1
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Du Q, Zhang M, Gao A, He T, Guo M. Epigenetic silencing ZSCAN23 promotes pancreatic cancer growth by activating Wnt signaling. Cancer Biol Ther 2024; 25:2302924. [PMID: 38226836 PMCID: PMC10793710 DOI: 10.1080/15384047.2024.2302924] [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: 11/06/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most malignant tumor. Zinc finger and SCAN domain-containing protein 23 (ZSCAN23) is a new member of the SCAN domain family. The expression regulation and biological function remain to be elucidated. In this study, we explored the epigenetic regulation and the function of ZSCAN23 in PDAC. ZSCAN23 was methylated in 60.21% (171/284) of PDAC and its expression was regulated by promoter region methylation. The expression of ZSCAN23 inhibited cell proliferation, colony formation, migration, invasion, and induced apoptosis and G1/S phase arrest. ZSCAN23 suppressed Panc10.05 cell xenograft growth in mice. Mechanistically, ZSCAN23 inhibited Wnt signaling by interacting with myosin heavy chain 9 (MYH9) in pancreatic cancer cells. ZSCAN23 is frequently methylated in PDAC and may serve as a detective marker. ZSCAN23 suppresses PDAC cell growth both in vitro and in vivo.
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Affiliation(s)
- Qian Du
- Department of Gastroenterology and Hepatology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, People's Republic of China
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Meiying Zhang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Aiai Gao
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Tao He
- Department of Pathology, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, People's Republic of China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
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2
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Cauret CMS, Jordan DC, Kukoly LM, Burton SR, Anele EU, Kwiecien JM, Gansauge MT, Senthillmohan S, Greenbaum E, Meyer M, Horb ME, Evans BJ. Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis. PLoS Genet 2023; 19:e1010990. [PMID: 37792893 PMCID: PMC10578606 DOI: 10.1371/journal.pgen.1010990] [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: 03/07/2023] [Revised: 10/16/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) and that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires dm-w but that scan-w and ccdc69-w are not essential for viability, female development, or fertility. Analysis of mesonephros+gonad transcriptomes during sexual differentiation illustrates masculinization of the dm-w knockout transcriptome, and identifies mostly non-overlapping sets of differentially expressed genes in separate knockout lines for each of these three W-specific gene compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of dm-w is present in only a subset of species that carry this gene. These findings map out a dynamic evolutionary history of a newly evolved W chromosome-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.
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Affiliation(s)
- Caroline M. S. Cauret
- Biology Department, McMaster University, Hamilton, Ontario, Canada
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Danielle C. Jordan
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
- The School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Sarah R. Burton
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
| | - Emmanuela U. Anele
- Biology Department, McMaster University, Hamilton, Ontario, Canada
- Department Zoology, Ahmadu Bello University, Zaria, Nigeria
| | - Jacek M. Kwiecien
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Eli Greenbaum
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marko E. Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
| | - Ben J. Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
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Li Q, Tan G, Wu F. The functions and roles of C2H2 zinc finger proteins in hepatocellular carcinoma. Front Physiol 2023; 14:1129889. [PMID: 37457025 PMCID: PMC10339807 DOI: 10.3389/fphys.2023.1129889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
C2H2 zinc finger (C2H2-ZF) proteins are the majority group of human transcription factors and they have many different molecular functions through different combinations of zinc finger domains. Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors and the main reason for cancer-related deaths worldwide. More and more findings support the abnormal expression of C2H2-ZF protein in the onset and progression of HCC. The C2H2-ZF proteins are involved in various biological functions in HCC, such as EMT, stemness maintenance, metabolic reprogramming, cell proliferation and growth, apoptosis, and genomic integrity. The study of anti-tumor drug resistance also highlights the pivotal roles of C2H2-ZF proteins at the intersection of biological functions (EMT, stemness maintenance, autophagy)and chemoresistance in HCC. The involvement of C2H2-ZF protein found recently in regulating different molecules, signal pathways and pathophysiological activities indicate these proteins as the possible therapeutic targets, and diagnostic or prognostic biomarkers for HCC.
