) through the exonization of a 41–amino acid motif (the D2 domain). Alx1 and Alx4 contain glutamine-50 paired-type homeodomains, which interact preferentially with palindromic binding sites in vitro. Chromatin immunoprecipitation sequencing (ChIP-seq) studies have shown, however, that Alx1 binds both to palindromic and half sites in vivo. To address this apparent discrepancy and explore the function of the D2 domain, we used an endogenous cis-regulatory module associated with Sp-mtmmpb, a gene that encodes a PMC-specific metalloprotease, to analyze the DNA-binding properties of Alx1. We find that Alx1 forms dimeric complexes on TAAT-containing half sites by a mechanism distinct from the well-known mechanism of dimerization on palindromic sites. We used transgenic reporter assays to analyze the functional roles of half sites in vivo and demonstrate that two sites with partially redundant functions are essential for the PMC-specific activity of the Sp-mtmmpb cis-regulatory module. Finally, we show that the D2 domain influences the DNA-binding properties of Alx1 in vitro, suggesting that the exonization of this motif may have facilitated the acquisition of new transcriptional targets and consequently a novel developmental function.
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Affiliation(s)
| | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Ayşe Haruka Açıkbaş
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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24
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A Family of Auxiliary Subunits of the TRP Cation Channel Encoded by the Complex inaF Locus. Genetics 2020; 215:713-728. [PMID: 32434796 DOI: 10.1534/genetics.120.303268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
TRP channels function in many types of sensory receptor cells. Despite extensive analyses, an open question is whether there exists a family of auxiliary subunits, which could influence localization, trafficking, and function of TRP channels. Here, using Drosophila melanogaster, we reveal a previously unknown TRP interacting protein, INAF-C, which is expressed exclusively in the ultraviolet-sensing R7 photoreceptor cells. INAF-C is encoded by an unusual locus comprised of four distinct coding regions, which give rise to four unique single-transmembrane-containing proteins. With the exception of INAF-B, roles for the other INAF proteins were unknown. We found that both INAF-B and INAF-C are required for TRP stability and localization in R7 cells. Conversely, loss of just INAF-B greatly reduced TRP from other types of photoreceptor cells, but not R7. The requirements for TRP and INAF are reciprocal, since loss of TRP decreased the concentrations of both INAF-B and INAF-C. INAF-A, which is not normally expressed in photoreceptor cells, can functionally substitute for INAF-B, indicating that it is a third TRP auxiliary protein. Reminiscent of the structural requirements between Kv channels and KCNE auxiliary subunits, the codependencies of TRP and INAF depended on several transmembrane domains (TMDs) in TRP, and the TMD and the C-terminus of INAF-B. Our studies support a model in which the inaF locus encodes a family of at least three TRP auxiliary subunits.
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25
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Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL. Nat Commun 2020; 11:2223. [PMID: 32376862 PMCID: PMC7203112 DOI: 10.1038/s41467-020-16024-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 04/08/2020] [Indexed: 11/09/2022] Open
Abstract
Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable to the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.
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26
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Baretić D, Jenkyn-Bedford M, Aria V, Cannone G, Skehel M, Yeeles JTP. Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. Mol Cell 2020; 78:926-940.e13. [PMID: 32369734 PMCID: PMC7276988 DOI: 10.1016/j.molcel.2020.04.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 12/15/2022]
Abstract
The eukaryotic replisome, organized around the Cdc45-MCM-GINS (CMG) helicase, orchestrates chromosome replication. Multiple factors associate directly with CMG, including Ctf4 and the heterotrimeric fork protection complex (Csm3/Tof1 and Mrc1), which has important roles including aiding normal replication rates and stabilizing stalled forks. How these proteins interface with CMG to execute these functions is poorly understood. Here we present 3 to 3.5 Å resolution electron cryomicroscopy (cryo-EM) structures comprising CMG, Ctf4, and the fork protection complex at a replication fork. The structures provide high-resolution views of CMG-DNA interactions, revealing a mechanism for strand separation, and show Csm3/Tof1 “grip” duplex DNA ahead of CMG via a network of interactions important for efficient replication fork pausing. Although Mrc1 was not resolved in our structures, we determine its topology in the replisome by cross-linking mass spectrometry. Collectively, our work reveals how four highly conserved replisome components collaborate with CMG to facilitate replisome progression and maintain genome stability. Cryo-EM structure of Csm3/Tof1 and Ctf4 bound to the eukaryotic CMG helicase Csm3/Tof1 are positioned at the front of the replisome where they grip duplex DNA High-resolution views of CMG-DNA contacts suggest a mechanism for strand separation Mrc1 binds across one side of CMG contacting the front and back of the replisome
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Affiliation(s)
- Domagoj Baretić
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | | | - Valentina Aria
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Giuseppe Cannone
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Mark Skehel
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
| | - Joseph T P Yeeles
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK.
