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Grochowska KM, Gomes GM, Raman R, Kaushik R, Sosulina L, Kaneko H, Oelschlegel AM, Yuanxiang P, Reyes‐Resina I, Bayraktar G, Samer S, Spilker C, Woo MS, Morawski M, Goldschmidt J, Friese MA, Rossner S, Navarro G, Remy S, Reissner C, Karpova A, Kreutz MR. Jacob-induced transcriptional inactivation of CREB promotes Aβ-induced synapse loss in Alzheimer's disease. EMBO J 2023; 42:e112453. [PMID: 36594364 PMCID: PMC9929644 DOI: 10.15252/embj.2022112453] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023] Open
Abstract
Synaptic dysfunction caused by soluble β-amyloid peptide (Aβ) is a hallmark of early-stage Alzheimer's disease (AD), and is tightly linked to cognitive decline. By yet unknown mechanisms, Aβ suppresses the transcriptional activity of cAMP-responsive element-binding protein (CREB), a master regulator of cell survival and plasticity-related gene expression. Here, we report that Aβ elicits nucleocytoplasmic trafficking of Jacob, a protein that connects a NMDA-receptor-derived signalosome to CREB, in AD patient brains and mouse hippocampal neurons. Aβ-regulated trafficking of Jacob induces transcriptional inactivation of CREB leading to impairment and loss of synapses in mouse models of AD. The small chemical compound Nitarsone selectively hinders the assembly of a Jacob/LIM-only 4 (LMO4)/ Protein phosphatase 1 (PP1) signalosome and thereby restores CREB transcriptional activity. Nitarsone prevents impairment of synaptic plasticity as well as cognitive decline in mouse models of AD. Collectively, the data suggest targeting Jacob protein-induced CREB shutoff as a therapeutic avenue against early synaptic dysfunction in AD.
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Affiliation(s)
- Katarzyna M Grochowska
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Leibniz Group ‘Dendritic Organelles and Synaptic Function’, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Guilherme M Gomes
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
| | - Rajeev Raman
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Rahul Kaushik
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Liudmila Sosulina
- Department of Cellular NeuroscienceLeibniz Institute for NeurobiologyMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
| | - Hiroshi Kaneko
- Department of Cellular NeuroscienceLeibniz Institute for NeurobiologyMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
| | | | - PingAn Yuanxiang
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | | | - Gonca Bayraktar
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Sebastian Samer
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Christina Spilker
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Marcel S Woo
- Institute of Neuroimmunology and Multiple Sclerosis, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Markus Morawski
- Molecular Imaging in NeurosciencesPaul Flechsig Institute of Brain ResearchLeipzigGermany
| | - Jürgen Goldschmidt
- Department of Systems Physiology of Learning and MemoryLeibniz Institute for NeurobiologyMagdeburgGermany
| | - Manuel A Friese
- Institute of Neuroimmunology and Multiple Sclerosis, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Steffen Rossner
- Molecular Imaging in NeurosciencesPaul Flechsig Institute of Brain ResearchLeipzigGermany
| | - Gemma Navarro
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food ScienceUniversity of BarcelonaBarcelonaSpain
- Institut de Neurociències de la Universitat de BarcelonaBarcelonaSpain
| | - Stefan Remy
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
- Department of Cellular NeuroscienceLeibniz Institute for NeurobiologyMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
| | - Carsten Reissner
- Institute of Anatomy and Molecular NeurobiologyWestfälische Wilhelms‐UniversityMünsterGermany
| | - Anna Karpova
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
| | - Michael R Kreutz
- RG NeuroplasticityLeibniz Institute for NeurobiologyMagdeburgGermany
- Leibniz Group ‘Dendritic Organelles and Synaptic Function’, Center for Molecular Neurobiology (ZMNH)University Medical Center Hamburg‐EppendorfHamburgGermany
- Center for Behavioral Brain SciencesOtto von Guericke UniversityMagdeburgGermany