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Sheta M, Yoshida K, Kanemoto H, Calderwood SK, Eguchi T. Stress-Inducible SCAND Factors Suppress the Stress Response and Are Biomarkers for Enhanced Prognosis in Cancers. Int J Mol Sci 2023; 24:ijms24065168. [PMID: 36982267 PMCID: PMC10049278 DOI: 10.3390/ijms24065168] [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: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
The cell stress response is an essential system present in every cell for responding and adapting to environmental stimulations. A major program for stress response is the heat shock factor (HSF)–heat shock protein (HSP) system that maintains proteostasis in cells and promotes cancer progression. However, less is known about how the cell stress response is regulated by alternative transcription factors. Here, we show that the SCAN domain (SCAND)-containing transcription factors (SCAN-TFs) are involved in repressing the stress response in cancer. SCAND1 and SCAND2 are SCAND-only proteins that can hetero-oligomerize with SCAN-zinc finger transcription factors, such as MZF1(ZSCAN6), for accessing DNA and transcriptionally co-repressing target genes. We found that heat stress induced the expression of SCAND1, SCAND2, and MZF1 bound to HSP90 gene promoter regions in prostate cancer cells. Moreover, heat stress switched the transcript variants’ expression from long noncoding RNA (lncRNA-SCAND2P) to protein-coding mRNA of SCAND2, potentially by regulating alternative splicing. High expression of HSP90AA1 correlated with poorer prognoses in several cancer types, although SCAND1 and MZF1 blocked the heat shock responsiveness of HSP90AA1 in prostate cancer cells. Consistent with this, gene expression of SCAND2, SCAND1, and MZF1 was negatively correlated with HSP90 gene expression in prostate adenocarcinoma. By searching databases of patient-derived tumor samples, we found that MZF1 and SCAND2 RNA were more highly expressed in normal tissues than in tumor tissues in several cancer types. Of note, high RNA expression of SCAND2, SCAND1, and MZF1 correlated with enhanced prognoses of pancreatic cancer and head and neck cancers. Additionally, high expression of SCAND2 RNA was correlated with better prognoses of lung adenocarcinoma and sarcoma. These data suggest that the stress-inducible SCAN-TFs can function as a feedback system, suppressing excessive stress response and inhibiting cancers.
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Affiliation(s)
- Mona Sheta
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Kunihiro Yoshida
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Hideka Kanemoto
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Takanori Eguchi
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Correspondence: ; Tel.: +81-86-235-6661
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Eguchi T, Csizmadia E, Kawai H, Sheta M, Yoshida K, Prince TL, Wegiel B, Calderwood SK. SCAND1 Reverses Epithelial-to-Mesenchymal Transition (EMT) and Suppresses Prostate Cancer Growth and Migration. Cells 2022; 11:cells11243993. [PMID: 36552758 PMCID: PMC9777339 DOI: 10.3390/cells11243993] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a reversible cellular program that transiently places epithelial (E) cells into pseudo-mesenchymal (M) cell states. The malignant progression and resistance of many carcinomas depend on EMT activation, partial EMT, or hybrid E/M status in neoplastic cells. EMT is activated by tumor microenvironmental TGFβ signal and EMT-inducing transcription factors, such as ZEB1/2, in tumor cells. However, reverse EMT factors are less studied. We demonstrate that prostate epithelial transcription factor SCAND1 can reverse the cancer cell mesenchymal and hybrid E/M phenotypes to a more epithelial, less invasive status and inhibit their proliferation and migration in DU-145 prostate cancer cells. SCAND1 is a SCAN domain-containing protein and hetero-oligomerizes with SCAN-zinc finger transcription factors, such as MZF1, for accessing DNA and the transcriptional co-repression of target genes. We found that SCAND1 expression correlated with maintaining epithelial features, whereas the loss of SCAND1 was associated with mesenchymal phenotypes of tumor cells. SCAND1 and MZF1 were mutually inducible and coordinately included in chromatin with hetero-chromatin protein HP1γ. The overexpression of SCAND1 reversed hybrid E/M status into an epithelial phenotype with E-cadherin and β-catenin relocation. Consistently, the co-expression analysis in TCGA PanCancer Atlas revealed that SCAND1 and MZF1 expression was negatively correlated with EMT driver genes, including CTNNB1, ZEB1, ZEB2 and TGFBRs, in prostate adenocarcinoma specimens. In addition, SCAND1 overexpression suppressed tumor cell proliferation by reducing the MAP3K-MEK-ERK signaling pathway. Of note, in a mouse tumor xenograft model, SCAND1 overexpression significantly reduced Ki-67(+) and Vimentin(+) tumor cells and inhibited migration and lymph node metastasis of prostate cancer. Kaplan-Meier analysis showed high expression of SCAND1 and MZF1 to correlate with better prognoses in pancreatic cancer and head and neck cancers, although with poorer prognosis in kidney cancer. Overall, these data suggest that SCAND1 induces expression and coordinated heterochromatin-binding of MZF1 to reverse the hybrid E/M status into an epithelial phenotype and, inhibits tumor cell proliferation, migration, and metastasis, potentially by repressing the gene expression of EMT drivers and the MAP3K-MEK-ERK signaling pathway.