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27
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Lee JK, Bosnakovski D, Toso EA, Dinh T, Banerjee S, Bohl TE, Shi K, Orellana K, Kyba M, Aihara H. Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA. Cell Rep 2019; 25:2955-2962.e3. [PMID: 30540931 DOI: 10.1016/j.celrep.2018.11.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 11/18/2022] Open
Abstract
Double homeobox (DUX) transcription factors are unique to eutherian mammals. DUX4 regulates expression of repetitive elements during early embryogenesis, but misexpression of DUX4 causes facioscapulohumeral muscular dystrophy (FSHD) and translocations overexpressing the DUX4 double homeodomain cause B cell leukemia. Here, we report the crystal structure of the tandem homeodomains of DUX4 bound to DNA. The homeodomains bind DNA in a head-to-head fashion, with the linker making anchoring DNA minor-groove interactions and unique protein contacts. Remarkably, despite being tandem duplicates, the DUX4 homeodomains recognize different core sequences. This results from an arginine-to-glutamate mutation, unique to primates, causing alternative positioning of a key arginine side chain in the recognition helix. Mutational studies demonstrate that this primate-specific change is responsible for the divergence in sequence recognition that likely drove coevolution of embryonically regulated repeats in primates. Our work provides a framework for understanding the endogenous function of DUX4 and its role in FSHD and cancer.
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Affiliation(s)
- John K Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Darko Bosnakovski
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Faculty of Medical Sciences, Goce Delcev University-Stip, Krste Misirkov b.b., 2000 Stip, Republic of Macedonia
| | - Erik A Toso
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tracy Dinh
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, IL 60439, USA
| | - Thomas E Bohl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kayo Orellana
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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28
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Poddar S, Chakravarty D, Chakrabarti P. Structural changes in DNA-binding proteins on complexation. Nucleic Acids Res 2019. [PMID: 29534202 PMCID: PMC6283420 DOI: 10.1093/nar/gky170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein–DNA docking benchmark that contains 66 binary protein–DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein–protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein–DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.
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Affiliation(s)
- Sayan Poddar
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Devlina Chakravarty
- Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.,Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India
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29
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Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis. Sci Rep 2018; 8:17421. [PMID: 30479355 PMCID: PMC6258689 DOI: 10.1038/s41598-018-35547-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/06/2018] [Indexed: 02/06/2023] Open
Abstract
Recently, human PAIRED-LIKE homeobox transcription factor (TF) genes were discovered whose expression is limited to the period of embryo genome activation up to the 8-cell stage. One of these TFs is LEUTX, but its importance for human embryogenesis is still subject to debate. We confirmed that human LEUTX acts as a TAATCC-targeting transcriptional activator, like other K50-type PAIRED-LIKE TFs. Phylogenetic comparisons revealed that Leutx proteins are conserved across Placentalia and comprise two conserved domains, the homeodomain, and a Leutx-specific domain containing putative transcriptional activation motifs (9aaTAD). Examination of human genotype resources revealed 116 allelic variants in LEUTX. Twenty-four variants potentially affect function, but they occur only heterozygously at low frequency. One variant affects a DNA-specificity determining residue, mutationally reachable by a one-base transition. In vitro and in silico experiments showed that this LEUTX mutation (alanine to valine at position 54 in the homeodomain) results in a transactivational loss-of-function to a minimal TAATCC-containing promoter and a 36 bp motif enriched in genes involved in embryo genome activation. A compensatory change in residue 47 restores function. The results support the notion that human LEUTX functions as a transcriptional activator important for human embryogenesis.
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30
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Lazzaretti D, Bandholz-Cajamarca L, Emmerich C, Schaaf K, Basquin C, Irion U, Bono F. The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity. Life Sci Alliance 2018; 1:e201800187. [PMID: 30456389 PMCID: PMC6238398 DOI: 10.26508/lsa.201800187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/29/2023] Open
Abstract
Combination of in vitro and in vivo data show that RNA sequence influences Staufen target recognition and that protein–RNA base contacts are required for Staufen function in Drosophila. During mRNA localization, RNA-binding proteins interact with specific structured mRNA localization motifs. Although several such motifs have been identified, we have limited structural information on how these interact with RNA-binding proteins. Staufen proteins bind structured mRNA motifs through dsRNA-binding domains (dsRBD) and are involved in mRNA localization in Drosophila and mammals. We solved the structure of two dsRBDs of human Staufen1 in complex with a physiological dsRNA sequence. We identified interactions between the dsRBDs and the RNA sugar–phosphate backbone and direct contacts of conserved Staufen residues to RNA bases. Mutating residues mediating nonspecific backbone interactions only affected Staufen function in Drosophila when in vitro binding was severely reduced. Conversely, residues involved in base-directed interactions were required in vivo even when they minimally affected in vitro binding. Our work revealed that Staufen can read sequence features in the minor groove of dsRNA and suggests that these influence target selection in vivo.
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Affiliation(s)
| | | | | | - Kristina Schaaf
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Claire Basquin
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Uwe Irion
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Fulvia Bono
- Max Planck Institute for Developmental Biology, Tübingen, Germany.,Living Systems Institute, University of Exeter, Exeter, UK
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31
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Structural basis for multiple gene regulation by human DUX4. Biochem Biophys Res Commun 2018; 505:1161-1167. [PMID: 30322619 DOI: 10.1016/j.bbrc.2018.10.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 11/22/2022]
Abstract
DUX4 plays critical role in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy and acute lymphoblastic leukemia in humans. As a master transcription regulator, DUX4 can also bind the promoters and activate the transcription of hundreds ZGA-associated genes. Here we report on the structural and biochemical studies of DUX4 double homeodomains (DUX4-DH), representing the only structures contain both homeodomain 1 (HD1) and homeodomain 2 (HD2). HD1 and HD2 adopt classical homeobox fold; via the helix inserted into the major groove and the N-terminal extended loop inserted into the minor groove, HD1 and HD2 recognize the box1 (5'-TAA-3') and box2 (5'-TGA-3') nucleotides of the consensus sequence, respectively. Among the box1 and box2 linking nucleotides (CCTAA), the two adenine residues are reported to be highly conserved; however, they are not directly recognized by DUX4-DH in the structures. Besides different nucleotides, our ITC analysis indicated that DUX4-DH can also tolerate various changes in the linker length. Our studies not only revealed the basis for target DNA recognition by DUX4, but also advanced our understanding on multiple gene activation by DUX4.
