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Alavanda C, Demir Ş, Güven S, Eltan M, Eltan SB, Sefer AP, Pul S, Güran T, Alpay H, Arman A, Ata P, Turan S. Expanding the Clinical Features of Schimke Immuno-osseous Dysplasia: a New Patient with a Novel Variant and Novel Clinical Findings. J Clin Res Pediatr Endocrinol 2025; 17:126-135. [PMID: 39113392 PMCID: PMC12118321 DOI: 10.4274/jcrpe.galenos.2024.2024-1-17] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/25/2024] [Indexed: 05/29/2025] Open
Abstract
Schimke immuno-osseous dysplasia (SIOD) (MIM:242900) is an ultra-rare, autosomal recessive, pan-ethnic pleiotropic disease. Typical findings of this syndrome are steroid-resistant nephrotic syndrome, cellular immunodeficiency, spondyloepiphyseal dysplasia (SED) and facial dysmorphism. Biallelic variants in the SMARCAL1 gene cause SIOD. The five-and-a-half-year-old female patient was evaluated because of short stature, dysmorphism, hypercalcemia, hypophosphatemia, and elevated follicle-stimulating hormone (FSH) levels. Karyotype analysis and array-CGH testing were normal. Clinical exome sequencing (CES) was performed to analyze genes associated with hypophosphatemia. No pathogenic variant was detected. The subsequent detection of proteinuria during follow-up for cross-fused ectopic left kidney ultimately facilitated the diagnosis of SIOD, although no obvious SED was detected. Re-analysis of CES revealed a novel homozygous c.2422_2427+9delinsA pathogenic variant in the SMARCAL1. The literature on SMARCAL1 gene pathogenic variants, including 125 SIOD cases from 38 articles was reviewed to investigate whether hypercalcemia, hypophosphatemia, and elevated FSH levels had been previously reported in SIOD patients. This review revealed that this was the first report of these findings in a patient with SIOD. Thus, this report expands both the phenotypic and genotypic spectrum of SIOD.
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Affiliation(s)
- Ceren Alavanda
- University of Health Sciences Türkiye, Van Training and Research Hospital, Clinic of Medical Genetics, Van, Türkiye
- Marmara University Faculty of Medicine, Department of Medical Genetics, İstanbul, Türkiye
| | - Şenol Demir
- Marmara University Faculty of Medicine, Department of Medical Genetics, İstanbul, Türkiye
| | - Serçin Güven
- Marmara University Faculty of Medicine, Department of Pediatric Nephrology, İstanbul, Türkiye
| | - Mehmet Eltan
- Marmara University Faculty of Medicine, Department of Pediatric Endocrinology, İstanbul, Türkiye
| | - Sevgi Bilgiç Eltan
- Marmara University Faculty of Medicine, Department of Pediatric Allergy and Immunology, İstanbul, Türkiye
| | - Asena Pınar Sefer
- Marmara University Faculty of Medicine, Department of Pediatric Allergy and Immunology, İstanbul, Türkiye
| | - Serim Pul
- Marmara University Faculty of Medicine, Department of Pediatric Nephrology, İstanbul, Türkiye
| | - Tülay Güran
- Marmara University Faculty of Medicine, Department of Pediatric Endocrinology, İstanbul, Türkiye
| | - Harika Alpay
- Marmara University Faculty of Medicine, Department of Pediatric Nephrology, İstanbul, Türkiye
| | - Ahmet Arman
- Marmara University Faculty of Medicine, Department of Medical Genetics, İstanbul, Türkiye
| | - Pınar Ata
- Marmara University Faculty of Medicine, Department of Medical Genetics, İstanbul, Türkiye
| | - Serap Turan
- Marmara University Faculty of Medicine, Department of Pediatric Endocrinology, İstanbul, Türkiye
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2
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Sun BB, Wang GZ, Han SC, Yang FY, Guo H, Liu J, Liu YT, Zhou GB. Oncogenic functions and therapeutic potentials of targeted inhibition of SMARCAL1 in small cell lung cancer. Cancer Lett 2024; 592:216929. [PMID: 38697461 DOI: 10.1016/j.canlet.2024.216929] [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: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
Small cell lung cancer (SCLC) is a recalcitrant cancer characterized by high frequency loss-of-function mutations in tumor suppressors with a lack of targeted therapy due to absence of high frequency gain-of-function abnormalities in oncogenes. SMARCAL1 is a member of the ATP-dependent chromatin remodeling protein SNF2 family that plays critical roles in DNA damage repair and genome stability maintenance. Here, we showed that SMARCAL1 was overexpressed in SCLC patient samples and was inversely associated with overall survival of the patients. SMARCAL1 was required for SCLC cell proliferation and genome integrity. Mass spectrometry revealed that PAR6B was a downstream SMARCAL1 signal molecule which rescued inhibitory effects caused by silencing of SMARCAL1. By screening of 36 FDA-approved clinically available agents related to DNA damage repair, we found that an aza-anthracenedione, pixantrone, was a potent SMARCAL1 inhibitor which suppressed the expression of SMARCAL1 and PAR6B at protein level. Pixantrone caused DNA damage and exhibited inhibitory effects on SCLC cells in vitro and in a patient-derived xenograft mouse model. These results indicated that SMARCAL1 functions as an oncogene in SCLC, and pixantrone as a SMARCAL1 inhibitor bears therapeutic potentials in this deadly disease.
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Affiliation(s)
- Bei-Bei Sun
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Gui-Zhen Wang
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Si-Chong Han
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fu-Ying Yang
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hua Guo
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yu-Tao Liu
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Guang-Biao Zhou
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Nagai TH, Hartigan C, Mizoguchi T, Yu H, Deik A, Bullock K, Wang Y, Cromley D, Schenone M, Cowan CA, Rader DJ, Clish CB, Carr SA, Xu YX. Chromatin regulator SMARCAL1 modulates cellular lipid metabolism. Commun Biol 2023; 6:1298. [PMID: 38129665 PMCID: PMC10739977 DOI: 10.1038/s42003-023-05665-6] [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: 05/25/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Biallelic mutations of the chromatin regulator SMARCAL1 cause Schimke Immunoosseous Dysplasia (SIOD), characterized by severe growth defects and premature mortality. Atherosclerosis and hyperlipidemia are common among SIOD patients, yet their onset and progression are poorly understood. Using an integrative approach involving proteomics, mouse models, and population genetics, we investigated SMARCAL1's role. We found that SmarcAL1 interacts with angiopoietin-like 3 (Angptl3), a key regulator of lipoprotein metabolism. In vitro and in vivo analyses demonstrate SmarcAL1's vital role in maintaining cellular lipid homeostasis. The observed translocation of SmarcAL1 to cytoplasmic peroxisomes suggests a potential regulatory role in lipid metabolism through gene expression. SmarcAL1 gene inactivation reduces the expression of key genes in cellular lipid catabolism. Population genetics investigations highlight significant associations between SMARCAL1 genetic variations and body mass index, along with lipid-related traits. This study underscores SMARCAL1's pivotal role in cellular lipid metabolism, likely contributing to the observed lipid phenotypes in SIOD patients.
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Affiliation(s)
- Taylor Hanta Nagai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | | | - Taiji Mizoguchi
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Haojie Yu
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Bullock
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yanyan Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Debra Cromley
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Monica Schenone
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Chad A Cowan
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Daniel J Rader
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yu-Xin Xu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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Bale A, Rambo R, Prior C. The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement. PLoS Comput Biol 2023; 19:e1011248. [PMID: 38011290 PMCID: PMC10703313 DOI: 10.1371/journal.pcbi.1011248] [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: 06/08/2023] [Revised: 12/07/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison. These are performed using the SKMT algorithm, a novel method of smoothing the Cα backbone to achieve a minimal complexity curve representation of the manner in which the protein's secondary structure elements fold to form its tertiary structure. Its subsequent complexity is characterised using measures based on the writhe and crossing number quantities heavily utilised in DNA topology studies, and which have shown promising results when applied to proteins recently. The SKMT smoothing is used to derive empirical bounds on a protein's entanglement relative to its number of secondary structure elements. We show that large scale helical geometries dominantly account for the maximum growth in entanglement of protein monomers, and further that this large scale helical geometry is present in a large array of proteins, consistent across a number of different protein structure types and sequences. We also show how these bounds can be used to constrain the search space of protein structure prediction from small angle x-ray scattering experiments, a method highly suited to determining the likely structure of proteins in solution where crystal structure or machine learning based predictions often fail to match experimental data. Finally we develop a structural comparison metric based on the SKMT smoothing which is used in one specific case to demonstrate significant structural similarity between Rossmann fold and TIM Barrel proteins, a link which is potentially significant as attempts to engineer the latter have in the past produced the former. We provide the SWRITHE interactive python notebook to calculate these metrics.