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Affiliation(s)
- Takanori Eguchi
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Correspondence: (T.E.); (S.K.C.); Tel.: +81-86-235-6661 (T.E.); +1-617-667-4240 (S.K.C.); Fax: +81-86-235-6664 (T.E.); +1-617-667-4245 (S.K.C.)
| | - Eva Csizmadia
- Division of Surgical Sciences, Department of Surgery, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Hotaka Kawai
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Mona Sheta
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Kunihiro Yoshida
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Oral and Craniofacial Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | | | - Barbara Wegiel
- Division of Surgical Sciences, Department of Surgery, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: (T.E.); (S.K.C.); Tel.: +81-86-235-6661 (T.E.); +1-617-667-4240 (S.K.C.); Fax: +81-86-235-6664 (T.E.); +1-617-667-4245 (S.K.C.)
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6
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Greenwell AM, Baughan S, Altinok D, Marupudi NI, Kupsky W, Kumar-Sinha C, Gorsi HS. Lorlatinib for the Treatment of ALK Fusion–Positive Infant-Type Hemispheric Glioma: A Case Report. JCO Precis Oncol 2022; 6:e2200255. [DOI: 10.1200/po.22.00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
| | - Scott Baughan
- Wayne State University School of Medicine, Detroit, MI
| | - Deniz Altinok
- Department of Radiology, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI
| | - Neena I. Marupudi
- Department of Pediatric Neurosurgery, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI
| | - William Kupsky
- Department of Pathology, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI
| | - Chandan Kumar-Sinha
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Hamza S. Gorsi
- Department of Hematology/Oncology, Children's Hospital of Michigan, Central Michigan University School of Medicine, Mount Pleasant, MI
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7
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Mandel‐Brehm C, Benson LA, Tran B, Kung AF, Mann SA, Vazquez SE, Retallack H, Sample HA, Zorn KC, Khan LM, Kerr LM, McAlpine PL, Zhang L, McCarthy F, Elias JE, Katwa U, Astley CM, Tomko S, Dalmau J, Seeley WW, Pleasure SJ, Wilson MR, Gorman MP, DeRisi JL. ZSCAN1 Autoantibodies Are Associated with Pediatric Paraneoplastic ROHHAD. Ann Neurol 2022; 92:279-291. [PMID: 35466441 PMCID: PMC9329235 DOI: 10.1002/ana.26380] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation and Autonomic Dysregulation (ROHHAD), is a severe pediatric disorder of uncertain etiology resulting in hypothalamic dysfunction and frequent sudden death. Frequent co-occurrence of neuroblastic tumors have fueled suspicion of an autoimmune paraneoplastic neurological syndrome (PNS); however, specific anti-neural autoantibodies, a hallmark of PNS, have not been identified. Our objective is to determine if an autoimmune paraneoplastic etiology underlies ROHHAD. METHODS Immunoglobulin G (IgG) from pediatric ROHHAD patients (n = 9), non-inflammatory individuals (n = 100) and relevant pediatric controls (n = 25) was screened using a programmable phage display of the human peptidome (PhIP-Seq). Putative ROHHAD-specific autoantibodies were orthogonally validated using radioactive ligand binding and cell-based assays. Expression of autoantibody targets in ROHHAD tumor and healthy brain tissue was assessed with immunohistochemistry and mass spectrometry, respectively. RESULTS Autoantibodies to ZSCAN1 were detected in ROHHAD patients by PhIP-Seq and orthogonally validated in 7/9 ROHHAD patients and 0/125 controls using radioactive ligand binding and cell-based assays. Expression of ZSCAN1 in ROHHAD tumor and healthy human brain tissue was confirmed. INTERPRETATION Our results support the notion that tumor-associated ROHHAD syndrome is a pediatric PNS, potentially initiated by an immune response to peripheral neuroblastic tumor. ZSCAN1 autoantibodies may aid in earlier, accurate diagnosis of ROHHAD syndrome, thus providing a means toward early detection and treatment. This work warrants follow-up studies to test sensitivity and specificity of a novel diagnostic test. Last, given the absence of the ZSCAN1 gene in rodents, our study highlights the value of human-based approaches for detecting novel PNS subtypes. ANN NEUROL 2022;92:279-291.