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32
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A novel PAX6 nonsense mutation identified in an Iranian family with various eye anomalies. J Curr Ophthalmol 2018; 30:234-238. [PMID: 30197953 PMCID: PMC6127359 DOI: 10.1016/j.joco.2017.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/18/2017] [Accepted: 12/12/2017] [Indexed: 12/03/2022] Open
Abstract
Purpose The aim of this study was to detect the genetic defects in a large pedigree of affected individuals with various phenotypes of ocular anomalies including partial aniridia, congenital cataract, and nystagmus. Methods The entire coding region of paired box gene 6 (PAX6) was amplified by polymerase chain reaction (PCR), sequenced, and compared with a GenBank database. Results A novel mutation (c.1170 C > T; p.Gln297X) was found in the proband and all affected members. This nonsense mutation leads to PAX6 protein truncation. Conclusions Our findings suggest that this novel mutation is most likely responsible for the pathogenesis of the congenital aniridia, cataract, and nystagmus in this pedigree. To the best of our knowledge, this is the first report of this mutation of PAX6 gene in a kindred pedigree with various ocular abnormalities.
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33
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Hughes AEO, Myers CA, Corbo JC. A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo. Genome Res 2018; 28:1520-1531. [PMID: 30158147 PMCID: PMC6169884 DOI: 10.1101/gr.231886.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Cone-rod homeobox (CRX) is a paired-like homeodomain transcription factor (TF) and a master regulator of photoreceptor development in vertebrates. The in vitro DNA binding preferences of CRX have been described in detail, but the degree to which in vitro binding affinity is correlated with in vivo enhancer activity is not known. In addition, paired-class homeodomain TFs can bind DNA cooperatively as both homodimers and heterodimers at inverted TAAT half-sites separated by 2 or 3 nucleotides. This dimeric configuration is thought to mediate target specificity, but whether monomeric and dimeric sites encode distinct levels of activity is not known. Here, we used a massively parallel reporter assay to determine how local sequence context shapes the regulatory activity of CRX binding sites in mouse photoreceptors. We assayed inactivating mutations in more than 1700 TF binding sites and found that dimeric CRX binding sites act as stronger enhancers than monomeric CRX binding sites. Furthermore, the activity of dimeric half-sites is cooperative, dependent on a strict 3-bp spacing, and tuned by the identity of the spacer nucleotides. Saturating single-nucleotide mutagenesis of 195 CRX binding sites showed that, on average, changes in TF binding site affinity are correlated with changes in regulatory activity, but this relationship is obscured when considering mutations across multiple cis-regulatory elements (CREs). Taken together, these results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.
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Affiliation(s)
- Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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34
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Syrimis A, Nicolaou N, Alexandrou A, Papaevripidou I, Nicolaou M, Loukianou E, Sismani C, Malas S, Christophidou-Anastasiadou V, Tanteles GA. Molecular analysis of Cypriot families with aniridia reveals a novel PAX6 mutation. Mol Med Rep 2018; 18:1623-1627. [PMID: 29901133 PMCID: PMC6072148 DOI: 10.3892/mmr.2018.9126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022] Open
Abstract
The present study investigated the clinical and mutational spectrum of aniridia in a cohort of 17 affected individuals from six families from Cyprus. Each proband was initially evaluated for copy number variants at the PAX6 locus and subsequently underwent PAX6 mutation screening. Sequence analysis of FOXC1 and PITX2 was performed in patients who did not carry a PAX6 mutation. The most common clinical features in the group of aniridia patients associated with aniridia were nystagmus, cataracts and glaucoma. PAX6 pathogenic mutations were identified in five out of six families (a diagnostic yield of 84%). Previously reported pathogenic mutations in PAX6 were identified in four families, which comprise p.R203*, p.R240* and p.R317*. In addition, a novel pathogenic variant (p.E220Gfs*23) was identified in a single family. No pathogenic mutations were detected in PAX6, FOXC1 or PITX2 in the only patient with a sporadic form of aniridia‑like phenotype, confirming the genetic heterogeneity associated with this disease. To the best of our knowledge this is the first report on the mutational spectrum of PAX6 in aniridia patients of Cypriot ancestry. Mutational screening of PAX6 serves a crucial role in distinguishing isolated from syndromic forms of aniridia, and it may therefore eliminate the need for renal ultrasound scan surveillance, delineate the phenotype and improve genetic counseling.