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Affiliation(s)
- Arron Bale
- Department of Mathematical Sciences, Durham University, Durham, United Kingdom
| | - Robert Rambo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Christopher Prior
- Department of Mathematical Sciences, Durham University, Durham, United Kingdom
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5
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Dewey EB, Korda Holsclaw J, Saghaey K, Wittmer ME, Sekelsky J. The effect of repeat length on Marcal1-dependent single-strand annealing in Drosophila. Genetics 2023; 223:iyac164. [PMID: 36303322 PMCID: PMC9836020 DOI: 10.1093/genetics/iyac164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/22/2022] [Indexed: 01/19/2023] Open
Abstract
Proper repair of DNA double-strand breaks is essential to the maintenance of genomic stability and avoidance of genetic disease. Organisms have many ways of repairing double-strand breaks, including the use of homologous sequences through homology-directed repair. While homology-directed repair is often error free, in single-strand annealing homologous repeats flanking a double-strand break are annealed to one another, leading to the deletion of one repeat and the intervening sequences. Studies in yeast have shown a relationship between the length of the repeat and single-strand annealing efficacy. We sought to determine the effects of homology length on single-strand annealing in Drosophila, as Drosophila uses a different annealing enzyme (Marcal1) than yeast. Using an in vivo single-strand annealing assay, we show that 50 base pairs are insufficient to promote single-strand annealing and that 500-2,000 base pairs are required for maximum efficiency. Loss of Marcal1 generally followed the same homology length trend as wild-type flies, with single-strand annealing frequencies reduced to about a third of wild-type frequencies regardless of homology length. Interestingly, we find a difference in single-strand annealing rates between 500-base pair homologies that align to the annealing target either nearer or further from the double-strand break, a phenomenon that may be explained by Marcal1 dynamics. This study gives insights into Marcal1 function and provides important information to guide the design of genome engineering strategies that use single-strand annealing to integrate linear DNA constructs into a chromosomal double-strand break.
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Affiliation(s)
- Evan B Dewey
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julie Korda Holsclaw
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kiyarash Saghaey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mackenzie E Wittmer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeff Sekelsky
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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6
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The Biochemical Mechanism of Fork Regression in Prokaryotes and Eukaryotes—A Single Molecule Comparison. Int J Mol Sci 2022; 23:ijms23158613. [PMID: 35955746 PMCID: PMC9368896 DOI: 10.3390/ijms23158613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 02/04/2023] Open
Abstract
The rescue of stalled DNA replication forks is essential for cell viability. Impeded but still intact forks can be rescued by atypical DNA helicases in a reaction known as fork regression. This reaction has been studied at the single-molecule level using the Escherichia coli DNA helicase RecG and, separately, using the eukaryotic SMARCAL1 enzyme. Both nanomachines possess the necessary activities to regress forks: they simultaneously couple DNA unwinding to duplex rewinding and the displacement of bound proteins. Furthermore, they can regress a fork into a Holliday junction structure, the central intermediate of many fork regression models. However, there are key differences between these two enzymes. RecG is monomeric and unidirectional, catalyzing an efficient and processive fork regression reaction and, in the process, generating a significant amount of force that is used to displace the tightly-bound E. coli SSB protein. In contrast, the inefficient SMARCAL1 is not unidirectional, displays limited processivity, and likely uses fork rewinding to facilitate RPA displacement. Like many other eukaryotic enzymes, SMARCAL1 may require additional factors and/or post-translational modifications to enhance its catalytic activity, whereas RecG can drive fork regression on its own.
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Bisht D, Patne K, Rakesh R, Muthuswami R. On the Interaction Between SMARCAL1 and BRG1. Front Cell Dev Biol 2022; 10:870815. [PMID: 35784471 PMCID: PMC9243424 DOI: 10.3389/fcell.2022.870815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
SMARCAL1 and BRG1, both classified as ATP-dependent chromatin remodeling proteins, play a role in double-strand break DNA damage response pathways. Mutations in SMARCAL1 cause Schimke Immuno-osseous Dysplasia (SIOD) while mutations in BRG1 are associated with Coffin-Siris Syndrome (CSS4). In HeLa cells, SMARCAL1 and BRG1 co-regulate the expression of ATM, ATR, and RNAi genes on doxorubicin-induced DNA damage. Both the proteins are found to be simultaneously present on the promoter of these genes. Based on these results we hypothesized that SMARCAL1 and BRG1 interact with each other forming a complex. In this paper, we validate our hypothesis and show that SMARCAL1 and BRG1 do indeed interact with each other both in the absence and presence of doxorubicin. The formation of these complexes is dependent on the ATPase activity of both SMARCAL1 and BRG1. Using deletion constructs, we show that the HARP domains of SMARCAL1 mediate interaction with BRG1 while multiple domains of BRG1 are probably important for binding to SMARCAL1. We also show that SIOD-associated mutants fail to form a complex with BRG1. Similarly, CSS4-associated mutants of BRG1 fail to interact with SMARCAL1, thus, possibly contributing to the failure of the DNA damage response pathway and pathophysiology associated with SIOD and CSS4.
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Expanding Phenotype of Schimke Immuno-Osseous Dysplasia: Congenital Anomalies of the Kidneys and of the Urinary Tract and Alteration of NK Cells. Int J Mol Sci 2020; 21:ijms21228604. [PMID: 33203071 PMCID: PMC7696905 DOI: 10.3390/ijms21228604] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 11/17/2022] Open
Abstract
Schimke immuno-osseous dysplasia (SIOD) is a rare multisystemic disorder with a variable clinical expressivity caused by biallelic variants in SMARCAL1. A phenotype-genotype correlation has been attempted and variable expressivity of biallelic SMARCAL1 variants may be associated with environmental and genetic disturbances of gene expression. We describe two siblings born from consanguineous parents with a diagnosis of SIOD revealed by whole exome sequencing (WES). Results: A homozygous missense variant in the SMARCAL1 gene (c.1682G>A; p.Arg561His) was identified in both patients. Despite carrying the same variant, the two patients showed substantial renal and immunological phenotypic differences. We describe features not previously associated with SIOD-both patients had congenital anomalies of the kidneys and of the urinary tract and one of them succumbed to a classical type congenital mesoblastic nephroma. We performed an extensive characterization of the immunophenotype showing combined immunodeficiency characterized by a profound lymphopenia, lack of thymic output, defective IL-7Rα expression, and disturbed B plasma cells differentiation and immunoglobulin production in addition to an altered NK-cell phenotype and function. Conclusions: Overall, our results contribute to extending the phenotypic spectrum of features associated with SMARCAL1 mutations and to better characterizing the underlying immunologic disorder with critical implications for therapeutic and management strategies.
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Bansal R, Hussain S, Chanana UB, Bisht D, Goel I, Muthuswami R. SMARCAL1, the annealing helicase and the transcriptional co-regulator. IUBMB Life 2020; 72:2080-2096. [PMID: 32754981 DOI: 10.1002/iub.2354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
The ATP-dependent chromatin remodeling proteins play an important role in DNA repair. The energy released by ATP hydrolysis is used for myriad functions ranging from nucleosome repositioning and nucleosome eviction to histone variant exchange. In addition, the distant member of the family, SMARCAL1, uses the energy to reanneal stalled replication forks in response to DNA damage. Biophysical studies have shown that this protein has the unique ability to recognize and bind specifically to DNA structures possessing double-strand to single-strand transition regions. Mutations in SMARCAL1 have been linked to Schimke immuno-osseous dysplasia, an autosomal recessive disorder that exhibits variable penetrance and expressivity. It has long been hypothesized that the variable expressivity and pleiotropic phenotypes observed in the patients might be due to the ability of SMARCAL1 to co-regulate the expression of a subset of genes within the genome. Recently, the role of SMARCAL1 in regulating transcription has been delineated. In this review, we discuss the biophysical and functional properties of the protein that help it to transcriptionally co-regulate DNA damage response as well as to bind to the stalled replication fork and stabilize it, thus ensuring genomic stability. We also discuss the role of SMARCAL1 in cancer and the possibility of using this protein as a chemotherapeutic target.
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Affiliation(s)
- Ritu Bansal
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Saddam Hussain
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Upasana Bedi Chanana
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Deepa Bisht
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Isha Goel
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Muthuswami
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Zhang Y, Chen Q, Zhu G, Zhang F, Fang X, Ren H, Jiang J, Yang F, Zhang D, Chen F. CHR721, interacting with OsRPA1a, is essential for both male and female reproductive development in rice. PLANT MOLECULAR BIOLOGY 2020; 103:473-487. [PMID: 32266647 DOI: 10.1007/s11103-020-01004-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
CHR721 functions as a chromatin remodeler and interacts with a known single-stranded binding protein, OsRPA1a, to regulate both male and female reproductive development in rice. Reproductive development and fertility are important for seed production in rice. Here, we identified a sterile rice mutant, chr721, that exhibited defects in both male and female reproductive development. Approximately 5% of the observed defects in chr721, such as asynchronous dyad division, occurred during anaphase II of meiosis. During the mitotic stage, approximately 80% of uninucleate microspores failed to develop into tricellular pollen, leading to abnormal development. In addition, defects in megaspore development were detected after functional megaspore formation. CHR721, which encodes a nuclear protein belonging to the SNF2 subfamily SMARCAL1, was identified by map-based cloning. CHR721 was expressed in various tissues, especially in spikelets. CHR721 was found to interact with replication protein A (OsRPA1a), which is involved in DNA repair. The expressions of genes involved in DNA repair and cell-cycle checkpoints were consistently upregulated in chr721. Although numerous genes involved in male and female development have been identified, the mode of participation of chromatin-remodeling factors in reproductive development is still not well understood. Our results suggest that CHR721, a novel gene cloned from rice, plays a vital role in both male and female reproductive development.