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Affiliation(s)
- Caleigh Mandel‐Brehm
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | | | - Baouyen Tran
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Andrew F. Kung
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Sabrina A. Mann
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Sara E. Vazquez
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Hanna Retallack
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Hannah A. Sample
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Kelsey C. Zorn
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Lillian M. Khan
- Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
| | - Lauren M. Kerr
- Department of NeurologyBoston Children's HospitalBostonMAUSA
| | - Patrick L. McAlpine
- Otolaryngology Head and Neck Surgery Research DivisionStanford UniversityStanfordCAUSA
| | | | | | | | - Umakanth Katwa
- Department of Pulmonary MedicineSleep Center, Boston Children's HospitalBostonMAUSA
| | - Christina M. Astley
- Division of Endocrinology & Computational EpidemiologyBoston Children's HospitalBostonMAUSA
| | - Stuart Tomko
- Department of NeurologyWashington UniversitySt. LouisMOUSA
| | - Josep Dalmau
- Catalan Institution for Research and Advanced Studies (ICREA), Hospital Clinic‐IdibapsUniversity of BarcelonaBarcelonaSpain
| | - William W. Seeley
- Memory and Aging Center, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Michael R. Wilson
- MAS, Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Mark P. Gorman
- Department of NeurologyHarvard Medical SchoolBostonMAUSA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoCAUSA
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8
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Nakamura-Utsunomiya A. Autoimmunity Related to Adipsic Hypernatremia and ROHHAD Syndrome. Int J Mol Sci 2022; 23:ijms23136899. [PMID: 35805903 PMCID: PMC9266522 DOI: 10.3390/ijms23136899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
Specific antibody responses to subfornical organs, including Nax antibody, have been reported in patients with adipsic hypernatremia of unknown etiology who do not have structural lesions in the hypothalamic–pituitary gland. The subfornical organ, also referred to as the window of the brain, is a sensing site that monitors sodium and osmotic pressure levels. On the other hand, ROHHAD syndrome is a rare disease for which the etiology of the hypothalamic disorder is unknown, and there have been some reports in recent years describing its association with autoimmune mechanisms. In addition, abnormal Na levels, including hypernatremia, are likely to occur in this syndrome. When comparing the clinical features of adipsic hypernatremia due to autoimmune mechanisms and ROHHAD syndrome, there are similar hypothalamic–pituitary dysfunction symptoms in addition to abnormal Na levels. Since clinical diagnoses of autoimmunological adipsic hypernatremia and ROHAD syndrome might overlap, we need to understand the essential etiology and carry out precise assessments to accurately diagnose patients and provide effective treatment. In this review, I review the literature on the autoimmune mechanism reported in recent years and describe the findings obtained so far and future directions.