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Affiliation(s)
- Andreas Syrimis
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Nayia Nicolaou
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Michael Nicolaou
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Eleni Loukianou
- Department of Ophthalmology, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Stavros Malas
- Department of Developmental and Functional Genetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Violetta Christophidou-Anastasiadou
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Department of Clinical Genetics, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - George A. Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
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35
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Dong X, Zhang W, Wu H, Huang J, Zhang M, Wang P, Zhang H, Chen Z, Chen SJ, Meng G. Structural basis of DUX4/IGH-driven transactivation. Leukemia 2018; 32:1466-1476. [PMID: 29572508 PMCID: PMC5990521 DOI: 10.1038/s41375-018-0093-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/10/2018] [Accepted: 02/20/2018] [Indexed: 01/10/2023]
Abstract
Oncogenic fusions are major drivers in leukemogenesis and may serve as potent targets for treatment. DUX4/IGHs have been shown to trigger the abnormal expression of ERGalt through binding to DUX4-Responsive-Element (DRE), which leads to B-cell differentiation arrest and a full-fledged B-ALL. Here, we determined the crystal structures of Apo- and DNADRE-bound DUX4HD2 and revealed a clamp-like transactivation mechanism via the double homeobox domain. Biophysical characterization showed that mutations in the interacting interfaces significantly impaired the DNA binding affinity of DUX4 homeobox. These mutations, when introduced into DUX4/IGH, abrogated its transactivation activity in Reh cells. More importantly, the structure-based mutants significantly impaired the inhibitory effects of DUX4/IGH upon B-cell differentiation in mouse progenitor cells. All these results help to define a key DUX4/IGH-DRE recognition/step in B-ALL.
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Affiliation(s)
- Xue Dong
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Weina Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Haiyan Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Ming Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Pengran Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Hao Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Sai-Juan Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China. .,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China.
| | - Guoyu Meng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China. .,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China.
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Novel PAX6 mutation reported in an aniridia patient. Hum Genome Var 2017; 4:17053. [PMID: 29238604 PMCID: PMC5719187 DOI: 10.1038/hgv.2017.53] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/09/2017] [Accepted: 09/15/2017] [Indexed: 01/17/2023] Open
Abstract
An aniridia patient was found to have a novel PAX6 mutation. A genetic duplication within PAX6, which caused a frameshift mutation, ultimately created a nonsense stop codon and premature truncation of the protein. Consequently, the patient presented with a clouded cornea as a result of partial limbal stem cell deficiency, foveal hypoplasia, nystagmus and a pale, cupped optic disc caused by glaucoma.
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Moir L, Bochukova EG, Dumbell R, Banks G, Bains RS, Nolan PM, Scudamore C, Simon M, Watson KA, Keogh J, Henning E, Hendricks A, O'Rahilly S, Barroso I, Sullivan AE, Bersten DC, Whitelaw ML, Kirsch S, Bentley E, Farooqi IS, Cox RD. Disruption of the homeodomain transcription factor orthopedia homeobox (Otp) is associated with obesity and anxiety. Mol Metab 2017; 6:1419-1428. [PMID: 29107289 PMCID: PMC5681237 DOI: 10.1016/j.molmet.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022] Open
Abstract
Objective Genetic studies in obese rodents and humans can provide novel insights into the mechanisms involved in energy homeostasis. Methods In this study, we genetically mapped the chromosomal region underlying the development of severe obesity in a mouse line identified as part of a dominant N-ethyl-N-nitrosourea (ENU) mutagenesis screen. We characterized the metabolic and behavioral phenotype of obese mutant mice and examined changes in hypothalamic gene expression. In humans, we examined genetic data from people with severe early onset obesity. Results We identified an obese mouse heterozygous for a missense mutation (pR108W) in orthopedia homeobox (Otp), a homeodomain containing transcription factor required for the development of neuroendocrine cell lineages in the hypothalamus, a region of the brain important in the regulation of energy homeostasis. OtpR108W/+ mice exhibit increased food intake, weight gain, and anxiety when in novel environments or singly housed, phenotypes that may be partially explained by reduced hypothalamic expression of oxytocin and arginine vasopressin. R108W affects the highly conserved homeodomain, impairs DNA binding, and alters transcriptional activity in cells. We sequenced OTP in 2548 people with severe early-onset obesity and found a rare heterozygous loss of function variant in the homeodomain (Q153R) in a patient who also had features of attention deficit disorder. Conclusions OTP is involved in mammalian energy homeostasis and behavior and appears to be necessary for the development of hypothalamic neural circuits. Further studies will be needed to investigate the contribution of rare variants in OTP to human energy homeostasis. A mouse Otp mutation alters hypothalamic neuropeptide expression leading to increased food intake, obesity and anxiety. In severe early onset obesity, we found a heterozygous LOF variant in a patient with attention deficit disorder features. These studies show for the first time that mutations in the Otp/OTP gene cause obesity.
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Affiliation(s)
- Lee Moir
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Elena G Bochukova
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Rebecca Dumbell
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Gareth Banks
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Rasneer S Bains
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Patrick M Nolan
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Cheryl Scudamore
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Kimberly A Watson
- School of Biological Sciences, University of Reading, Reading, Berkshire, UK
| | - Julia Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Audrey Hendricks
- Wellcome Trust Sanger Institute, Cambridge, UK; Department of Mathematical and Statistical Sciences, University of Colorado-Denver, Denver, CO 80204, USA
| | - Stephen O'Rahilly
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | | | - Adrienne E Sullivan
- Department Molecular and Cellular Biology, University of Adelaide, Adelaide, Australia
| | - David C Bersten
- Department Molecular and Cellular Biology, University of Adelaide, Adelaide, Australia
| | - Murray L Whitelaw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department Molecular and Cellular Biology, University of Adelaide, Adelaide, Australia
| | - Susan Kirsch
- Department of Endocrinology, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
| | - Elizabeth Bentley
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
| | - Roger D Cox
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK.