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Affiliation(s)
- Yushun Zhang
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Qiong Chen
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Guanlin Zhu
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Fang Zhang
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Xiaohua Fang
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Haibo Ren
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Jun'e Jiang
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, People's Republic of China
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, No. 8 Daxue Road, Yichang, 443002, Hubei, People's Republic of China.
| | - Fan Chen
- National Centre for Plant Gene Research, State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China.
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11
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Buhl M, Kästle C, Geyer A, Autenrieth IB, Peter S, Willmann M. Molecular Evolution of Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa Strains From Patients and Hospital Environment in a Prolonged Outbreak. Front Microbiol 2019; 10:1742. [PMID: 31440214 PMCID: PMC6694792 DOI: 10.3389/fmicb.2019.01742] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/15/2019] [Indexed: 11/24/2022] Open
Abstract
In this study, we aimed to elucidate a prolonged outbreak of extensively drug-resistant (XDR) Pseudomonas aeruginosa, at two adjacent hospitals over a time course of 4 years. Since all strains exhibited a similar antibiotic susceptibility pattern and carried the carbapenemase gene blaVIM, a monoclonal outbreak was assumed. To shed light on the intra-hospital evolution of these strains over time, whole genome sequence (WGS) analysis of 100 clinical and environmental outbreak strains was employed. Phylogenetic analysis of the core genome revealed the outbreak to be polyclonal, rather than monoclonal as initially suggested. The vast majority of strains fell into one of two major clusters, composed of 27 and 59 strains, and their accessory genome each revealed over 400 and 600 accessory genes, respectively, thus indicating an unexpectedly high structural diversity among phylogenetically clustered strains. Further analyses focused on the cluster with 59 strains, representing the hospital from which both clinical and environmental strains were available. Our investigation clearly shows both accumulation and loss of genes occur very frequently over time, as reflected by analysis of protein enrichment as well as functional enrichment. In addition, we investigated adaptation through single nucleotide polymorphisms (SNPs). Among the genes affected by SNPs, there are a multidrug efflux pump (mexZ) and a mercury detoxification operon (merR) with deleterious mutations, potentially leading to loss of repression with resistance against antibiotics and disinfectants. Our results not only confirm WGS to be a powerful tool for epidemiologic analyses, but also provide insights into molecular evolution during an XDR P. aeruginosa hospital outbreak. Genome mutation unveiled a striking genetic plasticity on an unexpectedly high level, mostly driven by horizontal gene transfer. Our study adds valuable information to the molecular understanding of “real-world” Intra-hospital P. aeruginosa evolution and is a step forward toward more personalized medicine in infection control.
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Affiliation(s)
- Michael Buhl
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Christina Kästle
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - André Geyer
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
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12
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Yuruk Yildirim Z, Ozkan M, Yilmaz A, Kayserili H, Pehlivanoglu C, Emre S, Nayir A. An unusual cause of nephrotic syndrome: Answers. Pediatr Nephrol 2019; 34:819-821. [PMID: 30406368 DOI: 10.1007/s00467-018-4115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/27/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Zeynep Yuruk Yildirim
- Istanbul Faculty of Medicine, Pediatric Nephrology Department, Istanbul University, Istanbul, Turkey.
| | - Melis Ozkan
- Istanbul Faculty of Medicine, Department of Pediatrics, Istanbul University, Istanbul, Turkey
| | - Alev Yilmaz
- Istanbul Faculty of Medicine, Pediatric Nephrology Department, Istanbul University, Istanbul, Turkey
| | - Hülya Kayserili
- Istanbul Faculty of Medicine, Medical Genetics Department, Istanbul University, Istanbul, Turkey.,Medical Genetics Department & Genetic Diagnosis Center, Koç University School of Medicine, Istanbul, Turkey
| | - Cemile Pehlivanoglu
- Istanbul Faculty of Medicine, Pediatric Nephrology Department, Istanbul University, Istanbul, Turkey
| | - Sevinc Emre
- Istanbul Faculty of Medicine, Pediatric Nephrology Department, Istanbul University, Istanbul, Turkey
| | - Ahmet Nayir
- Istanbul Faculty of Medicine, Pediatric Nephrology Department, Istanbul University, Istanbul, Turkey
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13
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Bansal R, Arya V, Sethy R, Rakesh R, Muthuswami R. RecA-like domain 2 of DNA-dependent ATPase A domain, a SWI2/SNF2 protein, mediates conformational integrity and ATP hydrolysis. Biosci Rep 2018; 38:BSR20180568. [PMID: 29748240 PMCID: PMC6019379 DOI: 10.1042/bsr20180568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/27/2022] Open
Abstract
ATP-dependent chromatin remodeling proteins use the energy released from ATP hydrolysis to reposition nucleosomes in DNA-dependent processes. These proteins are classified as SF2 helicases. SMARCAL1, a member of this protein family, is known to modulate both DNA repair and transcription by specifically recognizing DNA molecules possessing double-strand to single-strand transition regions. Mutations in this gene cause a rare autosomal recessive disorder known as Schimke Immuno-Osseous Dysplasia (SIOD).Structural studies have shown that the ATP-dependent chromatin remodeling proteins possess two RecA-like domains termed as RecA-like domain 1 and RecA-like domain 2. Using Active DNA-dependent ATPase A domain (ADAAD), the bovine homolog of SMARCAL1, as a model system we had previously shown that the RecA-like domain 1 containing helicase motifs Q, I, Ia, II, and III are sufficient for ligand binding; however, the Rec A-like domain 2 containing motifs IV, V, and VI are needed for ATP hydrolysis. In the present study, we have focused on the motifs present in the RecA-like domain 2. Our studies demonstrate that the presence of an aromatic residue in motif IV is needed for interaction with DNA in the presence of ATP. We also show that the motif V is required for the catalytic efficiency of the protein and motif VI is needed for interaction with DNA in the presence of ATP. Finally, we show that the SIOD-associated mutation, R820H, present in motif VI results in loss of ATPase activity, and therefore, reduced response to DNA damage.
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Affiliation(s)
- Ritu Bansal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vijendra Arya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ramesh Sethy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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14
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Abstract
A large number of SNF2 family, DNA and ATP-dependent motor proteins are needed during transcription, DNA replication, and DNA repair to manipulate protein-DNA interactions and change DNA structure. SMARCAL1, ZRANB3, and HLTF are three related members of this family with specialized functions that maintain genome stability during DNA replication. These proteins are recruited to replication forks through protein-protein interactions and bind DNA using both their motor and substrate recognition domains (SRDs). The SRD provides specificity to DNA structures like forks and junctions and confers DNA remodeling activity to the motor domains. Remodeling reactions include fork reversal and branch migration to promote fork stabilization, template switching, and repair. Regulation ensures these powerful activities remain controlled and restricted to damaged replication forks. Inherited mutations in SMARCAL1 cause a severe developmental disorder and mutations in ZRANB3 and HLTF are linked to cancer illustrating the importance of these enzymes in ensuring complete and accurate DNA replication. In this review, we examine how these proteins function, concentrating on their common and unique attributes and regulatory mechanisms.
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Affiliation(s)
- Lisa A Poole
- a Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
| | - David Cortez
- a Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
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15
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Burnham DR, Nijholt B, De Vlaminck I, Quan J, Yusufzai T, Dekker C. Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively. Nucleic Acids Res 2017; 45:4687-4695. [PMID: 28334870 PMCID: PMC5416776 DOI: 10.1093/nar/gkx147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis–Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands.
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Affiliation(s)
- Daniel R Burnham
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Bas Nijholt
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Iwijn De Vlaminck
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Jinhua Quan
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Timur Yusufzai
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
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16
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Annealing of Complementary DNA Sequences During Double-Strand Break Repair in Drosophila Is Mediated by the Ortholog of SMARCAL1. Genetics 2017; 206:467-480. [PMID: 28258182 DOI: 10.1534/genetics.117.200238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 12/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) pose a serious threat to genomic integrity. If unrepaired, they can lead to chromosome fragmentation and cell death. If repaired incorrectly, they can cause mutations and chromosome rearrangements. DSBs are repaired using end-joining or homology-directed repair strategies, with the predominant form of homology-directed repair being synthesis-dependent strand annealing (SDSA). SDSA is the first defense against genomic rearrangements and information loss during DSB repair, making it a vital component of cell health and an attractive target for chemotherapeutic development. SDSA has also been proposed to be the primary mechanism for integration of large insertions during genome editing with CRISPR/Cas9. Despite the central role for SDSA in genome stability, little is known about the defining step: annealing. We hypothesized that annealing during SDSA is performed by the annealing helicase SMARCAL1, which can anneal RPA-coated single DNA strands during replication-associated DNA damage repair. We used unique genetic tools in Drosophila melanogaster to test whether the fly ortholog of SMARCAL1, Marcal1, mediates annealing during SDSA. Repair that requires annealing is significantly reduced in Marcal1 null mutants in both synthesis-dependent and synthesis-independent (single-strand annealing) assays. Elimination of the ATP-binding activity of Marcal1 also reduced annealing-dependent repair, suggesting that the annealing activity requires translocation along DNA. Unlike the null mutant, however, the ATP-binding defect mutant showed reduced end joining, shedding light on the interaction between SDSA and end-joining pathways.