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Affiliation(s)
- Akari Nakamura-Utsunomiya
- Department of Genetic Medicine, Hiroshima University Graduate School, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8511, Japan;
- Department of Pediatrics, Hiroshima University Graduate School, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8511, Japan
- Division of Neonatal Screening, National Center for Child Health and Development, 2 Chome-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
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9
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Bonchuk AN, Boyko KM, Nikolaeva AY, Burtseva AD, Popov VO, Georgiev PG. Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity. Structure 2022; 30:1004-1015.e4. [DOI: 10.1016/j.str.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
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10
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Zurowska K, Alam A, Ganser-Pornillos BK, Pornillos O. Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins. Proteins 2022; 90:309-313. [PMID: 34357660 PMCID: PMC8671222 DOI: 10.1002/prot.26204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 01/03/2023]
Abstract
The Gag proteins of retroviruses play an essential role in virus particle assembly by forming a protein shell or capsid and thus generating the virion compartment. A variety of human proteins have now been identified with structural similarity to one or more of the major Gag domains. These human proteins are thought to have been evolved or "domesticated" from ancient integrations due to retroviral infections or retrotransposons. Here, we report that X-ray crystal structures of stably folded domains of MOAP1 (modulator of apoptosis 1) and PEG10 (paternally expressed gene 10) are highly similar to the C-terminal capsid (CA) domains of cognate Gag proteins. The structures confirm classification of MOAP1 and PEG10 as domesticated Gags, and suggest that these proteins may have preserved some of the key interactions that facilitated assembly of their ancestral Gags into capsids.
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Affiliation(s)
- Katarzyna Zurowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ayaan Alam
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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11
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Bai L, Yang G, Qin Z, Lyu J, Wang Y, Feng J, Liu M, Gong T, Li X, Li Z, Li J, Qin J, Yang W, Ding C. Proteome-Wide Profiling of Readers for DNA Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101426. [PMID: 34351703 PMCID: PMC8498917 DOI: 10.1002/advs.202101426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Indexed: 05/13/2023]
Abstract
DNA modifications, represented by 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), play important roles in epigenetic regulation of biological processes. The specific recognition of DNA modifications by the transcriptional protein machinery is thought to be a potential mechanism for epigenetic-driven gene regulation, and many modified DNA-specific binding proteins have been uncovered. However, the panoramic view of the roles of DNA modification readers at the proteome level remains largely unclear. Here, a recently developed concatenated tandem array of consensus transcription factor (TF) response elements (catTFREs) approach is employed to profile the binding activity of TFs at DNA modifications. Modified DNA-binding activity is quantified for 1039 TFs, representing 70% of the TFs in the human genome. Additionally, the modified DNA-binding activity of 600 TFs is monitored during the mouse brain development from the embryo to the adult stages. Readers of these DNA modifications are predicted, and the hierarchical networks between the transcriptional protein machinery and modified DNA are described. It is further demonstrated that ZNF24 and ZSCAN21 are potential readers of 5fC-modified DNA. This study provides a landscape of TF-DNA modification interactions that can be used to elucidate the epigenetic-related transcriptional regulation mechanisms under physiological conditions.
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Affiliation(s)
- Lin Bai
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Guojian Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Jiacheng Lyu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Jinwen Feng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Mingwei Liu
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein Sciences (The PHOENIX Center, Beijing)Institute of LifeomicsBeijing102206China
| | - Tongqing Gong
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein Sciences (The PHOENIX Center, Beijing)Institute of LifeomicsBeijing102206China
| | - Xianju Li
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein Sciences (The PHOENIX Center, Beijing)Institute of LifeomicsBeijing102206China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
| | - Jun Qin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein Sciences (The PHOENIX Center, Beijing)Institute of LifeomicsBeijing102206China
| | - Wenjun Yang
- Department of Pediatric OrthopedicsXin Hua Hospital AffiliatedShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesInstitute of Biomedical SciencesHuman Phenome InstituteZhongshan HospitalFudan UniversityShanghai200433China
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12
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Abstract
LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.