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Transcription factor Hlx controls a systematic switch from white to brown fat through Prdm16-mediated co-activation. Nat Commun 2017; 8:68. [PMID: 28701693 PMCID: PMC5507986 DOI: 10.1038/s41467-017-00098-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/30/2017] [Indexed: 11/30/2022] Open
Abstract
Browning of subcutaneous white fat (iWAT) involves several reprograming events, but the underlying mechanisms are incompletely understood. Here we show that the transcription factor Hlx is selectively expressed in brown adipose tissue (BAT) and iWAT, and is translationally upregulated by β3-adrenergic signaling-mediated suppression of the translational inhibitor 4E-BP1. Hlx interacts with and is co-activated by Prdm16 to control BAT-selective gene expression and mitochondrial biogenesis. Hlx heterozygous knockout mice have defects in brown-like adipocyte formation in iWAT, and develop glucose intolerance and high fat-induced hepatic steatosis. Conversely, transgenic expression of Hlx at a physiological level drives a full program of thermogenesis and converts iWAT to brown-like fat, which improves glucose homeostasis and prevents obesity and hepatic steatosis. The adipose remodeling phenotypes are recapitulated by fat-specific injection of Hlx knockdown and overexpression viruses, respectively. Our studies establish Hlx as a powerful regulator for systematic white adipose tissue browning and offer molecular insights into the underlying transcriptional mechanism. The transcriptional co-activator Prdm16 regulates browning of white adipose tissue (WAT). Here, the authors show that Prdm16 interacts with the transcription factor Hlx, which is stabilized in response to β3-adrenergic signaling, to increase thermogenic gene expression and mitochondrial biogenesis in subcutaneous WAT.
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Watanabe M, Yasuoka Y, Mawaribuchi S, Kuretani A, Ito M, Kondo M, Ochi H, Ogino H, Fukui A, Taira M, Kinoshita T. Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis. Dev Biol 2017; 426:301-324. [DOI: 10.1016/j.ydbio.2016.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/27/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
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Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors. Sci Rep 2017; 7:43184. [PMID: 28256534 PMCID: PMC5335693 DOI: 10.1038/srep43184] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
Rod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an ‘inverted’ nuclear architecture, with a dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the periphery. To test if this unique nuclear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rods and their most closely related cell type, cone photoreceptors. We find that thousands of loci are selectively closed in rods relative to cones as well as >60 additional cell types. Furthermore, we find that the open chromatin profile of photoreceptors lacking the rod master regulator Nrl is nearly indistinguishable from that of native cones, indicating that Nrl is required for selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, revealing key differences in the cis-regulatory grammar of these cell types. Taken together, these data provide insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in gene regulation.
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New Insights into Cooperative Binding of Homeodomain Transcription Factors PREP1 and PBX1 to DNA. Sci Rep 2017; 7:40665. [PMID: 28094776 PMCID: PMC5240567 DOI: 10.1038/srep40665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/09/2016] [Indexed: 01/13/2023] Open
Abstract
PREP1 and PBX1 are homeodomain (HD) transcription factors that play crucial roles in embryonic development. Here, we present the first biophysical characterization of a PREP1 HD, and the NMR spectroscopic study of its DNA binding pocket. The data show that residues flanking the HD participate in DNA binding. The kinetic parameters for DNA binding of individual PREP1 and PBX1 HDs, and of their combination, show that isolated PREP1 and PBX1 HDs bind to DNA in a cooperative manner. A novel PREP1 motif, flanking the HD at the C-terminus, is required for cooperativity.
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Kim CH, An MJ, Kim DH, Kim JW. Histone deacetylase 1 (HDAC1) regulates retinal development through a PAX6-dependent pathway. Biochem Biophys Res Commun 2016; 482:735-741. [PMID: 27871855 DOI: 10.1016/j.bbrc.2016.11.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
Abstract
Cell fate determination is tightly controlled by the expression of transcription factors and gene regulatory networks. PAX6 is a transcription factor containing a DNA-binding paired-box domain and homeobox domain that plays a key role in the development of the eye, brain, and pancreas. Here, we showed that histone deacetyltransferase 1 (HDAC1) is a novel binding partner of PAX6 in newborn mouse retinas. We also showed that HDAC1 specifically binds to the paired and transactivation domains of PAX6, and these physical interactions were required for effective repression of PAX6 transcriptional activity during retinal development. Furthermore, HDAC1 preferentially regulates the transcriptional activity of PAX6 when it binds to paired-domain (P6CON and chimeric pCON/P3) PAX6 responsive elements compared to homeodomain (pP3) PAX6 responsive elements. The repressive effect of HDAC1 on the transcriptional activity of PAX6 was reversed by knockdown of HDAC1 or treatment with an HDAC inhibitor, TSA. Taken together, these results show that HDAC1 binds PAX6 and that protein-protein interaction leads to transcriptional repression of PAX6 target genes during mouse retinal development.