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17
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The effect of ovine oocyte vitrification on expression of subset of genes involved in epigenetic modifications during oocyte maturation and early embryo development. Theriogenology 2016; 86:2136-2146. [DOI: 10.1016/j.theriogenology.2016.07.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 11/20/2022]
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18
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Sharma T, Bansal R, Haokip DT, Goel I, Muthuswami R. SMARCAL1 Negatively Regulates C-Myc Transcription By Altering The Conformation Of The Promoter Region. Sci Rep 2015; 5:17910. [PMID: 26648259 PMCID: PMC4673416 DOI: 10.1038/srep17910] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/09/2015] [Indexed: 12/18/2022] Open
Abstract
SMARCAL1, a member of the SWI2/SNF2 protein family, stabilizes replication forks during DNA damage. In this manuscript, we provide the first evidence that SMARCAL1 is also a transcriptional co-regulator modulating the expression of c-Myc, a transcription factor that regulates 10-15% genes in the human genome. BRG1, SMARCAL1 and RNAPII were found localized onto the c-myc promoter. When HeLa cells were serum starved, the occupancy of SMARCAL1 on the c-myc promoter increased while that of BRG1 and RNAPII decreased correlating with repression of c-myc transcription. Using Active DNA-dependent ATPase A Domain (ADAAD), the bovine homolog of SMARCAL1, we show that the protein can hydrolyze ATP using a specific region upstream of the CT element of the c-myc promoter as a DNA effector. The energy, thereby, released is harnessed to alter the conformation of the promoter DNA. We propose that SMARCAL1 negatively regulates c-myc transcription by altering the conformation of its promoter region during differentiation.
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Affiliation(s)
| | - Ritu Bansal
- School of Life Sciences, JNU, New Delhi 110067
| | | | - Isha Goel
- School of Life Sciences, JNU, New Delhi 110067
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19
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Sanyal M, Morimoto M, Baradaran-Heravi A, Choi K, Kambham N, Jensen K, Dutt S, Dionis-Petersen KY, Liu LX, Felix K, Mayfield C, Dekel B, Bokenkamp A, Fryssira H, Guillen-Navarro E, Lama G, Brugnara M, Lücke T, Olney AH, Hunley TE, Polat AI, Yis U, Bogdanovic R, Mitrovic K, Berry S, Najera L, Najafian B, Gentile M, Nur Semerci C, Tsimaratos M, Lewis DB, Boerkoel CF. Lack of IL7Rα expression in T cells is a hallmark of T-cell immunodeficiency in Schimke immuno-osseous dysplasia (SIOD). Clin Immunol 2015; 161:355-65. [DOI: 10.1016/j.clim.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 10/16/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
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20
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Sarin S, Javidan A, Boivin F, Alexopoulou I, Lukic D, Svajger B, Chu S, Baradaran-Heravi A, Boerkoel CF, Rosenblum ND, Bridgewater D. Insights into the renal pathogenesis in Schimke immuno-osseous dysplasia: A renal histological characterization and expression analysis. J Histochem Cytochem 2014; 63:32-44. [PMID: 25319549 DOI: 10.1369/0022155414558335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Schimke immuno-osseous dysplasia (SIOD) is a pleiotropic disorder caused by mutations in the SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like-1 (SMARCAL1) gene, with multiple clinical features, notably end-stage renal disease. Here we characterize the renal pathology in SIOD patients. Our analysis of SIOD patient renal biopsies demonstrates the tip and collapsing variants of focal segmental glomerulosclerosis (FSGS). Additionally, electron microscopy revealed numerous glomerular abnormalities most notably in the podocyte and Bowman's capsule. To better understand the role of SMARCAL1 in the pathogenesis of FSGS, we defined SMARCAL1 expression in the developing and mature kidney. In the developing fetal kidney, SMARCAL1 is expressed in the ureteric epithelium, stroma, metanephric mesenchyme, and in all stages of the developing nephron, including the maturing glomerulus. In postnatal kidneys, SMARCAL1 expression is localized to epithelial tubules of the nephron, collecting ducts, and glomerulus (podocytes and endothelial cells). Interestingly, not all cells within the same lineage expressed SMARCAL1. In renal biopsies from SIOD patients, TUNEL analysis detected marked increases in DNA fragmentation. Our results highlight the cells that may contribute to the renal pathogenesis in SIOD. Further, we suggest that disruptions in genomic integrity during fetal kidney development contribute to the pathogenesis of FSGS in SIOD patients.
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Affiliation(s)
- Sanjay Sarin
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Ashkan Javidan
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Felix Boivin
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Iakovina Alexopoulou
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Dusan Lukic
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Bruno Svajger
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Stephanie Chu
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada (ABH, CFB)
| | - Cornelius F Boerkoel
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada (ABH, CFB),Department of Medical Genetics, University of British Columbia, Vancouver, Canada (CFB)
| | - Norman D Rosenblum
- Department of Pediatrics, Division of Nephrology, The Hospital for Sick Children, University of Toronto, Toronto, Canada (NDR)
| | - Darren Bridgewater
- Program in Pathology and Molecular Medicine, McMaster University, Hamilton, Canada (SS, AJ, FB, IA, BS, SC, DL, DB)
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21
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Feldkamp MD, Mason AC, Eichman BF, Chazin WJ. Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1. Biochemistry 2014; 53:3052-61. [PMID: 24730652 PMCID: PMC4020579 DOI: 10.1021/bi500252w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
SWI/SNF-related,
matrix-associated, actin-dependent regulator of
chromatin, subfamily A-like1 (SMARCAL1) is a recently identified DNA
damage response protein involved in remodeling stalled replication
forks. The eukaryotic single-strand DNA binding protein replication
protein A (RPA) recruits SMARCAL1 to stalled forks in vivo and facilitates regression of forks containing leading strand gaps.
Both activities are mediated by a direct interaction between an RPA
binding motif (RBM) at the N-terminus of SMARCAL1 and the C-terminal
winged-helix domain of the RPA 32 kDa subunit (RPA32C). Here we report
a biophysical and structural characterization of the SMARCAL1–RPA
interaction. Isothermal titration calorimetry and circular dichroism
spectroscopy revealed that RPA32C binds SMARCAL1-RBM with a Kd of 2.5 μM and induces a disorder-to-helix
transition. The crystal structure of RPA32C was refined to 1.4 Å
resolution, and the SMARCAL1-RBM binding site was mapped on the structure
on the basis of nuclear magnetic resonance chemical shift perturbations.
Conservation of the interaction surface to other RBM-containing proteins
allowed construction of a model for the RPA32C/SMARCAL1-RBM complex.
The implications of our results are discussed with respect to the
recruitment of SMARCAL1 and other DNA damage response and repair proteins
to stalled replication forks.
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Affiliation(s)
- Michael D Feldkamp
- Department of Biochemistry, ‡Department of Biological Sciences, §Department of Chemistry, and ∥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
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22
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Santangelo L, Gigante M, Netti GS, Diella S, Puteo F, Carbone V, Grandaliano G, Giordano M, Gesualdo L. A novel SMARCAL1 mutation associated with a mild phenotype of Schimke immuno-osseous dysplasia (SIOD). BMC Nephrol 2014; 15:41. [PMID: 24589093 PMCID: PMC3973878 DOI: 10.1186/1471-2369-15-41] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/25/2014] [Indexed: 11/17/2022] Open
Abstract
Background Schimke immuno-osseous dysplasia (SIOD, OMIM #242900) is an autosomal-recessive pleiotropic disorder characterized by spondyloepiphyseal dysplasia, renal dysfunction and T-cell immunodeficiency. SIOD is caused by mutations in the gene SMARCAL1. Case presentation We report the clinical and genetic diagnosis of a 5-years old girl with SIOD, referred to our Center because of nephrotic-range proteinuria occasionally detected during the follow-up for congenital hypothyroidism. Mutational analysis of SMARCAL1 gene was performed by polymerase chain reaction (PCR) and bidirectional sequencing. Sequence analysis revealed that patient was compound heterozygous for two SMARCAL1 mutations: a novel missense change (p.Arg247Pro) and a well-known nonsense mutation (p.Glu848*). Conclusion This report provided the clinical and genetic description of a mild phenotype of Schimke immuno-osseous dysplasia associated with nephrotic proteinuria, decreasing after combined therapy with ACE inhibitors and sartans. Our experience highlighted the importance of detailed clinical evaluation, appropriate genetic counseling and molecular testing, to provide timely treatment and more accurate prognosis.
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Affiliation(s)
| | | | | | | | | | | | | | - Mario Giordano
- Unit of Pediatric Nephrology, University Hospital "Policlinico Consorziale - Giovanni XXIII", Bari, Italy.
