1
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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024; 32:2470-2488. [PMID: 38910326 DOI: 10.1016/j.ymthe.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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2
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Celona B, Salomonsson SE, Wu H, Dang B, Kratochvil HT, Clelland CD, DeGrado WF, Black BL. Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats. Proc Natl Acad Sci U S A 2024; 121:e2220020121. [PMID: 39042693 PMCID: PMC11295049 DOI: 10.1073/pnas.2220020121] [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: 12/16/2022] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Expansion of intronic GGGGCC repeats in the C9orf72 gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Transcription of the expanded repeats results in the formation of RNA-containing nuclear foci and altered RNA metabolism. In addition, repeat-associated non-AUG (RAN) translation of the expanded GGGGCC-repeat sequence results in the production of highly toxic dipeptide-repeat (DPR) proteins. GGGGCC repeat-containing transcripts form G-quadruplexes, which are associated with formation of RNA foci and RAN translation. Zfp106, an RNA-binding protein essential for motor neuron survival in mice, suppresses neurotoxicity in a Drosophila model of C9orf72 ALS. Here, we show that Zfp106 inhibits formation of RNA foci and significantly reduces RAN translation caused by GGGGCC repeats in cultured mammalian cells, and we demonstrate that Zfp106 coexpression reduces the levels of DPRs in C9orf72 patient-derived cells. Further, we show that Zfp106 binds to RNA G-quadruplexes and causes a conformational change in the G-quadruplex structure formed by GGGGCC repeats. Together, these data demonstrate that Zfp106 suppresses the formation of RNA foci and DPRs caused by GGGGCC repeats and suggest that the G-quadruplex RNA-binding function of Zfp106 contributes to its suppression of GGGGCC repeat-mediated cytotoxicity.
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Affiliation(s)
- Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
| | - Sally E. Salomonsson
- Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Memory & Aging Center, Department of Neurology, University of California, San Francisco, CA94143
| | - Haifan Wu
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bobo Dang
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Huong T. Kratochvil
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Claire D. Clelland
- Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Memory & Aging Center, Department of Neurology, University of California, San Francisco, CA94143
| | - William F. DeGrado
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
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3
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Cheng R, Zheng X, Wang Y, Ma X, Liu X, Xu W, Wang M, Gao Y, Xing X, Zhou C, Sun H, Guo Z, Quan F, Liu J, Hua S, Wang Y, Zhang Y, Liu X. Modification of alternative splicing in bovine somatic cell nuclear transfer embryos using engineered CRISPR-Cas13d. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2257-2268. [PMID: 35524909 DOI: 10.1007/s11427-021-2060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Animal cloning can be achieved by somatic cell nuclear transfer (SCNT), but the resulting live birth rate is relatively low. We previously improved the efficiency of bovine SCNT by exogenous melatonin treatment or by overexpression of lysine-specific demethylase 4D (KDM4D) and 4E (KDM4E). In this study, we revealed abundant alternative splicing (AS) transitions during fertilization and embryonic genome activation, and demonstrated abnormal AS in bovine SCNT embryos compared with in vitro fertilized embryos. We used the CRISPR-Cas13d RNA-targeting system to target cis-elements of ABI2 and ZNF106 pre-mRNA to modify AS, thus reducing the ratio of abnormal-isoform SCNT embryos by nearly 50% and achieving a high survival rate (11%-19%). These results indicate that this system may provide an efficient method for bovine cloning, while also paving the way for further improvements in the efficiency of SCNT.