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Affiliation(s)
- Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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13
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Neill T, Kapoor A, Xie C, Buraschi S, Iozzo RV. A functional outside-in signaling network of proteoglycans and matrix molecules regulating autophagy. Matrix Biol 2021; 100-101:118-149. [PMID: 33838253 PMCID: PMC8355044 DOI: 10.1016/j.matbio.2021.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023]
Abstract
Proteoglycans and selected extracellular matrix constituents are emerging as intrinsic and critical regulators of evolutionarily conversed, intracellular catabolic pathways. Often, these secreted molecules evoke sustained autophagy in a variety of cell types, tissues, and model systems. The unique properties of proteoglycans have ushered in a paradigmatic shift to broaden our understanding of matrix-mediated signaling cascades. The dynamic cellular pathway controlling autophagy is now linked to an equally dynamic and fluid signaling network embedded in a complex meshwork of matrix molecules. A rapidly emerging field of research encompasses multiple matrix-derived candidates, representing a menagerie of soluble matrix constituents including decorin, biglycan, endorepellin, endostatin, collagen VI and plasminogen kringle 5. These matrix constituents are pro-autophagic and simultaneously anti-angiogenic. In contrast, perlecan, laminin α2 chain, and lumican have anti-autophagic functions. Mechanistically, each matrix constituent linked to intracellular catabolic events engages a specific cell surface receptor that often converges on a common core of the autophagic machinery including AMPK, Peg3 and Beclin 1. We consider this matrix-evoked autophagy as non-canonical given that it occurs in an allosteric manner and is independent of nutrient availability or prevailing bioenergetics control. We propose that matrix-regulated autophagy is an important outside-in signaling mechanism for proper tissue homeostasis that could be therapeutically leveraged to combat a variety of diseases.
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Affiliation(s)
- Thomas Neill
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| | - Aastha Kapoor
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Christopher Xie
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Simone Buraschi
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Renato V Iozzo
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
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14
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Bonchuk A, Boyko K, Fedotova A, Nikolaeva A, Lushchekina S, Khrustaleva A, Popov V, Georgiev P. Structural basis of diversity and homodimerization specificity of zinc-finger-associated domains in Drosophila. Nucleic Acids Res 2021; 49:2375-2389. [PMID: 33638995 PMCID: PMC7913770 DOI: 10.1093/nar/gkab061] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
In arthropods, zinc finger-associated domains (ZADs) are found at the N-termini of many DNA-binding proteins with tandem arrays of Cys2-His2 zinc fingers (ZAD-C2H2 proteins). ZAD-C2H2 proteins undergo fast evolutionary lineage-specific expansion and functional diversification. Here, we show that all ZADs from Drosophila melanogaster form homodimers, but only certain ZADs with high homology can also heterodimerize. CG2712, for example, is unable to heterodimerize with its paralog, the previously characterized insulator protein Zw5, with which it shares 46% homology. We obtained a crystal structure of CG2712 protein's ZAD domain that, in spite of a low sequence homology, has similar spatial organization with the only known ZAD structure (from Grauzone protein). Steric clashes prevented the formation of heterodimers between Grauzone and CG2712 ZADs. Using detailed structural analysis, site-directed mutagenesis, and molecular dynamics simulations, we demonstrated that rapid evolutionary acquisition of interaction specificity was mediated by the more energy-favorable formation of homodimers in comparison to heterodimers, and that this specificity was achieved by multiple amino acid substitutions resulting in the formation or breaking of stabilizing interactions. We speculate that specific homodimerization of ZAD-C2H2 proteins is important for their architectural role in genome organization.
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Affiliation(s)
- Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Konstantin Boyko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anna Fedotova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alena Nikolaeva
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- National Research Center «Kurchatov Institute», Moscow 123182, Russia
| | - Sofya Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anastasia Khrustaleva
- Department of the Bioinformatics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladimir Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
- National Research Center «Kurchatov Institute», Moscow 123182, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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15
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Brix DM, Bundgaard Clemmensen KK, Kallunki T. Zinc Finger Transcription Factor MZF1-A Specific Regulator of Cancer Invasion. Cells 2020; 9:cells9010223. [PMID: 31963147 PMCID: PMC7016646 DOI: 10.3390/cells9010223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022] Open
Abstract
Over 90% of cancer deaths are due to cancer cells metastasizing into other organs. Invasion is a prerequisite for metastasis formation. Thus, inhibition of invasion can be an efficient way to prevent disease progression in these patients. This could be achieved by targeting the molecules regulating invasion. One of these is an oncogenic transcription factor, Myeloid Zinc Finger 1 (MZF1). Dysregulated transcription factors represent a unique, increasing group of drug targets that are responsible for aberrant gene expression in cancer and are important nodes driving cancer malignancy. Recent studies report of a central involvement of MZF1 in the invasion and metastasis of various solid cancers. In this review, we summarize the research on MZF1 in cancer including its function and role in lysosome-mediated invasion and in the expression of genes involved in epithelial to mesenchymal transition. We also discuss possible means to target it on the basis of the current knowledge of its function in cancer.