- German Center for Neurodegenerative Diseases (DZNE)MagdeburgGermany
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Wu L, Huang J, Trivedi P, Sun X, Yu H, He Z, Zhang X. Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis. Discov Oncol 2022; 13:139. [PMID: 36520265 PMCID: PMC9755447 DOI: 10.1007/s12672-022-00597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Morphogenesis and organogenesis in the low organisms have been found to be modulated by a number of proteins, and one of such factor, deformed epidermal auto-regulatory factor-1 (DEAF-1) has been initially identified in Drosophila. The mammalian homologue of DEAF-1 and structurally related proteins have been identified, and they formed a family with over 20 members. The factors regulate gene expression through association with co-repressors, recognition of genomic marker, to exert histone modification by catalyze addition of some chemical groups to certain amino acid residues on histone and non-histone proteins, and degradation host proteins, so as to regulate cell cycle progression and execution of cell death. The formation of fused genes during chromosomal translocation, exemplified with myeloid transforming gene on chromosome 8 (MTG8)/eight-to-twenty one translocation (ETO) /ZMYND2, MTG receptor 1 (MTGR1)/ZMYND3, MTG on chromosome 16/MTGR2/ZMYND4 and BS69/ZMYND11 contributes to malignant transformation. Other anomaly like copy number variation (CNV) of BS69/ZMYND11 and promoter hyper methylation of BLU/ZMYND10 has been noted in malignancies. It has been reported that when fusing with Runt-related transcription factor 1 (RUNX1), the binding of MTG8/ZMYND2 with co-repressors is disturbed, and silencing of BLU/ZMYND10 abrogates its ability to inhibition of cell cycle and promotion of apoptotic death. Further characterization of the implication of ZMYND proteins in carcinogenesis would enhance understanding of the mechanisms of occurrence and early diagnosis of tumors, and effective antitumor efficacy.
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Affiliation(s)
- Longji Wu
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
- Institute of Modern Biology, Nanjing University, Nanjing, Jiangsu, China
| | - Jing Huang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Pankaj Trivedi
- Department of Experimental Medicine, La Sapienza University, Rome, Italy
| | - Xuerong Sun
- Institute of Aging, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Hongbing Yu
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Zhiwei He
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Xiangning Zhang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China.
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China.
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hSSB2 (NABP1) is required for the recruitment of RPA during the cellular response to DNA UV damage. Sci Rep 2021; 11:20256. [PMID: 34642383 PMCID: PMC8511049 DOI: 10.1038/s41598-021-99355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
Maintenance of genomic stability is critical to prevent diseases such as cancer. As such, eukaryotic cells have multiple pathways to efficiently detect, signal and repair DNA damage. One common form of exogenous DNA damage comes from ultraviolet B (UVB) radiation. UVB generates cyclobutane pyrimidine dimers (CPD) that must be rapidly detected and repaired to maintain the genetic code. The nucleotide excision repair (NER) pathway is the main repair system for this type of DNA damage. Here, we determined the role of the human Single-Stranded DNA Binding protein 2, hSSB2, in the response to UVB exposure. We demonstrate that hSSB2 levels increase in vitro and in vivo after UVB irradiation and that hSSB2 rapidly binds to chromatin. Depletion of hSSB2 results in significantly decreased Replication Protein A (RPA32) phosphorylation and impaired RPA32 localisation to the site of UV-induced DNA damage. Delayed recruitment of NER protein Xeroderma Pigmentosum group C (XPC) was also observed, leading to increased cellular sensitivity to UVB. Finally, hSSB2 was shown to have affinity for single-strand DNA containing a single CPD and for duplex DNA with a two-base mismatch mimicking a CPD moiety. Altogether our data demonstrate that hSSB2 is involved in the cellular response to UV exposure.