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Affiliation(s)
- Rui Cheng
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xiaoman Zheng
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Yingmei Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xing Ma
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xin Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Wenjun Xu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Mengyun Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Yuanpeng Gao
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xupeng Xing
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Chuan Zhou
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Hongzheng Sun
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Fusheng Quan
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Jun Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Song Hua
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Xu Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
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4
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The putative role of zinc homeostasis in grain formation by Madurella mycetomatis during mycetoma infection. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Korn SM, Schlundt A. Structures and nucleic acid-binding preferences of the eukaryotic ARID domain. Biol Chem 2022; 403:731-747. [PMID: 35119801 DOI: 10.1515/hsz-2021-0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022]
Abstract
The DNA-binding AT-rich interactive domain (ARID) exists in a wide range of proteins throughout eukaryotic kingdoms. ARID domain-containing proteins are involved in manifold biological processes, such as transcriptional regulation, cell cycle control and chromatin remodeling. Their individual domain composition allows for a sub-classification within higher mammals. ARID is categorized as binder of double-stranded AT-rich DNA, while recent work has suggested ARIDs as capable of binding other DNA motifs and also recognizing RNA. Despite a broad variability on the primary sequence level, ARIDs show a highly conserved fold, which consists of six α-helices and two loop regions. Interestingly, this minimal core domain is often found extended by helices at the N- and/or C-terminus with potential roles in target specificity and, subsequently function. While high-resolution structural information from various types of ARIDs has accumulated over two decades now, there is limited access to ARID-DNA complex structures. We thus find ourselves left at the beginning of understanding ARID domain target specificities and the role of accompanying domains. Here, we systematically summarize ARID domain conservation and compare the various types with a focus on their structural differences and DNA-binding preferences, including the context of multiple other motifs within ARID domain containing proteins.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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6
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Scoville DW, Kang HS, Jetten AM. Transcription factor GLIS3: Critical roles in thyroid hormone biosynthesis, hypothyroidism, pancreatic beta cells and diabetes. Pharmacol Ther 2020; 215:107632. [PMID: 32693112 PMCID: PMC7606550 DOI: 10.1016/j.pharmthera.2020.107632] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/15/2020] [Indexed: 12/16/2022]
Abstract
GLI-Similar 3 (GLIS3) is a member of the GLIS subfamily of Krüppel-like zinc finger transcription factors that functions as an activator or repressor of gene expression. Study of GLIS3-deficiency in mice and humans revealed that GLIS3 plays a critical role in the regulation of several biological processes and is implicated in the development of various diseases, including hypothyroidism and diabetes. This was supported by genome-wide association studies that identified significant associations of common variants in GLIS3 with increased risk of these pathologies. To obtain insights into the causal mechanisms underlying these diseases, it is imperative to understand the mechanisms by which this protein regulates the development of these pathologies. Recent studies of genes regulated by GLIS3 led to the identification of a number of target genes and have provided important molecular insights by which GLIS3 controls cellular processes. These studies revealed that GLIS3 is essential for thyroid hormone biosynthesis and identified a critical function for GLIS3 in the generation of pancreatic β cells and insulin gene transcription. These observations raised the possibility that the GLIS3 signaling pathway might provide a potential therapeutic target in the management of diabetes, hypothyroidism, and other diseases. To develop such strategies, it will be critical to understand the upstream signaling pathways that regulate the activity, expression and function of GLIS3. Here, we review the recent progress on the molecular mechanisms by which GLIS3 controls key functions in thyroid follicular and pancreatic β cells and how this causally relates to the development of hypothyroidism and diabetes.
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Affiliation(s)
- David W Scoville
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hong Soon Kang
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Anton M Jetten
- Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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7
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Ahmed JN, Diamand KEM, Bellchambers HM, Arkell RM. Systematized reporter assays reveal ZIC protein regulatory abilities are Subclass-specific and dependent upon transcription factor binding site context. Sci Rep 2020; 10:13130. [PMID: 32753700 PMCID: PMC7403390 DOI: 10.1038/s41598-020-69917-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
The ZIC proteins are a family of transcription regulators with a well-defined zinc finger DNA-binding domain and there is evidence that they elicit functional DNA binding at a ZIC DNA binding site. Little is known, however, regarding domains within ZIC proteins that confer trans-activation or -repression. To address this question, a new cell-based trans-activation assay system suitable for ZIC proteins in HEK293T cells was constructed. This identified two previously unannotated evolutionarily conserved regions of ZIC3 that are necessary for trans-activation. These domains are found in all Subclass A ZIC proteins, but not in the Subclass B proteins. Additionally, the Subclass B proteins fail to elicit functional binding at a multimerised ZIC DNA binding site. All ZIC proteins, however, exhibit functional binding when the ZIC DNA binding site is embedded in a multiple transcription factor locus derived from ZIC target genes in the mouse genome. This ability is due to several domains, some of which are found in all ZIC proteins, that exhibit context dependent trans-activation or -repression activity. This knowledge is valuable for assessing the likely pathogenicity of variant ZIC proteins associated with human disorders and for determining factors that influence functional transcription factor binding.