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Affiliation(s)
- Ditte Marie Brix
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (D.M.B.); (K.K.B.C.)
- Danish Medicines Council, Dampfærgevej 27-29, 2100 Copenhagen, Denmark
| | - Knut Kristoffer Bundgaard Clemmensen
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (D.M.B.); (K.K.B.C.)
| | - Tuula Kallunki
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; (D.M.B.); (K.K.B.C.)
- Department of Drug Design and Pharmacology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: ; Tel.: +45-35-25-7746
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16
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Lambrughi M, Tiberti M, Allega MF, Sora V, Nygaard M, Toth A, Salamanca Viloria J, Bignon E, Papaleo E. Analyzing Biomolecular Ensembles. Methods Mol Biol 2019; 2022:415-451. [PMID: 31396914 DOI: 10.1007/978-1-4939-9608-7_18] [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] [Indexed: 06/10/2023]
Abstract
Several techniques are available to generate conformational ensembles of proteins and other biomolecules either experimentally or computationally. These methods produce a large amount of data that need to be analyzed to identify structure-dynamics-function relationship. In this chapter, we will cover different tools to unveil the information hidden in conformational ensemble data and to guide toward the rationalization of the data. We included routinely used approaches such as dimensionality reduction, as well as new methods inspired by high-order statistics and graph theory.
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Affiliation(s)
- Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Maria Francesca Allega
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Valentina Sora
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mads Nygaard
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Agota Toth
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Juan Salamanca Viloria
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emmanuelle Bignon
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.
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17
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Zhang X, Zhou H, Zhang Y, Cai L, Jiang G, Li A, Miao Y, Li Q, Qiu X, Wang E. ZNF452 facilitates tumor proliferation and invasion via activating AKT-GSK3β signaling pathway and predicts poor prognosis of non-small cell lung cancer patients. Oncotarget 2018; 8:38863-38875. [PMID: 28418919 PMCID: PMC5503578 DOI: 10.18632/oncotarget.16408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/24/2017] [Indexed: 01/05/2023] Open
Abstract
ZNF452 is a zinc-finger protein family member which contains an isolated SCAN (SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) zinc-finger domain. Despite the SCAN N-terminus domain is known to play a role in transcriptional regulation of genes involved in cell survival and differentiation, there are no precise cellular functions that have been assigned to ZNF452. In the present study, we found that either endogenous or exogenous ZNF452 was overexpressed in the cytoplasm of NSCLC cells and positive ratio of ZNF452 in NSCLC samples (50.8%, 93/183) was significantly higher than that in normal lung tissues (22.4%, 13/58, P<0.001). ZNF452 overexpression was correlated with advanced TNM stage (P=0.033), positive lymph node metastasis (P=0.002) and predicted poor overall survival of NSCLC patients (P<0.001). ZNF452 facilitated tumor growth, colony formation, G1-S phase arrest, migration and invasion through upregulating the levels of CyclinD1, CyclinE1, p-Rb, or Snail, and downregulating the expression of Zo-1. In nude mice xenografts, overexpressing ZNF452 also promoted tumor proliferation and metastasis. Subsequently, we found that the effect of ZNF452 on facilitating tumor proliferation and invasion was through activating its downstream AKT-GSK3β signaling pathway. Treatment of AKT inhibitor markedly prevented the phosphorylation of AKT and GSK3β which subsequently counteracted increasing expression of CyclinD1, CyclinE1 or Snail and restored the decreasing expression of Zo-1, as well as the upregulation of tumor proliferation and invasion, caused by ZNF452 overexpression. Taken together, the present study indicated that ZNF452 may be an upstream regulator of AKT-GSK3β signaling pathway and facilitates proliferation and invasion of NSCLC.