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23
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Dutta P, Tanti GK, Sharma S, Goswami SK, Komath SS, Mayo MW, Hockensmith JW, Muthuswami R. Global epigenetic changes induced by SWI2/SNF2 inhibitors characterize neomycin-resistant mammalian cells. PLoS One 2012; 7:e49822. [PMID: 23209606 PMCID: PMC3509132 DOI: 10.1371/journal.pone.0049822] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 10/17/2012] [Indexed: 11/24/2022] Open
Abstract
Background Previously, we showed that aminoglycoside phosphotransferases catalyze the formation of a specific inhibitor of the SWI2/SNF2 proteins. Aminoglycoside phosphotransferases, for example neomycin-resistant genes, are used extensively as selection markers in mammalian transfections as well as in transgenic studies. However, introduction of the neomycin-resistant gene is fraught with variability in gene expression. We hypothesized that the introduction of neomycin-resistant genes into mammalian cells results in inactivation of SWI2/SNF2 proteins thereby leading to global epigenetic changes. Methodology Using fluorescence spectroscopy we have shown that the inhibitor, known as Active DNA-dependent ATPase ADomain inhibitor (ADAADi), binds to the SWI2/SNF2 proteins in the absence as well as presence of ATP and DNA. This binding occurs via a specific region known as Motif Ia leading to a conformational change in the SWI2/SNF2 proteins that precludes ATP hydrolysis. ADAADi is produced from a plethora of aminoglycosides including G418 and Streptomycin, two commonly used antibiotics in mammalian cell cultures. Mammalian cells are sensitive to ADAADi; however, cells stably transfected with neomycin-resistant genes are refractory to ADAADi. In resistant cells, endogenous SWI2/SNF2 proteins are inactivated which results in altered histone modifications. Microarray data shows that the changes in the epigenome are reflected in altered gene expression. The microarray data was validated using real-time PCR. Finally, we show that the epigenetic changes are quantized. Significance The use of neomycin-resistant genes revolutionized mammalian transfections even though questions linger about efficacy. In this study, we have demonstrated that selection of neomycin-resistant cells results in survival of only those cells that have undergone epigenetic changes, and therefore, data obtained using these resistant genes as selection markers need to be cautiously evaluated.
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Affiliation(s)
- Popy Dutta
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Goutam Kumar Tanti
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Soni Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Shyamal K. Goswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Sneha Sudha Komath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Marty W. Mayo
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joel W. Hockensmith
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail: (JWH); (RM)
| | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
- * E-mail: (JWH); (RM)
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24
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Targeting SMARCAL1 as a novel strategy for cancer therapy. Biochem Biophys Res Commun 2012; 427:232-5. [PMID: 22995303 DOI: 10.1016/j.bbrc.2012.09.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 09/08/2012] [Indexed: 12/20/2022]
Abstract
SMARCAL1 is a SNF2 chromatin-remodeling protein with ATP-dependent annealing helicase activity. Recent studies have shown that SMARCAL1 is involved in DNA damage repair and cell cycle progression. Deficiency of SMARCAL1 enhances the anticancer activity of chemotherapy agents and reverses cancer cell resistance to these agents. Therefore, targeting SMARCAL1 is an attractive therapeutic approach for cancers with defects in DNA damage repair or cell cycle checkpoints. Here, we review advances in our understanding of the biochemical and cellular functions of SMARCAL1 made over the recent years and discuss the rationale for development of SMARCAL1 inhibitors as novel anticancer therapies.
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25
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Baradaran-Heravi A, Raams A, Lubieniecka J, Cho KS, DeHaai KA, Basiratnia M, Mari PO, Xue Y, Rauth M, Olney AH, Shago M, Choi K, Weksberg RA, Nowaczyk MJM, Wang W, Jaspers NGJ, Boerkoel CF. SMARCAL1 deficiency predisposes to non-Hodgkin lymphoma and hypersensitivity to genotoxic agents in vivo. Am J Med Genet A 2012; 158A:2204-13. [PMID: 22888040 DOI: 10.1002/ajmg.a.35532] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/16/2012] [Indexed: 12/19/2022]
Abstract
Schimke immuno-osseous dysplasia (SIOD) is a multisystemic disorder with prominent skeletal, renal, immunological, and ectodermal abnormalities. It is caused by mutations of SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1), which encodes a DNA stress response protein. To determine the relationship of this function to the SIOD phenotype, we profiled the cancer prevalence in SIOD and assessed if defects of nucleotide excision repair (NER) and nonhomologous end joining (NHEJ), respectively, explained the ectodermal and immunological features of SIOD. Finally, we determined if Smarcal1(del/del) mice had hypersensitivity to irinotecan (CPT-11), etoposide, and hydroxyurea (HU) and whether exposure to these agents induced features of SIOD. Among 71 SIOD patients, three had non-Hodgkin lymphoma (NHL) and one had osteosarcoma. We did not find evidence of defective NER or NHEJ; however, Smarcal1-deficient mice were hypersensitive to several genotoxic agents. Also, CPT-11, etoposide, and HU caused decreased growth and loss of growth plate chondrocytes. These data, which identify an increased prevalence of NHL in SIOD and confirm hypersensitivity to DNA damaging agents in vivo, provide guidance for the management of SIOD patients.
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Affiliation(s)
- Alireza Baradaran-Heravi
- Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Yuan J, Ghosal G, Chen J. The HARP-like domain-containing protein AH2/ZRANB3 binds to PCNA and participates in cellular response to replication stress. Mol Cell 2012; 47:410-21. [PMID: 22705370 DOI: 10.1016/j.molcel.2012.05.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 03/03/2012] [Accepted: 05/17/2012] [Indexed: 10/28/2022]
Abstract
Proteins with annealing activity are newly identified ATP-dependent motors that can rewind RPA-coated complementary single-stranded DNA bubbles. AH2 (annealing helicase 2, also named as ZRANB3) is the second protein with annealing activity, the function of which is still unknown. Here, we report that AH2 is recruited to stalled replication forks and that cells depleted of AH2 are hypersensitive to replication stresses. Furthermore, AH2 binds to PCNA, which is crucial for its function at stalled replication forks. Interestingly, we identified a HARP-like (HPL) domain in AH2 that is indispensible for its annealing activity in vitro and its function in vivo. Moreover, searching of HPL domain in SNF2 family of proteins led to the identification of SMARCA1 and RAD54L, both of which possess annealing activity. Thus, this study not only demonstrates the in vivo functions of AH2, but also reveals a common feature of this new subfamily of proteins with annealing activity.
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Affiliation(s)
- Jingsong Yuan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Elizondo LI, Jafar-Nejad P, Clewing JM, Boerkoel CF. Gene clusters, molecular evolution and disease: a speculation. Curr Genomics 2011; 10:64-75. [PMID: 19721813 PMCID: PMC2699835 DOI: 10.2174/138920209787581271] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 12/20/2008] [Accepted: 12/21/2008] [Indexed: 01/10/2023] Open
Abstract
Traditionally eukaryotic genes are considered independently expressed under the control of their promoters and cis-regulatory domains. However, recent studies in worms, flies, mice and humans have shown that genes co-habiting a chromatin domain or “genomic neighborhood” are frequently co-expressed. Often these co-expressed genes neither constitute part of an operon nor function within the same biological pathway. The mechanisms underlying the partitioning of the genome into transcriptional genomic neighborhoods are poorly defined. However, cross-species analyses find that the linkage among the co-expressed genes of these clusters is significantly conserved and that the expression patterns of genes within clusters have coevolved with the clusters. Such selection could be mediated by chromatin interactions with the nuclear matrix and long-range remodeling of chromatin structure. In the context of human disease, we propose that dysregulation of gene expression across genomic neighborhoods will cause highly pleiotropic diseases. Candidate genomic neighborhood diseases include the nuclear laminopathies, chromosomal translocations and genomic instability disorders, imprinting disorders of errant insulator function, syndromes from impaired cohesin complex assembly, as well as diseases of global covalent histone modifications and DNA methylation. The alteration of transcriptional genomic neighborhoods provides an exciting and novel model for studying epigenetic alterations as quantitative traits in complex common human diseases.
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The HARP domain dictates the annealing helicase activity of HARP/SMARCAL1. EMBO Rep 2011; 12:574-80. [PMID: 21525954 DOI: 10.1038/embor.2011.74] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 03/07/2011] [Accepted: 03/22/2011] [Indexed: 11/08/2022] Open
Abstract
Mutations in HepA-related protein (HARP, or SMARCAL1) cause Schimke immunoosseous dysplasia (SIOD). HARP has ATP-dependent annealing helicase activity, which helps to stabilize stalled replication forks and facilitate DNA repair during replication. Here, we show that the conserved tandem HARP (2HP) domain dictates this annealing helicase activity. Furthermore, chimeric proteins generated by fusing the 2HP domain of HARP with the SNF2 domain of BRG1 or HELLS show annealing helicase activity in vitro and, when targeted to replication forks, mimic the functions of HARP in vivo. We propose that the HARP domain endows HARP with this ATP-driven annealing helicase activity.
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Abstract
The proper resolution of branched DNA molecules, which arise during processes such as DNA replication, DNA repair, and transcription, is critical for the maintenance of the genome. Disruption of this process can lead to genome instability and cancer progression. In this review, we describe recent progress on several interesting and biologically important enzymes that act upon different types of branched DNA substrates.