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Affiliation(s)
- Jehangir N Ahmed
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Koula E M Diamand
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Helen M Bellchambers
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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8
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Yasuoka Y, Matsumoto M, Yagi K, Okazaki Y. Evolutionary History of GLIS Genes Illuminates Their Roles in Cell Reprograming and Ciliogenesis. Mol Biol Evol 2020; 37:100-109. [PMID: 31504761 PMCID: PMC6984359 DOI: 10.1093/molbev/msz205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The GLIS family transcription factors, GLIS1 and GLIS3, potentiate generation of induced pluripotent stem cells (iPSCs). In contrast, another GLIS family member, GLIS2, suppresses cell reprograming. To understand how these disparate roles arose, we examined evolutionary origins and genomic organization of GLIS genes. Comprehensive phylogenetic analysis shows that GLIS1 and GLIS3 originated during vertebrate whole genome duplication, whereas GLIS2 is a sister group to the GLIS1/3 and GLI families. This result is consistent with their opposing functions in cell reprograming. Glis1 evolved faster than Glis3, losing many protein-interacting motifs. This suggests that Glis1 acquired new functions under weakened evolutionary constraints. In fact, GLIS1 induces induced pluripotent stem cells more strongly. Transcriptomic data from various animal embryos demonstrate that glis1 is maternally expressed in some tetrapods, whereas vertebrate glis3 and invertebrate glis1/3 genes are rarely expressed in oocytes, suggesting that vertebrate (or tetrapod) Glis1 acquired a new expression domain and function as a maternal factor. Furthermore, comparative genomic analysis reveals that glis1/3 is part of a bilaterian-specific gene cluster, together with rfx3, ndc1, hspb11, and lrrc42. Because known functions of these genes are related to cilia formation and function, the last common ancestor of bilaterians may have acquired this cluster by shuffling gene order to establish more sophisticated epithelial tissues involving cilia. This evolutionary study highlights the significance of GLIS1/3 for cell reprograming, development, and diseases in ciliated organs such as lung, kidney, and pancreas.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahito Matsumoto
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Advanced Diabetic Therapeutics, Department of Metabolic Endocrinology, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Yagi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
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9
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Palencia-Campos A, Martínez-Fernández ML, Altunoglu U, Soto-Bielicka P, Torres A, Marín P, Aller E, Şentürk L, Berköz Ö, Yıldıran M, Kayserili H, Gil-Camarero E, Colli-Lista G, Sanchís-Calvo A, Carretero A, Guillén-Navarro E, López-González V, Ballesta-Martínez M, Rosell J, Aglan MS, Temtamy S, Otaify GA, Cuevas-Catalina L, Torres-Saavedra MN, Nevado J, Tenorio J, Lapunzina P, Bermejo-Sánchez E, Ruiz-Pérez VL. Heterozygous pathogenic variants in GLI1 are a common finding in isolated postaxial polydactyly A/B. Hum Mutat 2019; 41:265-276. [PMID: 31549748 DOI: 10.1002/humu.23921] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/24/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Postaxial polydactyly (PAP) is a frequent limb malformation consisting in the duplication of the fifth digit of the hand or foot. Morphologically, this condition is divided into type A and B, with PAP-B corresponding to a more rudimentary extra-digit. Recently, biallelic truncating variants in the transcription factor GLI1 were reported to be associated with a recessive disorder, which in addition to PAP-A, may include syndromic features. Moreover, two heterozygous subjects carrying only one inactive copy of GLI1 were also identified with PAP. Herein, we aimed to determine the level of involvement of GLI1 in isolated PAP, a condition previously established to be autosomal dominantly inherited with incomplete penetrance. We analyzed the coding region of GLI1 in 95 independent probands with nonsyndromic PAP and found 11.57% of these subjects with single heterozygous pathogenic variants in this gene. The detected variants lead to premature termination codons or result in amino acid changes in the DNA-binding domain of GLI1 that diminish its transactivation activity. Family segregation analysis of these variants was consistent with dominant inheritance with incomplete penetrance. We conclude that heterozygous changes in GLI1 underlie a significant proportion of sporadic or familial cases of isolated PAP-A/B.