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Shamilov R, Robinson VL, Aneskievich BJ. Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder. Int J Mol Sci 2021; 22:ijms22157912. [PMID: 34360678 PMCID: PMC8348711 DOI: 10.3390/ijms22157912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Epidermal keratinocyte proteins include many with an eccentric amino acid content (compositional bias), atypical ultrastructural fate (built-in protease sensitivity), or assembly visible at the light microscope level (cytoplasmic granules). However, when considered through the looking glass of intrinsic disorder (ID), these apparent oddities seem quite expected. Keratinocyte proteins with highly repetitive motifs are of low complexity but high adaptation, providing polymers (e.g., profilaggrin) for proteolysis into bioactive derivatives, or monomers (e.g., loricrin) repeatedly cross-linked to self and other proteins to shield underlying tissue. Keratohyalin granules developing from liquid–liquid phase separation (LLPS) show that unique biomolecular condensates (BMC) and proteinaceous membraneless organelles (PMLO) occur in these highly customized cells. We conducted bioinformatic and in silico assessments of representative keratinocyte differentiation-dependent proteins. This was conducted in the context of them having demonstrated potential ID with the prospect of that characteristic driving formation of distinctive keratinocyte structures. Intriguingly, while ID is characteristic of many of these proteins, it does not appear to guarantee LLPS, nor is it required for incorporation into certain keratinocyte protein condensates. Further examination of keratinocyte-specific proteins will provide variations in the theme of PMLO, possibly recognizing new BMC for advancements in understanding intrinsically disordered proteins as reflected by keratinocyte biology.
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Affiliation(s)
- Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA;
| | - Victoria L. Robinson
- Department of Molecular and Cellular Biology, College of Liberal Arts & Sciences, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269, USA;
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
- Correspondence: ; Tel.: +1-860-486-3053
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Structural and Functional Characterization of Host FHL1 Protein Interaction with Hypervariable Domain of Chikungunya Virus nsP3 Protein. J Virol 2020; 95:JVI.01672-20. [PMID: 33055253 DOI: 10.1128/jvi.01672-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/10/2020] [Indexed: 11/20/2022] Open
Abstract
Decades of insufficient control have resulted in unprecedented spread of chikungunya virus (CHIKV) around the globe, and millions have suffered from the highly debilitating disease. Nevertheless, the current understanding of CHIKV-host interactions and adaptability of the virus to replication in mosquitoes and mammalian hosts is still elusive. Our new study shows that four-and-a-half LIM domain protein (FHL1) is one of the host factors that interact with the hypervariable domain (HVD) of CHIKV nsP3. Unlike G3BPs, FHL1 is not a prerequisite of CHIKV replication, and many commonly used cell lines do not express FHL1. However, its expression has a detectable stimulatory effect(s) on CHIKV replication, and Fhl1 knockout (KO) cell lines demonstrate slower infection spread. Nuclear magnetic resonance (NMR)-based studies revealed that the binding site of FHL1 in CHIKV nsP3 HVD overlaps that of another proviral host factor, CD2AP. The structural data also demonstrated that FHL1-HVD interaction is mostly determined by the LIM1 domain of FHL1. However, it does not mirror binding of the entire protein, suggesting that other LIM domains are involved. In agreement with previously published data, our biological experiments showed that interactions of CHIKV HVD with CD2AP and FHL1 have additive effects on the efficiency of CHIKV replication. This study shows that CHIKV mutants with extensive modifications of FHL1- or both FHL1- and CD2AP-binding sites remain viable and develop spreading infection in multiple cell types. Our study also demonstrated that other members of the FHL family can bind to CHIKV HVD and thus may be involved in viral replication.IMPORTANCE Replication of chikungunya virus (CHIKV) is determined by a wide range of host factors. Previously, we have demonstrated that the hypervariable domain (HVD) of CHIKV nsP3 contains linear motifs that recruit defined families of host proteins into formation of functional viral replication complexes. Now, using NMR-based structural and biological approaches, we have characterized the binding site of the cellular FHL1 protein in CHIKV HVD and defined the biological significance of this interaction. In contrast to previously described binding of G3BP to CHIKV HVD, the FHL1-HVD interaction was found to not be a prerequisite of viral replication. However, the presence of FHL1 has a stimulatory effect on CHIKV infectivity and, subsequently, the infection spread. FHL1 and CD2AP proteins were found to have overlapping binding sites in CHIKV HVD and additive proviral functions. Elimination of the FHL1-binding site in the nsP3 HVD can be used for the development of stable, attenuated vaccine candidates.