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Affiliation(s)
- Timur Yusufzai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
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30
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Abstract
The structure and integrity of DNA is of considerable biological and biomedical importance, and it is therefore critical to identify and to characterize enzymes that alter DNA structure. DNA helicases are ATP-driven motor proteins that unwind DNA. Conversely, HepA-related protein (HARP) protein (also known as SMARCAL1 and DNA-dependent ATPase A) is an annealing helicase that rewinds DNA in an ATP-dependent manner. To date, HARP is the only known annealing helicase. Here we report the identification of a second annealing helicase, which we term AH2, for annealing helicase 2. Like HARP, AH2 catalyzes the ATP-dependent rewinding of replication protein A (RPA)-bound complementary single-stranded DNA, but does not exhibit any detectable helicase activity. Unlike HARP, however, AH2 lacks a conserved RPA-binding domain and does not interact with RPA. In addition, AH2 contains an HNH motif, which is commonly found in bacteria and fungi and is often associated with nuclease activity. AH2 appears to be the only vertebrate protein with an HNH motif. Contrary to expectations, purified AH2 does not exhibit nuclease activity, but it remains possible that AH2 contains a latent nuclease that is activated under specific conditions. These structural and functional differences between AH2 and HARP suggest that different annealing helicases have distinct functions in the cell.
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Affiliation(s)
- Timur Yusufzai
- Section of Molecular Biology, 0347, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
| | - James T. Kadonaga
- Section of Molecular Biology, 0347, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
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Postow L, Woo EM, Chait BT, Funabiki H. Identification of SMARCAL1 as a component of the DNA damage response. J Biol Chem 2010; 284:35951-61. [PMID: 19841479 DOI: 10.1074/jbc.m109.048330] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SMARCAL1 (also known as HARP) is a SWI/SNF family protein with an ATPase activity stimulated by DNA containing both single-stranded and double-stranded regions. Mutations in SMARCAL1 are associated with the disease Schimke immuno-osseous dysplasia, a multisystem autosomal recessive disorder characterized by T cell immunodeficiency, growth inhibition, and renal dysfunction. The cellular function of SMARCAL1, however, is unknown. Here, using Xenopus egg extracts and mass spectrometry, we identify SMARCAL1 as a protein recruited to double-stranded DNA breaks. SMARCAL1 binds to double-stranded breaks and stalled replication forks in both egg extract and human cells, specifically colocalizing with the single-stranded DNA binding factor RPA. In addition, SMARCAL1 interacts physically with RPA independently of DNA. SMARCAL1 is phosphorylated in a caffeine-sensitive manner in response to double-stranded breaks and stalled replication forks. It has been suggested that stalled forks can be stabilized by a mechanism involving caffeine-sensitive kinases, or they collapse and subsequently recruit Rad51 to promote homologous recombination repair. We show that depletion of SMARCAL1 from U2OS cells leads to increased frequency of RAD51 foci upon generation of stalled replication forks, indicating that fork breakdown is more prevalent in the absence of SMARCAL1. We propose that SMARCAL1 is a novel DNA damage-binding protein involved in replication fork stabilization.
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Affiliation(s)
- Lisa Postow
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York 10065, USA.
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Abstract
Schimke immunoosseous dysplasia (SIOD) is an autosomal recessive multisystem disorder characterized by prominent spondyloepiphyseal dysplasia, T cell deficiency, and focal segmental glomerulosclerosis. Biallelic mutations in swi/snf-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1 (SMARCAL1) are the only identified cause of SIOD, but approximately half of patients referred for molecular studies do not have detectable mutations in SMARCAL1. We hypothesized that skeletal features distinguish between those with or without SMARCAL1 mutations. Therefore, we analyzed the skeletal radiographs of 22 patients with and 11 without detectable SMARCAL1 mutations. We found that patients with SMARCAL1 mutations have a spondyloepiphyseal dysplasia (SED) essentially limited to the spine, pelvis, capital femoral epiphyses, and possibly the sella turcica, whereas the hands and other long bones are basically normal. Additionally, we found that several of the adolescent and young adult patients developed osteoporosis and coxarthrosis. Of the 11 patients without detectable SMARCAL1 mutations, seven had a SED indistinguishable from patients with SMARCAL1 mutations. We conclude therefore that SED is a feature of patients with SMARCAL1 mutations and that skeletal features do not distinguish who of those with SED have SMARCAL1 mutations.
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Huang C, Gu S, Yu P, Yu F, Feng C, Gao N, Du J. Deficiency of smarcal1 causes cell cycle arrest and developmental abnormalities in zebrafish. Dev Biol 2009; 339:89-100. [PMID: 20036229 DOI: 10.1016/j.ydbio.2009.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 12/14/2009] [Accepted: 12/15/2009] [Indexed: 11/19/2022]
Abstract
Mutations in SMARCAL1 cause Schimke Immuno-Osseous Dysplasia (SIOD), an autosomal recessive multisystem developmental disease characterized by growth retardation, T-cell deficiency, bone marrow failure, anemia and renal failure. SMARCAL1 encodes an ATP-driven annealing helicase. However, the biological function of SMARCAL1 and the molecular basis of SIOD remain largely unclear. In this work, we cloned the zebrafish homologue of the human SMARCAL1 gene and found that smarcal1 regulated cell cycle progression. Morpholino knockdown of smarcal1 in zebrafish recapitulated developmental abnormalities in SIOD patients, including growth retardation, craniofacial abnormality, and haematopoietic and vascular defects. Lack of smarcal1 caused G0/G1 cell cycle arrest and induced cell apoptosis. Furthermore, using Electrophoretic Mobility Shift Assay and reporter assay, we found that SMARCAL1 was transcriptionally inhibited by E2F6, an important cell cycle regulator. Over-expression of E2F6 in zebrafish embryos reduced the expression of smarcal1 mRNA and induced developmental defects similar to those in smarcal1 morphants. These results suggest that SIOD may be caused by defects in cell cycle regulation. Our study provides a model of SIOD and reveals its cellular and molecular bases.
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Affiliation(s)
- Cheng Huang
- Institute for Nutritional Sciences and Key Laboratory of Nutrition and Metabolism, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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Ciccia A, Bredemeyer AL, Sowa ME, Terret ME, Jallepalli PV, Harper JW, Elledge SJ. The SIOD disorder protein SMARCAL1 is an RPA-interacting protein involved in replication fork restart. Genes Dev 2009; 23:2415-25. [PMID: 19793862 DOI: 10.1101/gad.1832309] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The integrity of genomic DNA is continuously challenged by the presence of DNA base lesions or DNA strand breaks. Here we report the identification of a new DNA damage response protein, SMARCAL1 (SWI/SNF-related, matrix associated, actin-dependent regulator of chromatin, subfamily a-like 1), which is a member of the SNF2 family and is mutated in Schimke immunoosseous dysplasia (SIOD). We demonstrate that SMARCAL1 directly interacts with Replication protein A (RPA) and is recruited to sites of DNA damage in an RPA-dependent manner. SMARCAL1-depleted cells display sensitivity to DNA-damaging agents that induce replication fork collapse, and exhibit slower fork recovery and delayed entry into mitosis following S-phase arrest. Furthermore, SIOD patient fibroblasts reconstituted with SMARCAL1 exhibit faster cell cycle progression after S-phase arrest. Thus, the symptoms of SIOD may be caused, at least in part, by defects in the cellular response to DNA replication stress.
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Affiliation(s)
- Alberto Ciccia
- Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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36
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Yuan J, Ghosal G, Chen J. The annealing helicase HARP protects stalled replication forks. Genes Dev 2009; 23:2394-9. [PMID: 19793864 DOI: 10.1101/gad.1836409] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mutations in HepA-related protein (HARP) are the only identified causes of Schimke immunoosseous dysplasia (SIOD). HARP has a unique annealing helicase activity in vitro, but the in vivo functional significance remains unknown. Here, we demonstrated that HARP is recruited to stalled replication forks via its direct interaction with Replication protein A (RPA). Cells with HARP depletion displayed increased spontaneous DNA damage and G2/M arrest, suggesting that HARP normally acts to stabilize stalled replication forks. Our data place the annealing helicase activity of HARP at replication forks and propose that SIOD syndrome may be caused by the destabilization of replication forks during cell proliferation.
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Affiliation(s)
- Jingsong Yuan
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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37
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Yusufzai T, Kong X, Yokomori K, Kadonaga JT. The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA. Genes Dev 2009; 23:2400-4. [PMID: 19793863 DOI: 10.1101/gad.1831509] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
HepA-related protein (HARP) (also known as SMARCAL1) is an ATP-driven annealing helicase that catalyzes the formation of dsDNA from complementary Replication protein A (RPA)-bound ssDNA. Here we find that HARP contains a conserved N-terminal motif that is necessary and sufficient for binding to RPA. This RPA-binding motif is not required for annealing helicase activity, but is essential for the recruitment of HARP to sites of laser-induced DNA damage. These findings suggest that the interaction of HARP with RPA increases the concentration of annealing helicase activity in the vicinity of ssDNA regions to facilitate processes such as DNA repair.