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Affiliation(s)
- Chul-Hong Kim
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Mi-Jin An
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae-Hyun Kim
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung-Woong Kim
- Genome Dynamics Laboratory, Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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Ang SF, Lim SC, Tan CS, Fong JC, Kon WY, Lian JX, Subramanium T, Sum CF. A preliminary study to evaluate the strategy of combining clinical criteria and next generation sequencing (NGS) for the identification of monogenic diabetes among multi-ethnic Asians. Diabetes Res Clin Pract 2016; 119:13-22. [PMID: 27420379 DOI: 10.1016/j.diabres.2016.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 05/05/2016] [Accepted: 06/06/2016] [Indexed: 11/18/2022]
Abstract
AIMS Diabetes is increasing globally and Asia is the epicenter. Among those with young-onset diabetes (<45years), the prevalence of monogenic diabetes is estimated to be non-trivial (∼5%). An accurate diagnosis of monogenic diabetes is important to inform treatment, prognosis and genetic counseling. Therefore, a robust clinical algorithm to identify probands for testing is needed. Our aims are (1) to select probands for genetic testing and variant identification based on their clinical phenotype and (2) to evaluate the MODY probability calculator in our multi-ethnic Asian population. METHODS Eighty-four potential probands, identified in accordance with clinical practice guidelines, were subjected to re-sequencing of 16 monogenic diabetes genes and targeted genotyping for mitochondrial 3243A>G point-mutation. Variants, confirmed by bi-directional Sanger sequencing, were classified as pathogenic if they fulfilled the criteria adapted from American College of Medical Genetics. Performance of MODY calculator (with positive-predictive threshold set at >62.4%) for those with diabetes-onset ⩽35years (data input-limit) (n=71) was also evaluated. RESULTS Thirteen subjects (15.5%) harbored likely pathogenic/pathogenic variants: 6 (2 novel) in HNF1A (1 subject concomitantly had another HNF4A variant), 1 in HNF4A, 2 in mt3243A>G and 1 each in GCK, KCNJ11 (novel), ABCC8 (novel) and PAX4 (novel). Performance of the MODY calculator was: sensitivity 0.769, specificity 0.603 and negative predictive value 0.921. When analysis was restricted to MODY1-3, the performance was: 0.875, 0.587 and 0.974, respectively. CONCLUSIONS The prevalence of MODY is non-trivial (∼15%) among Asians with young-onset diabetes. MODY calculator performs well in our population in nominating probands for genetic testing.
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Affiliation(s)
- Su Fen Ang
- Clinical Research Unit, Khoo Teck Puat Hospital (KTPH), Singapore
| | - Su Chi Lim
- Diabetes Center, Khoo Teck Puat Hospital (KTPH), Singapore.
| | - Clara Sh Tan
- Clinical Research Unit, Khoo Teck Puat Hospital (KTPH), Singapore
| | - Jessie Cw Fong
- Clinical Research Unit, Khoo Teck Puat Hospital (KTPH), Singapore
| | - Winston Yc Kon
- Department of Endocrinology, Tan Tock Seng Hospital (TTSH), Singapore
| | - Joyce X Lian
- Department of Endocrinology, Tan Tock Seng Hospital (TTSH), Singapore
| | | | - Chee Fang Sum
- Diabetes Center, Khoo Teck Puat Hospital (KTPH), Singapore
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Yoshida S, Kato T, Nishimura N, Kanno N, Chen M, Ueharu H, Nishihara H, Kato Y. Transcription of follicle-stimulating hormone subunit genes is modulated by porcine LIM homeobox transcription factors, LHX2 and LHX3. J Reprod Dev 2016; 62:241-8. [PMID: 26853788 PMCID: PMC4919287 DOI: 10.1262/jrd.2015-163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The LIM-homeobox transcription factors LHX2 and LHX3s (LHX3a and LHX3b) are thought to be involved in
regulating the pituitary glycoprotein hormone subunit genes Cga and Fshβ.
These two factors show considerable differences in their amino acid sequences for DNA binding and
protein-protein interactions and in their vital function in pituitary development. Hence, we compared the DNA
binding properties and transcriptional activities of Cga and Fshβ between
LHX2 and LHX3s. A gel mobility shift assay for approximately 1.1 kb upstream of Cga and 2.0
kb upstream of Fshβ varied in binding profiles between LHX2 and LHX3s. DNase I footprinting
revealed DNA binding sites in 8 regions of the Cga promoter for LHX2 and LHX3s with small
differences in the binding range and strength. In the Fshβ promoter, 14 binding sites were
identified for LHX2 and LHX3, respectively. There were alternative binding sites to either gene in addition to
similar differences observed in the Cga promoter. The transcriptional activities of LHX2 and
LHX3s according to a reporter assay showed cell-type dependent activity with repression in the pituitary
gonadotrope lineage LβT2 cells and stimulation in Chinese hamster ovary lineage CHO cells. Reactivity of LHX2
and LHX3s was observed in all regions, and differences were observed in the 5'-upstream region of
Fshβ. However, immunohistochemistry showed that LHX2 resides in a small number of
gonadotropes in contrast to LHX3. Thus, LHX3 mainly controls Cga and Fshβ
expression.