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Affiliation(s)
- Adrián Palencia-Campos
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain
| | - María-Luisa Martínez-Fernández
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies, Institute of Health Carlos III, Madrid, Spain
| | - Umut Altunoglu
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | - Antonio Torres
- Paediatric Unit, Hospital San Juan de La Cruz, Úbeda, Spain
| | - Purificación Marín
- Dysmorphology and Neonatology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Elena Aller
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Genetic Unit, Hospital La Fe, Valencia, Spain
| | - Leyli Şentürk
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Ömer Berköz
- Department of Reconstructive and aesthetic Surgery, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Mehmet Yıldıran
- Department of Reconstructive and aesthetic Surgery, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Hülya Kayserili
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Medical Genetics Department, Koç University School of Medicine, Istanbul, Turkey
| | | | | | | | - Alba Carretero
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain
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- Paediatric Units from different hospitals, all part of ECEMC (Spanish Collaborative Study of Congenital Malformations) Clinical Network, Spain
| | - Encarna Guillén-Navarro
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Genetic Medicine Unit, Paediatric Unit, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain
| | - Vanesa López-González
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Genetic Medicine Unit, Paediatric Unit, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain
| | - María Ballesta-Martínez
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Genetic Medicine Unit, Paediatric Unit, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain
| | - Jordi Rosell
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Genetic Unit, Hospital Son Espases, Palma de Mallorca, Spain
| | - Mona S Aglan
- Department of Clinical Genetics, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Samia Temtamy
- Department of Clinical Genetics, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Ghada A Otaify
- Department of Clinical Genetics, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Lourdes Cuevas-Catalina
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies, Institute of Health Carlos III, Madrid, Spain
| | - María-Nieves Torres-Saavedra
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies, Institute of Health Carlos III, Madrid, Spain.,CS Federica Montseny, Unidad Asistencial Sureste, Madrid, Spain
| | - Julian Nevado
- Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Jair Tenorio
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Pablo Lapunzina
- CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Eva Bermejo-Sánchez
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies, Institute of Health Carlos III, Madrid, Spain.,Institute of Rare Diseases Research (IIER), Institute of Health Carlos III, Madrid, Spain
| | - Víctor L Ruiz-Pérez
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain
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10
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Sun A, Li F, Liu Z, Jiang Y, Zhang J, Wu J, Shi Y. Structural and biochemical insights into human zinc finger protein AEBP2 reveals interactions with RBBP4. Protein Cell 2019; 9:738-742. [PMID: 29134516 PMCID: PMC6053351 DOI: 10.1007/s13238-017-0483-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Aiai Sun
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Zhonghua Liu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
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11
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Vicentefranqueira R, Leal F, Marín L, Sánchez CI, Calera JA. The interplay between zinc and iron homeostasis in
Aspergillus fumigatus
under zinc‐replete conditions relies on the iron‐mediated regulation of alternative transcription units of
zafA
and the basal amount of the ZafA zinc‐responsiveness transcription factor. Environ Microbiol 2019; 21:2787-2808. [DOI: 10.1111/1462-2920.14618] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Rocío Vicentefranqueira
- Instituto de Biología Funcional y Genómica (IBFG‐CSIC)Universidad de Salamanca Salamanca Spain
| | - Fernando Leal
- Instituto de Biología Funcional y Genómica (IBFG‐CSIC)Universidad de Salamanca Salamanca Spain
- Departamento de Microbiología y GenéticaUniversidad de Salamanca Salamanca Spain
| | - Laura Marín
- Instituto de Biología Funcional y Genómica (IBFG‐CSIC)Universidad de Salamanca Salamanca Spain
| | - Clara Inés Sánchez
- Instituto de Biología Funcional y Genómica (IBFG‐CSIC)Universidad de Salamanca Salamanca Spain
| | - José Antonio Calera
- Instituto de Biología Funcional y Genómica (IBFG‐CSIC)Universidad de Salamanca Salamanca Spain
- Departamento de Microbiología y GenéticaUniversidad de Salamanca Salamanca Spain
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12
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Tohmonda T, Kamiya A, Ishiguro A, Iwaki T, Fujimi TJ, Hatayama M, Aruga J. Identification and Characterization of Novel Conserved Domains in Metazoan Zic Proteins. Mol Biol Evol 2018; 35:2205-2229. [DOI: 10.1093/molbev/msy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Takahide Tohmonda