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Affiliation(s)
- Timur Yusufzai
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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38
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Uzun A, Rodriguez-Osorio N, Kaya A, Wang H, Parrish JJ, Ilyin VA, Memili E. Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis. BMC Genomics 2009; 10:183. [PMID: 19393058 PMCID: PMC2684548 DOI: 10.1186/1471-2164-10-183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 04/24/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Embryonic genome activation (EGA) is a critical event for the preimplantation embryo, which is manifested by changes in chromatin structure, transcriptional machinery, expression of embryonic genes, and degradation of maternal transcripts. The objectives of this study were to determine transcript abundance of HMGN3a and SMARCAL1 in mature bovine oocytes and early bovine embryos, to perform comparative functional genomics analysis of these genes across mammals. RESULTS New annotations of both HMGN3a and SMARCAL1 were submitted to the Bovine Genome Annotation Submission Database at BovineGenome.org. Careful analysis of the bovine SMARCAL1 consensus gene set for this protein (GLEAN_20241) showed that the NCBI protein contains sequencing errors, and that the actual bovine protein has a high degree of homology to the human protein. Our results showed that there was a high degree of structural conservation of HMGN3a and SMARCAL1 in the mammalian species studied. HMGN3a transcripts were present at similar levels in bovine matured oocytes and 2-4-cell embryos but at higher levels in 8-16-cell embryos, morulae and blastocysts. On the other hand, transcript levels of SMARCAL1 decreased throughout preimplantation development. CONCLUSION The high levels of structural conservation of these proteins highlight the importance of chromatin remodeling in the regulation of gene expression, particularly during early mammalian embryonic development. The greater similarities of human and bovine HMGN3a and SMARCAL1 proteins may suggest the cow as a valuable model to study chromatin remodeling at the onset of mammalian development. Understanding the roles of chromatin remodeling proteins during embryonic development emphasizes the importance of epigenetics and could shed light on the underlying mechanisms of early mammalian development.
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Affiliation(s)
- Alper Uzun
- Department of Biology, Northeastern University, Boston, MA, USA.
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39
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Nongkhlaw M, Dutta P, Hockensmith JW, Komath SS, Muthuswami R. Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family. Nucleic Acids Res 2009; 37:3332-41. [PMID: 19324887 PMCID: PMC2691824 DOI: 10.1093/nar/gkp178] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The active DNA-dependent ATPase A domain (ADAAD), a member of the SWI2/SNF2 family, has been shown to bind DNA in a structure-specific manner, recognizing DNA molecules possessing double-stranded to single-stranded transition regions leading to ATP hydrolysis. Extending these studies we have delineated the structural requirements of the DNA effector for ADAAD and have shown that the single-stranded and double-stranded regions both contribute to binding affinity while the double-stranded region additionally plays a role in determining the rate of ATP hydrolysis. We have also investigated the mechanism of interaction of DNA and ATP with ADAAD and shown that each can interact independently with ADAAD in the absence of the other. Furthermore, the protein can bind to dsDNA as well as ssDNA molecules. However, the conformation change induced by the ssDNA is different from the conformational change induced by stem-loop DNA (slDNA), thereby providing an explanation for the observed ATP hydrolysis only in the presence of the double-stranded:single-stranded transition (i.e. slDNA).
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Affiliation(s)
- Macmillan Nongkhlaw
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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40
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Haseltine CA, Kowalczykowski SC. An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA. Nucleic Acids Res 2009; 37:2757-70. [PMID: 19282450 PMCID: PMC2677860 DOI: 10.1093/nar/gkp068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rad54 protein is a key member of the RAD52 epistasis group required for homologous recombination in eukaryotes. Rad54 is a duplex DNA translocase that remodels both DNA and protein–DNA complexes, and functions at multiple steps in the recombination process. Here we use biochemical criteria to demonstrate the existence of this important protein in a prokaryotic organism. The Sulfolobus solfataricus Rad54 (SsoRad54) protein is a double-strand DNA-dependent ATPase that can alter the topology of duplex DNA. Like its eukaryotic homolog, it interacts directly with the S. solfataricus Rad51 homologue, SsoRadA, to stimulate DNA strand exchange. Confirmation of this protein as an authentic Rad54 homolog establishes an essential phylogenetic bridge for identifying Rad54 homologs in the archaeal and bacterial domains.
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Affiliation(s)
- Cynthia A Haseltine
- Department of Microbiology, University of California, Davis, CA 95616-8665, USA
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41
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Abstract
DNA-dependent adenosine triphosphatases (ATPases) participate in a broad range of biological processes including transcription, DNA repair, and chromatin dynamics. Mutations in the HepA-related protein (HARP) ATPase are responsible for Schimke immuno-osseous dysplasia (SIOD), but the function of the protein is unknown. We found that HARP is an ATP-dependent annealing helicase that rewinds single-stranded DNA bubbles that are stably bound by replication protein A. Other related ATPases, including the DNA translocase Rad54, did not exhibit annealing helicase activity. Analysis of mutant HARP proteins suggests that SIOD is caused by a deficiency in annealing helicase activity. Moreover, the pleiotropy of HARP mutations is consistent with the function of HARP as an annealing helicase that acts throughout the genome to oppose the action of DNA-unwinding activities in the nucleus.
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Affiliation(s)
- Timur Yusufzai
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347 USA
| | - James T. Kadonaga
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347 USA
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Neurologic phenotype of Schimke immuno-osseous dysplasia and neurodevelopmental expression of SMARCAL1. J Neuropathol Exp Neurol 2008; 67:565-77. [PMID: 18520775 DOI: 10.1097/nen.0b013e3181772777] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Schimke immuno-osseous dysplasia (OMIM 242900) is an uncommon autosomal-recessive multisystem disease caused by mutations in SMARCAL1 (swi/snf-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1), a gene encoding a putative chromatin remodeling protein. Neurologic manifestations identified to date relate to enhanced atherosclerosis and cerebrovascular disease. Based on a clinical survey, we determined that half of Schimke immuno-osseous dysplasia patients have a small head circumference, and 15% have social, language, motor, or cognitive abnormalities. Postmortem examination of 2 Schimke immuno-osseous dysplasia patients showed low brain weights and subtle brain histologic abnormalities suggestive of perturbed neuron-glial migration such as heterotopia, irregular cortical thickness, incomplete gyral formation, and poor definition of cortical layers. We found that SMARCAL1 is highly expressed in the developing and adult mouse and human brain, including neural precursors and neuronal lineage cells. These observations suggest that SMARCAL1 deficiency may influence brain development and function in addition to its previously recognized effect on cerebral circulation.
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Clewing JM, Fryssira H, Goodman D, Smithson SF, Sloan EA, Lou S, Huang Y, Choi K, Lücke T, Alpay H, André JL, Asakura Y, Biebuyck-Gouge N, Bogdanovic R, Bonneau D, Cancrini C, Cochat P, Cockfield S, Collard L, Cordeiro I, Cormier-Daire V, Cransberg K, Cutka K, Deschenes G, Ehrich JHH, Fründ S, Georgaki H, Guillen-Navarro E, Hinkelmann B, Kanariou M, Kasap B, Kilic SS, Lama G, Lamfers P, Loirat C, Majore S, Milford D, Morin D, Ozdemir N, Pontz BF, Proesmans W, Psoni S, Reichenbach H, Reif S, Rusu C, Saraiva JM, Sakallioglu O, Schmidt B, Shoemaker L, Sigaudy S, Smith G, Sotsiou F, Stajic N, Stein A, Stray-Pedersen A, Taha D, Taque S, Tizard J, Tsimaratos M, Wong NACS, Boerkoel CF. Schimke immunoosseous dysplasia: suggestions of genetic diversity. Hum Mutat 2007; 28:273-83. [PMID: 17089404 DOI: 10.1002/humu.20432] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Schimke immunoosseous dysplasia (SIOD), which is characterized by prominent spondyloepiphyseal dysplasia, T-cell deficiency, and focal segmental glomerulosclerosis, is a panethnic autosomal recessive multisystem disorder with variable expressivity. Biallelic mutations in switch/sucrose nonfermenting (swi/snf) related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1 (SMARCAL1) are the only identified cause of SIOD. However, among 72 patients from different families, we identified only 38 patients with biallelic mutations in the coding exons and splice junctions of the SMARCAL1 gene. This observation, the variable expressivity, and poor genotype-phenotype correlation led us to test several hypotheses including modifying haplotypes, oligogenic inheritance, or locus heterogeneity in SIOD. Haplotypes associated with the two more common mutations, R820H and E848X, did not correlate with phenotype. Also, contrary to monoallelic SMARCAL1 coding mutations indicating oligogenic inheritance, we found that all these patients did not express RNA and/or protein from the other allele and thus have biallelic SMARCAL1 mutations. We hypothesize therefore that the variable expressivity among patients with biallelic SMARCAL1 mutations arises from environmental, genetic, or epigenetic modifiers. Among patients without detectable SMARCAL1 coding mutations, our analyses of cell lines from four of these patients showed that they expressed normal levels of SMARCAL1 mRNA and protein. This is the first evidence for nonallelic heterogeneity in SIOD. From analysis of the postmortem histopathology from two patients and the clinical data from most patients, we propose the existence of endophenotypes of SIOD.