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Affiliation(s)
- Saishu Yoshida
- Division of Life Science, Graduate School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
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Rister J, Razzaq A, Boodram P, Desai N, Tsanis C, Chen H, Jukam D, Desplan C. Single-base pair differences in a shared motif determine differential Rhodopsin expression. Science 2016; 350:1258-61. [PMID: 26785491 DOI: 10.1126/science.aab3417] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The final identity and functional properties of a neuron are specified by terminal differentiation genes, which are controlled by specific motifs in compact regulatory regions. To determine how these sequences integrate inputs from transcription factors that specify cell types, we compared the regulatory mechanism of Drosophila Rhodopsin genes that are expressed in subsets of photoreceptors to that of phototransduction genes that are expressed broadly, in all photoreceptors. Both sets of genes share an 11-base pair (bp) activator motif. Broadly expressed genes contain a palindromic version that mediates expression in all photoreceptors. In contrast, each Rhodopsin exhibits characteristic single-bp substitutions that break the symmetry of the palindrome and generate activator or repressor motifs critical for restricting expression to photoreceptor subsets. Sensory neuron subtypes can therefore evolve through single-bp changes in short regulatory motifs, allowing the discrimination of a wide spectrum of stimuli.
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Affiliation(s)
- Jens Rister
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Ansa Razzaq
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Pamela Boodram
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Nisha Desai
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Cleopatra Tsanis
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Hongtao Chen
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - David Jukam
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA
| | - Claude Desplan
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003-6688, USA.
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AlQuraishi M, Tang S, Xia X. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics 2015; 16:390. [PMID: 26586237 PMCID: PMC4653904 DOI: 10.1186/s12859-015-0819-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 11/11/2015] [Indexed: 11/28/2022] Open
Abstract
Background Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. Description We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Conclusions This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.
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Affiliation(s)
- Mohammed AlQuraishi
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA. .,HMS Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA.
| | - Shengdong Tang
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,HMS Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Xide Xia
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,HMS Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
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Schulte D. Meis: New friends of Pax. NEUROGENESIS 2014; 1:e976014. [PMID: 27502016 PMCID: PMC4973581 DOI: 10.4161/23262133.2014.976014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 08/04/2014] [Accepted: 10/08/2014] [Indexed: 12/27/2022]
Abstract
The generation of neuronal diversity in the mammalian brain is a multistep process, beginning with the regional patterning of neural stem- and progenitor cell domains, the commitment of these cells toward a general neuronal fate, followed by the selection of a particular neuronal subtype and the differentiation of postmitotic neurons. Each of these steps as well as the transitions between them require precisely controlled changes in transcriptional programs. Although a large number of transcription factors are known to regulate neurogenesis in the embryonic and adult central nervous system, the sheer number of neuronal cell types in the brain and the complexity of the cellular processes that accompany their production suggest that transcription factors act cooperatively to control individual steps in neurogenesis. In fact, combinatorial regulation by sets of transcription factors has emerged as a versatile mode to control cell fate specification. Here, I discuss our recent finding that members of the MEIS-subfamily of TALE-transcription factors, originally identified as HOX cofactors in non-neural tissues, function in concert with PAX-proteins in the regulation of cell fate specification and neuronal differentiation in the embryonic and adult brain.
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Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute); University Hospital Goethe University ; Frankfurt, Germany
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Forsdahl S, Kiselev Y, Hogseth R, Mjelle JE, Mikkola I. Pax6 regulates the expression of Dkk3 in murine and human cell lines, and altered responses to Wnt signaling are shown in FlpIn-3T3 cells stably expressing either the Pax6 or the Pax6(5a) isoform. PLoS One 2014; 9:e102559. [PMID: 25029272 PMCID: PMC4100929 DOI: 10.1371/journal.pone.0102559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023] Open
Abstract
Pax6 is a transcription factor important for early embryo development. It is expressed in several cancer cell lines and tumors. In glioblastoma, PAX6 has been shown to function as a tumor suppressor. Dickkopf 3 (Dkk3) is well established as a tumor suppressor in several tumor types, but not much is known about the regulation of its expression. We have previously found that Pax6 and Pax6(5a) increase the expression of the Dkk3 gene in two stably transfected mouse fibroblast cell lines. In this study the molecular mechanism behind this regulation is looked at. Western blot and reverse transcriptase quantitative PCR (RT-qPCR) confirmed higher level of Dkk3 expression in both Pax6 and Pax6(5a) expressing cell lines compared to the control cell line. By the use of bioinformatics and electrophoretic mobility shift assay (EMSA) we have mapped a functional Pax6 binding site in the mouse Dkk3 promoter. The minimal Dkk3 promoter fragment required for transcriptional activation by Pax6 and Pax6(5a) was a 200 bp region just upstream of the transcriptional start site. Mutation of the evolutionary conserved binding site in this region abrogated transcriptional activation and binding of Pax6/Pax6(5a) to the mouse Dkk3 promoter. Since the identified Pax6 binding site in this promoter is conserved, RT-qPCR and Western blot were used to look for regulation of Dkk3/REIC expression in human cell lines. Six of eight cell lines tested showed changes in Dkk3/REIC expression after PAX6 siRNA knockdown. Interestingly, we observed that the Pax6/Pax6(5a) expressing mouse fibroblast cell lines were less responsive to canonical Wnt pathway stimulation than the control cell line when TOP/FOP activity and the levels of active β-catenin and GSK3-β Ser9 phosphorylation were measured after LiCl stimulation.