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6
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The Transcription Factor Deaf1 Modulates Engrailed-1 Expression to Regulate Skin Appendage Fate. J Invest Dermatol 2019; 139:2378-2381.e4. [PMID: 31145909 DOI: 10.1016/j.jid.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/29/2019] [Accepted: 05/10/2019] [Indexed: 12/23/2022]
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Bhati M, Llamosas E, Jacques DA, Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM. Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans. Sci Rep 2017; 7:4579. [PMID: 28676648 PMCID: PMC5496915 DOI: 10.1038/s41598-017-04587-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional ‘LIM code’ that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species.
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Affiliation(s)
- Mugdha Bhati
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Teva Pharmaceuticals Australia Pty Ltd, Macquarie Park, NSW, 2113, Australia
| | - Estelle Llamosas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,School of Women's and Children's Health, University of New South Wales, NSW, Australia
| | - David A Jacques
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,iThree Institute, University of Technology, NSW, 2007, Australia
| | - Cy M Jeffries
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center and School of Pharmacy, Tabritz Univeristy of Medical Science, Tabritz, Iran
| | - Nina Ripin
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Department of Biology, ETH, Zurich, 8093, Switzerland
| | - Hannah R Nicholas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
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8
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Robertson NO, Shah M, Matthews JM. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Neil O. Robertson
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | - Manan Shah
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
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9
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Robertson NO, Shah M, Matthews JM. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions. Angew Chem Int Ed Engl 2016; 55:13236-13239. [DOI: 10.1002/anie.201605964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Neil O. Robertson
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | - Manan Shah
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
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hSSB1 (NABP2/OBFC2B) is regulated by oxidative stress. Sci Rep 2016; 6:27446. [PMID: 27273218 PMCID: PMC4897654 DOI: 10.1038/srep27446] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/18/2016] [Indexed: 12/17/2022] Open
Abstract
The maintenance of genome stability is an essential cellular process to prevent the development of diseases including cancer. hSSB1 (NABP2/ OBFC2A) is a critical component of the DNA damage response where it participates in the repair of double-strand DNA breaks and in base excision repair of oxidized guanine residues (8-oxoguanine) by aiding the localization of the human 8-oxoguanine glycosylase (hOGG1) to damaged DNA. Here we demonstrate that following oxidative stress, hSSB1 is stabilized as an oligomer which is required for hSSB1 to function in the removal of 8-oxoguanine. Monomeric hSSB1 shows a decreased affinity for oxidized DNA resulting in a cellular 8-oxoguanine-repair defect and in the absence of ATM signaling initiation. While hSSB1 oligomerization is important for the removal of 8-oxoguanine from the genome, it is not required for the repair of double-strand DNA-breaks by homologous recombination. These findings demonstrate a novel hSSB1 regulatory mechanism for the repair of damaged DNA.
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Jensik PJ, Vargas JD, Reardon SN, Rajamanickam S, Huggenvik JI, Collard MW. DEAF1 binds unmethylated and variably spaced CpG dinucleotide motifs. PLoS One 2014; 9:e115908. [PMID: 25531106 PMCID: PMC4274154 DOI: 10.1371/journal.pone.0115908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 11/19/2022] Open
Abstract
DEAF1 is a transcriptional regulator associated with autoimmune and neurological disorders and is known to bind TTCG motifs. To further ascertain preferred DEAF1 DNA ligands, we screened a random oligonucleotide library containing an "anchored" CpG motif. We identified a binding consensus that generally conformed to a repeated TTCGGG motif, with the two invariant CpG dinucleotides separated by 6-11 nucleotides. Alteration of the consensus surrounding the dual CpG dinucleotides, or cytosine methylation of a single CpG half-site, eliminated DEAF1 binding. A sequence within the Htr1a promoter that resembles the binding consensus but contains a single CpG motif was confirmed to have low affinity binding with DEAF1. A DEAF1 binding consensus was identified in the EIF4G3 promoter and ChIP assay showed endogenous DEAF1 was bound to the region. We conclude that DEAF1 preferentially binds variably spaced and unmethylated CpG-containing half-sites when they occur within an appropriate consensus.
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Affiliation(s)
- Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
- * E-mail:
| | - Jesse D. Vargas
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Sara N. Reardon
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Jodi I. Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Michael W. Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
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