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Affiliation(s)
- J Marietta Clewing
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Misirlioglu M, Page GP, Sagirkaya H, Kaya A, Parrish JJ, First NL, Memili E. Dynamics of global transcriptome in bovine matured oocytes and preimplantation embryos. Proc Natl Acad Sci U S A 2006; 103:18905-10. [PMID: 17142320 PMCID: PMC1748150 DOI: 10.1073/pnas.0608247103] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Global activation of the embryonic genome is the most critical event in early mammalian development. After fertilization, a rich supply of maternal proteins and RNAs support development whereas a number of zygotic and embryonic genes are expressed in a stage-specific manner leading to embryonic genome activation (EGA). However, the identities of embryonic genes expressed and the mechanism(s) of EGA are poorly defined in the bovine. Using the Affymetrix bovine-specific DNA microarray as the biggest available array at present, we analyzed gene expression at two key stages of bovine development, matured oocytes (MII) and 8-cell-stage embryos, constituting the ultimate reservoir for life and a stage during which EGA takes place, respectively. Key genes in regulation of transcription, chromatin-structure cell adhesion, and signal transduction were up-regulated at the 8-cell stage as compared with 8-cell embryos treated with alpha-amanitin and MII. Genes controlling DNA methylation and metabolism were up-regulated in MII. These changes in gene expression, related to transcriptional machinery, chromatin structure, and the other cellular functions occurring during several cleavage stages, are expected to result in a unique chromatin structure capable of maintaining totipotency during embryogenesis and leading to differentiation during postimplantation development. Dramatic reprogramming of gene expression at the onset of development also has implications for cell plasticity in somatic cell nuclear transfer, genomic imprinting, and cancer.
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Affiliation(s)
| | - G. P. Page
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294-0022; and
| | | | - A. Kaya
- Department of Animal Sciences, University of Wisconsin, Madison, WI 53706
| | - J. J. Parrish
- Department of Animal Sciences, University of Wisconsin, Madison, WI 53706
| | - N. L. First
- Biological Sciences, Mississippi State University, Mississippi State, MS 39762
- To whom correspondence may be addressed. E-mail:
or
| | - E. Memili
- Departments of *Animal and Dairy Sciences and
- To whom correspondence may be addressed. E-mail:
or
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Clewing JM, Antalfy BC, Lücke T, Najafian B, Marwedel KM, Hori A, Powel RM, Do AFS, Najera L, SantaCruz K, Hicks MJ, Armstrong DL, Boerkoel CF. Schimke immuno-osseous dysplasia: a clinicopathological correlation. J Med Genet 2006; 44:122-30. [PMID: 16840568 PMCID: PMC2598061 DOI: 10.1136/jmg.2006.044313] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Schimke immuno-osseous dysplasia (SIOD) is a fatal autosomal recessive disorder caused by loss-of-function mutations in swi/snf-related matrix-associated actin-dependent regulator of chromatin, subfamily a-like 1 (SMARCAL1). METHODS Analysis of detailed autopsies to correlate clinical and pathological findings in two men severely affected with SIOD. RESULTS As predicted by the clinical course, T cell deficiency in peripheral lymphoid organs, defective chondrogenesis, focal segmental glomerulosclerosis, cerebral ischaemic lesions and premature atherosclerosis were identified. Clinically unexpected findings included a paucity of B cells in the peripheral lymphoid organs, emperipolesis-like (penetration of one cell by another) abnormalities in the adenohypophysis, fatty infiltration of the cardiac right ventricular wall, pulmonary emphysema, testicular hypoplasia with atrophy and azospermia, and clustering of small cerebral vessels. CONCLUSIONS A regulatory role for the SMARCAL1 protein in the proliferation of chondrocytes, lymphocytes and spermatozoa, as well as in the development or maintenance of cardiomyocytes and in vascular homoeostasis, is suggested. Additional clinical management guidelines are recommended as this study has shown that patients with SIOD may be at risk of pulmonary hypertension, combined immunodeficiency, subcortical ischaemic dementia and cardiac dysfunction.
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Affiliation(s)
- J Marietta Clewing
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Flaus A, Martin DMA, Barton GJ, Owen-Hughes T. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res 2006; 34:2887-905. [PMID: 16738128 PMCID: PMC1474054 DOI: 10.1093/nar/gkl295] [Citation(s) in RCA: 534] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 03/18/2006] [Accepted: 04/05/2006] [Indexed: 12/14/2022] Open
Abstract
The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.
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Affiliation(s)
- Andrew Flaus
- Division of Gene Regulation and Expression, University of DundeeDundee DD1 5EH, Scotland, UK
- Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of DundeeDundee DD1 5EH, Scotland, UK
| | - David M. A. Martin
- Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of DundeeDundee DD1 5EH, Scotland, UK
| | - Geoffrey J. Barton
- Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of DundeeDundee DD1 5EH, Scotland, UK
| | - Tom Owen-Hughes
- To whom correspondence should be addressed. Tel: +44 0 1382 385796; Fax: +44 0 1382 388702;
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Affiliation(s)
- Smita S Patel
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA.
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Elizondo LI, Huang C, Northrop JL, Deguchi K, Clewing JM, Armstrong DL, Boerkoel CF. Schimke immuno-osseous dysplasia: a cell autonomous disorder? Am J Med Genet A 2006; 140:340-8. [PMID: 16419127 DOI: 10.1002/ajmg.a.31089] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like protein 1) encodes a SWI/SNF ATP-dependent chromatin remodeling protein. Mutations in SMARCAL1 cause the autosomal-recessive multisystem disorder Schimke immuno-osseous dysplasia (SIOD); this suggests that the SMARCAL1 protein is involved in the development or maintenance of multiple organs. Disease within these many tissues could arise by a cell autonomous or a cell non-autonomous mechanism. Consistent with a cell autonomous mechanism, we did not find any disease recurrence in transplanted organs or protection of other tissues by the organ grafts. In order to better understand the role of SMARCAL1 during normal development and in the pathogenesis of SIOD, we characterized the spatial and temporal expression of the murine homolog (Smarcal1). The Smarcal1 mRNA and protein were expressed throughout development and in all tissues affected in patients with SIOD including the bone, kidney, thymus, thyroid, tooth, bone marrow, hair, eye, and blood vessels. Significantly, the expression profile of Smarcal1 in the mouse has led us to reexamine and identify novel pathology in our patient population resulting in changes in the clinical management of SIOD. The expression of Smarcal1 in affected tissues and the non-recurrence of disease in grafted organs lead us to hypothesize a cell autonomous function for SMARCAL1 and to propose tissue-specific mechanisms for the pathophysiology of SIOD.
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Affiliation(s)
- Leah I Elizondo
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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Bökenkamp A, deJong M, van Wijk JAE, Block D, van Hagen JM, Ludwig M. R561C missense mutation in the SMARCAL1 gene associated with mild Schimke immuno-osseous dysplasia. Pediatr Nephrol 2005; 20:1724-8. [PMID: 16237566 DOI: 10.1007/s00467-005-2047-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 05/08/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Autosomal-recessive Schimke immuno-osseous dysplasia (SIOD) characterized by spondyloepiphyseal dysplasia, focal-segmental glomerulosclerosis (FSGS), T-cell immunodeficiency and facial dysmorphism is caused by defects in the SMARCAL1 gene. The gene product is involved in the transcriptional regulation of other genes. A 12-year-old boy of consanginous Turkish descent developed disproportionate short stature from spondyloepiphyseal dysplasia at the age of 6 and nephrotic syndrome at the age of 10 years. Renal biopsy revealed FSGS, the kidney function was normal, T-lymphocytes were diminished without infectious complications, and he has had no cerebral ischemia. Analysis of the patient's SMARCAL1 gene revealed a novel homozygous C1798T transition leading to a R561C substitution. The parents and two healthy sisters were found to be heterozygous. A younger brother, who is also homozygous for the mutation, is clinically asymptomatic and has no proteinuria at the age of 18 months. Still, his CD4 cells are diminished. For SMARCAL1 mutations a clear genotype-phenotype correlation has been reported: severe SIOD with in utero or early-childhood onset leading to end-stage renal disease within a few years is caused by nonsense, frame shift or splice mutations. Many patients die from infections and cerebrovascular insults during childhood. Mild SIOD manifests later and progresses more slowly without infectious or cerebral vascular complications--the underlying defect being missense mutations in all three patients reported so far. The novel R561C missense mutation in our patient with mild SIOD is additional evidence for the genotype-phenotype correlation reported for SMARCAL1 mutations.
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Affiliation(s)
- Arend Bökenkamp
- Department of Pediatrics, Vrije University Medical Center, Amsterdam, The Netherlands.
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50
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Bakshi R, Mehta AK, Sharma R, Maiti S, Pasha S, Brahmachari V. Characterization of a human SWI2/SNF2 like protein hINO80: demonstration of catalytic and DNA binding activity. Biochem Biophys Res Commun 2005; 339:313-20. [PMID: 16298340 DOI: 10.1016/j.bbrc.2005.10.206] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2005] [Accepted: 10/27/2005] [Indexed: 11/29/2022]
Abstract
The proteins belonging to SWI2/SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. We have identified a human gene with a putative DNA binding domain, which belongs to the INO80 subfamily of SWI2/SNF2 proteins. Here we report the cloning, expression, and functional activity of the domains from hINO80 gene both in terms of the DNA dependent ATPase as well as DNA binding activity. A differential expression of the various domains within this gene is detected in human tissues while a ubiquitous expression is detected in mice. The intranuclear localization is demonstrated using antibodies directed against the DBINO domain of hINO80.
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Affiliation(s)
- Rachit Bakshi
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
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