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akiko Kamiya
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akira Ishiguro
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Takashi Iwaki
- Meguro Parasitological Museum, Meguro-Ku, Tokyo, Japan
| | - Takahiko J Fujimi
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Minoru Hatayama
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
| | - Jun Aruga
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
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13
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Garcia Silva-Bailão M, Lobato Potenciano da Silva K, Raniere Borges dos Anjos L, de Sousa Lima P, de Melo Teixeira M, Maria de Almeida Soares C, Melo Bailão A. Mechanisms of copper and zinc homeostasis in pathogenic black fungi. Fungal Biol 2018; 122:526-537. [DOI: 10.1016/j.funbio.2017.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 02/08/2023]
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14
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Role of Zic Family Proteins in Transcriptional Regulation and Chromatin Remodeling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:353-380. [DOI: 10.1007/978-981-10-7311-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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15
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Link between the causative genes of holoprosencephaly: Zic2 directly regulates Tgif1 expression. Sci Rep 2018; 8:2140. [PMID: 29391420 PMCID: PMC5794963 DOI: 10.1038/s41598-018-20242-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/15/2018] [Indexed: 02/07/2023] Open
Abstract
One of the causal genes for holoprosencephaly (HPE) is ZIC2 (HPE5). It belongs to the zinc finger protein of the cerebellum (Zic) family of genes that share a C2H2-type zinc finger domain, similar to the GLI family of genes. In order to clarify the role of Zic2 in gene regulation, we searched for its direct target genes using chromatin immunoprecipitation (ChIP). We identified TGIF1 (HPE4), another holoprosencephaly-causative gene in humans. We identified Zic2-binding sites (ZBS) on the 5′ flanking region of Tgif1 by in vitro DNA binding assays. ZBS were essential for Zic2-dependent transcriptional activation in reporter gene assays. Zic2 showed a higher affinity to ZBS than GLI-binding sequences. Zic2-binding to the cis-regulatory element near the Tgif1 promoter may be involved in the mechanism underlying forebrain development and incidences of HPE.
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16
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Abstract
Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene. The Gli-Glis-Nkl-Zic superfamily and some other eukaryotic zinc finger proteins share a tandem CWCH2 (tCWCH2) motif, a hallmark for inter-zinc finger interaction between two adjacent C2H2 zinc fingers. In Zic family proteins, there exist additional evolutionally conserved domains known as ZOC and ZFNC, both of which may have appeared before cnidarian-bilaterian divergence. Comparison of the exon-intron boundaries in the Zic zinc finger domains revealed an intron (A-intron) that was absolutely conserved in bilaterians (metazoans with bilateral symmetry) and a placozoan (a simple nonparasitic metazoan). In vertebrates, there are five to seven Zic paralogs among which Zic1, Zic2, and Zic3 are generated through a tandem gene duplication and carboxy-terminal truncation in a vertebrate common ancestor, sharing a conserved carboxy-terminal sequence. Several hypotheses have been proposed to explain the Zic family phylogeny, including their origin, unique features in the first and second zinc finger motif, evolution of the nuclear localization signal, significance of the animal taxa-selective degeneration, gene multiplication in the vertebrate lineage, and involvement in the evolutionary alteration of the animal body plan.
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17
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Diamand KEM, Barratt KS, Arkell RM. Overview of Rodent Zic Genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:179-207. [PMID: 29442323 DOI: 10.1007/978-981-10-7311-3_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The five murine Zic genes encode multifunctional transcriptional regulator proteins important for a large number of processes during embryonic development. The genes and proteins are highly conserved with respect to the orthologous human genes, an attribute evidently mirrored by functional conservation, since the murine and human genes mutate to give the same phenotypes. Each ZIC protein contains a zinc finger domain that participates in both protein-DNA and protein-protein interactions. The ZIC proteins are capable of interacting with the key transcriptional mediators of the SHH, WNT and NODAL signalling pathways as well as with components of the transcriptional machinery and chromatin-modifying complexes. It is possible that this diverse range of protein partners underlies characteristics uncovered by mutagenesis and phenotyping of the murine Zic genes. These features include redundant and unique roles for ZIC proteins, regulatory interdependencies amongst family members and pleiotropic Zic gene function. Future investigations into the complex nature of the Zic gene family activity should be facilitated by recent advances in genome engineering and functional genomics.