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Affiliation(s)
- Siri Forsdahl
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
| | - Yury Kiselev
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
- Norwegian Translational Cancer Research Center, Department of Medical Biology, UiT – The Arctic University of Norway, Tromsoe, Norway
| | - Rune Hogseth
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
| | - Janne E. Mjelle
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
| | - Ingvild Mikkola
- Research Group of Pharmacology, Department of Pharmacy, UiT – The Artic University of Norway, Tromsoe, Norway
- * E-mail:
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Pröpper K, Meindl K, Sammito M, Dittrich B, Sheldrick GM, Pohl E, Usón I. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1743-57. [PMID: 24914984 PMCID: PMC4051508 DOI: 10.1107/s1399004714007603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/04/2014] [Indexed: 11/11/2022]
Abstract
Protein-DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein-DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein-DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein-DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.
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Affiliation(s)
- Kevin Pröpper
- University of Göttingen, Germany
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Kathrin Meindl
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Massimo Sammito
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | | | | | | | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Spain
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50
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Cross SH, Macalinao DG, McKie L, Rose L, Kearney AL, Rainger J, Thaung C, Keighren M, Jadeja S, West K, Kneeland SC, Smith RS, Howell GR, Young F, Robertson M, van t' Hof R, John SWM, Jackson IJ. A dominant-negative mutation of mouse Lmx1b causes glaucoma and is semi-lethal via LDB1-mediated dimerization [corrected]. PLoS Genet 2014; 10:e1004359. [PMID: 24809698 PMCID: PMC4014447 DOI: 10.1371/journal.pgen.1004359] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/24/2014] [Indexed: 12/27/2022] Open
Abstract
Mutations in the LIM-homeodomain transcription factor LMX1B cause nail-patella syndrome, an autosomal dominant pleiotrophic human disorder in which nail, patella and elbow dysplasia is associated with other skeletal abnormalities and variably nephropathy and glaucoma. It is thought to be a haploinsufficient disorder. Studies in the mouse have shown that during development Lmx1b controls limb dorsal-ventral patterning and is also required for kidney and eye development, midbrain-hindbrain boundary establishment and the specification of specific neuronal subtypes. Mice completely deficient for Lmx1b die at birth. In contrast to the situation in humans, heterozygous null mice do not have a mutant phenotype. Here we report a novel mouse mutant Icst, an N-ethyl-N-nitrosourea-induced missense substitution, V265D, in the homeodomain of LMX1B that abolishes DNA binding and thereby the ability to transactivate other genes. Although the homozygous phenotypic consequences of Icst and the null allele of Lmx1b are the same, heterozygous Icst elicits a phenotype whilst the null allele does not. Heterozygous Icst causes glaucomatous eye defects and is semi-lethal, probably due to kidney failure. We show that the null phenotype is rescued more effectively by an Lmx1b transgene than is Icst. Co-immunoprecipitation experiments show that both wild-type and Icst LMX1B are found in complexes with LIM domain binding protein 1 (LDB1), resulting in lower levels of functional LMX1B in Icst heterozygotes than null heterozygotes. We conclude that Icst is a dominant-negative allele of Lmx1b. These findings indicate a reassessment of whether nail-patella syndrome is always haploinsufficient. Furthermore, Icst is a rare example of a model of human glaucoma caused by mutation of the same gene in humans and mice. Nail-patella syndrome is a human genetic disease caused by an inactivating mutation in one copy of a gene called LMX1B, with the amount of protein produced from the remaining copy of the gene not being enough for normal function. Patients with this disease have malformations of their nails, elbows and kneecaps. Some patients also develop kidney disease and glaucoma. LMX1B controls where and when other genes are expressed and it is important during development. Studies in mice have shown that complete absence of Lmx1b is lethal at birth. In contrast to humans, mice with only one copy of the gene are normal. Here we describe a new mutant mouse, Icst, which has a mutation in Lmx1b that abolishes the ability of the protein to bind near genes that it controls. Mice with one normal and one copy of Lmx1b with the Icst mutation have eye defects and some die shortly after birth probably due to kidney failure. Therefore having one functional and one mutant copy of Lmx1b is more detrimental than having a half dose of functional protein. The Icst mouse is a model of human glaucoma where mutation of the same gene causes glaucoma in humans and mice.
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Affiliation(s)
- Sally H. Cross
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Danilo G. Macalinao
- The Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Lisa McKie
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Lorraine Rose
- Centre for Genomic and Experimental Medicine, IGMM, Edinburgh, United Kingdom
| | - Alison L. Kearney
- The Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Joe Rainger
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Margaret Keighren
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Shalini Jadeja
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Katrine West
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen C. Kneeland
- The Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Richard S. Smith
- The Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Gareth R. Howell
- The Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Fiona Young
- Electron Microscopy, Pathology, Western General Hospital, Edinburgh, United Kingdom
| | - Morag Robertson
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Rob van t' Hof
- Centre for Genomic and Experimental Medicine, IGMM, Edinburgh, United Kingdom
| | - Simon W. M. John
- The Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Ian J. Jackson
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
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