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Affiliation(s)
- Koula E M Diamand
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kristen S Barratt
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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18
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Job G, Brugger C, Xu T, Lowe BR, Pfister Y, Qu C, Shanker S, Baños Sanz JI, Partridge JF, Schalch T. SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules. Mol Cell 2017; 62:207-221. [PMID: 27105116 DOI: 10.1016/j.molcel.2016.03.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/27/2016] [Accepted: 03/11/2016] [Indexed: 11/18/2022]
Abstract
Nucleosome remodeling and deacetylation (NuRD) complexes are co-transcriptional regulators implicated in differentiation, development, and diseases. Methyl-CpG binding domain (MBD) proteins play an essential role in recruitment of NuRD complexes to their target sites in chromatin. The related SHREC complex in fission yeast drives transcriptional gene silencing in heterochromatin through cooperation with HP1 proteins. How remodeler and histone deacetylase (HDAC) cooperate within NuRD complexes remains unresolved. We determined that in SHREC the two modules occupy distant sites on the scaffold protein Clr1 and that repressive activity of SHREC can be modulated by the expression level of the HDAC-associated Clr1 domain alone. Moreover, the crystal structure of Clr2 reveals an MBD-like domain mediating recruitment of the HDAC module to heterochromatin. Thus, SHREC bi-functionality is organized in two separate modules with separate recruitment mechanisms, which work together to elicit transcriptional silencing at heterochromatic loci.
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Affiliation(s)
- Godwin Job
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Christiane Brugger
- Department of Molecular Biology, Science III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva 4, Switzerland
| | - Tao Xu
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Brandon R Lowe
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yvan Pfister
- Department of Molecular Biology, Science III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva 4, Switzerland
| | - Chunxu Qu
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sreenath Shanker
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - José I Baños Sanz
- Department of Molecular Biology, Science III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva 4, Switzerland
| | - Janet F Partridge
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Thomas Schalch
- Department of Molecular Biology, Science III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 1211 Geneva 4, Switzerland.
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19
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Zinc sensing and regulation in yeast model systems. Arch Biochem Biophys 2016; 611:30-36. [PMID: 26940262 DOI: 10.1016/j.abb.2016.02.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/23/2022]
Abstract
The Zap1 transcription factor of Saccharomyces cerevisiae and the Loz1 transcription factor of Schizosaccharomyces pombe both play a central role in zinc homeostasis by controlling the expression of genes necessary for zinc metabolism. Zap1 activates gene expression when cells are limited for zinc, while Loz1 is required for gene repression when zinc is in excess. In this review we highlight what is known about the underlying mechanisms by which these factors are regulated by zinc, and how transcriptional activation and repression in eukaryotic cells can be finely tuned according to intracellular zinc availability.
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20
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Joyce PI, Fratta P, Landman AS, Mcgoldrick P, Wackerhage H, Groves M, Busam BS, Galino J, Corrochano S, Beskina OA, Esapa C, Ryder E, Carter S, Stewart M, Codner G, Hilton H, Teboul L, Tucker J, Lionikas A, Estabel J, Ramirez-Solis R, White JK, Brandner S, Plagnol V, Bennet DLH, Abramov AY, Greensmith L, Fisher EMC, Acevedo-Arozena A. Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration. Hum Mol Genet 2015; 25:291-307. [PMID: 26604141 PMCID: PMC4706115 DOI: 10.1093/hmg/ddv471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/11/2015] [Indexed: 12/12/2022] Open
Abstract
Zinc finger motifs are distributed amongst many eukaryotic protein families, directing nucleic acid–protein and protein–protein interactions. Zinc finger protein 106 (ZFP106) has previously been associated with roles in immune response, muscle differentiation, testes development and DNA damage, although little is known about its specific function. To further investigate the function of ZFP106, we performed an in-depth characterization of Zfp106 deficient mice (Zfp106−/−), and we report a novel role for ZFP106 in motor and sensory neuronal maintenance and survival. Zfp106−/− mice develop severe motor abnormalities, major deficits in muscle strength and histopathological changes in muscle. Intriguingly, despite being highly expressed throughout the central nervous system, Zfp106−/− mice undergo selective motor and sensory neuronal and axonal degeneration specific to the spinal cord and peripheral nervous system. Neurodegeneration does not occur during development of Zfp106−/− mice, suggesting that ZFP106 is likely required for the maintenance of mature peripheral motor and sensory neurons. Analysis of embryonic Zfp106−/− motor neurons revealed deficits in mitochondrial function, with an inhibition of Complex I within the mitochondrial electron transport chain. Our results highlight a vital role for ZFP106 in sensory and motor neuron maintenance and reveal a novel player in mitochondrial dysfunction and neurodegeneration.
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Affiliation(s)
- Peter I Joyce
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Pietro Fratta
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Philip Mcgoldrick
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Michael Groves
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Jorge Galino
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | | | - Olga A Beskina
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Edward Ryder
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sarah Carter
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Gemma Codner
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Helen Hilton
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Lydia Teboul
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Jennifer Tucker
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Jeanne Estabel
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Ramiro Ramirez-Solis
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Jacqueline K White
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Sebastian Brandner
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - David L H Bennet
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Andrey Y Abramov
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | - Linda Greensmith
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
| | - Elizabeth M C Fisher
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
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21
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Houtmeyers R, Souopgui J, Tejpar S, Arkell R. The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis. Cell Mol Life Sci 2013; 70:3791-811. [PMID: 23443491 PMCID: PMC11113920 DOI: 10.1007/s00018-013-1285-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 01/16/2013] [Accepted: 01/28/2013] [Indexed: 12/18/2022]
Abstract
The zinc finger of the cerebellum gene (ZIC) discovered in Drosophila melanogaster (odd-paired) has five homologs in Xenopus, chicken, mice, and humans, and seven in zebrafish. This pattern of gene copy expansion is accompanied by a divergence in gene and protein structure, suggesting that Zic family members share some, but not all, functions. ZIC genes are implicated in neuroectodermal development and neural crest cell induction. All share conserved regions encoding zinc finger domains, however their heterogeneity and specification remain unexplained. In this review, the evolution, structure, and expression patterns of the ZIC homologs are described; specific functions attributable to individual family members are supported. A review of data from functional studies in Xenopus and murine models suggest that ZIC genes encode multifunctional proteins operating in a context-specific manner to drive critical events during embryogenesis. The identification of ZIC mutations in congenital syndromes highlights the relevance of these genes in human development.
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Affiliation(s)
- Rob Houtmeyers
- Department of Oncology, Katholieke Universiteit Leuven, O&N1, 3000, Leuven, Belgium,
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22
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Zhao H, Wang J, Han Y, Huang Z, Ying J, Bi X, Zhao J, Fang Y, Zhou H, Zhou J, Li Z, Zhang Y, Yang X, Yan T, Wang L, Torbenson MS, Cai J. ARID2: a new tumor suppressor gene in hepatocellular carcinoma. Oncotarget 2012; 2:886-91. [PMID: 22095441 PMCID: PMC3259997 DOI: 10.18632/oncotarget.355] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, however, genetic-environmental interactions and mechanisms associated with the development of HCC remains largely unclear. Our recent work described novel inactivating mutations of ARID2 (AT-rich interactive domain 2) in four major subtypes of HCC through exomic sequencing of ten HCV-associated HCCs and subsequent evaluation of the tumors from additional affected individuals. Here, we summarize the current knowledge about the relevance of ARID2 in HCC and the implication in future patient care.
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Affiliation(s)
- Hong Zhao
- Department of abdominal surgical oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, PR China
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23
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Abstract
Drosophila cubitus interruptus (Ci) and its vertebrate homologues, the glioblastoma (Gli) protein family, are the transcription factors belonging to the metazoan Gli/Glis/Zic ZF protein superfamily that shares similar five tandemly repeated C2H2-type zinc finger (ZF) motifs. Nuclear transport of Gli/Ci proteins is regulated by hedgehog (Hh) signaling and is an essential part of the Hh signal transduction pathway. Gli/Ci proteins possess a nuclear localization signal (NLS) and a nuclear export signal (NES), both of which are key signatures for controlling nucleocytoplasmic shuttling. The NLS of the Gli/Ci proteins has been mapped to the fifth ZF domain and its C-terminal side. It contains two clusters of basic residues (classical bipartite-type), which are conserved in metazoan Gli/Ci homologues, but which partially deviate from the intra-ZF domain NLSs in the Glis and Zic proteins. Recently, Importin α3 was identified as a nuclear transport protein for Ci. When we modeled the 3D structure of the Gli NLS-Importin α complex, the two basic clusters were predicted to fit in the two binding interfaces of Importin α. The mechanisms controlling the function of NLSs and NESs involve the elimination of the NES by Hh signaling-dependent protein cleavage in the Ci and the Gli3 proteins, and the phosphorylation of a threonine residue close to the NLS in Gli1. Both processes depend on the activity of protein kinase A, which has a critical role in Hh signaling in fly wing discs. In addition, the Roadkill protein, a substrate recognition component of E3 ubiquitin ligase, competes with the Ci protein to interact with Importin α3 resulting in inhibition of Ci protein nuclear import.
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Affiliation(s)
- Minoru Hatayama
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
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24
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Abstract
The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.
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Affiliation(s)
- B Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 45 Center Drive, Bethesda, MD 20892
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