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Affiliation(s)
- Xiupeng Zhang
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haijing Zhou
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yong Zhang
- Department of Pathology, Cancer Hospital of China Medical University, Shenyang, China
| | - Lin Cai
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Guiyang Jiang
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ailin Li
- Department of Radiotherapy, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yuan Miao
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qingchang Li
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueshan Qiu
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Enhua Wang
- Department of Pathology, College of Basic Medicine Science and First Affiliated Hospital of China Medical University, Shenyang, China
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18
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Fonseca LFS, Gimenez DFJ, Dos Santos Silva DB, Barthelson R, Baldi F, Ferro JA, Albuquerque LG. Differences in global gene expression in muscle tissue of Nellore cattle with divergent meat tenderness. BMC Genomics 2017; 18:945. [PMID: 29202705 PMCID: PMC5716225 DOI: 10.1186/s12864-017-4323-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
Background Meat tenderness is the consumer’s most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the high percentage of Zebu genes in the Brazilian cattle population, mainly Nellore cattle, the improvement of meat tenderness is important since the increasing proportion of Zebu genes in the population reduces meat tenderness. However, the measurement of this trait is difficult once it can only be made after animal slaughtering. New technologies such as RNA-Seq have been used to increase our understanding of the genetic processes regulating quantitative traits phenotypes. The objective of this study was to identify differentially expressed genes related to meat tenderness, in Nellore cattle in order to elucidate the genetic factors associated with meat quality. Samples were collected 24 h postmortem and the meat was not aged. Results We found 40 differentially expressed genes related to meat tenderness, 17 with known functions. Fourteen genes were up-regulated and 3 were down-regulated in the tender meat group. Genes related to ubiquitin metabolism, transport of molecules such as calcium and oxygen, acid-base balance, collagen production, actin, myosin, and fat were identified. The PCP4L1 (Purkinje cell protein 4 like 1) and BoLA-DQB (major histocompatibility complex, class II, DQ beta) genes were validated by qRT-PCR. The results showed relative expression values similar to those obtained by RNA-Seq, with the same direction of expression (i.e., the two techniques revealed higher expression of PCP4L1 in tender meat samples and of BoLA-DQB in tough meat samples). Conclusions This study revealed the differential expression of genes and functions in Nellore cattle muscle tissue, which may contain potential biomarkers involved in meat tenderness. Electronic supplementary material The online version of this article (10.1186/s12864-017-4323-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Fernando Baldi
- Faculty of Agricultural and Veterinary Sciences, São Paulo State University, FCAV/UNESP, Jaboticabal, São Paulo, Brazil
| | - Jesus Aparecido Ferro
- Faculty of Agricultural and Veterinary Sciences, São Paulo State University, FCAV/UNESP, Jaboticabal, São Paulo, Brazil
| | - Lucia Galvão Albuquerque
- Faculty of Agricultural and Veterinary Sciences, São Paulo State University, FCAV/UNESP, Jaboticabal, São Paulo, Brazil
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19
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Nygaard M, Terkelsen T, Vidas Olsen A, Sora V, Salamanca Viloria J, Rizza F, Bergstrand-Poulsen S, Di Marco M, Vistesen M, Tiberti M, Lambrughi M, Jäättelä M, Kallunki T, Papaleo E. The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer. Front Mol Biosci 2016; 3:78. [PMID: 28018905 PMCID: PMC5156680 DOI: 10.3389/fmolb.2016.00078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/17/2016] [Indexed: 11/24/2022] Open
Abstract
SCAN domains in zinc-finger transcription factors are crucial mediators of protein-protein interactions. Up to 240 SCAN-domain encoding genes have been identified throughout the human genome. These include cancer-related genes, such as the myeloid zinc finger 1 (MZF1), an oncogenic transcription factor involved in the progression of many solid cancers. The mechanisms by which SCAN homo- and heterodimers assemble and how they alter the transcriptional activity of zinc-finger transcription factors in cancer and other diseases remain to be investigated. Here, we provide the first description of the conformational ensemble of the MZF1 SCAN domain cross-validated against NMR experimental data, which are probes of structure and dynamics on different timescales. We investigated the protein-protein interaction network of MZF1 and how it is perturbed in different cancer types by the analyses of high-throughput proteomics and RNASeq data. Collectively, we integrated many computational approaches, ranging from simple empirical energy functions to all-atom microsecond molecular dynamics simulations and network analyses to unravel the effects of cancer-related substitutions in relation to MZF1 structure and interactions.
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Affiliation(s)
- Mads Nygaard
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Thilde Terkelsen
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - André Vidas Olsen
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Valentina Sora
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Juan Salamanca Viloria
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Fabio Rizza
- Department of Biomedical Sciences, University of Padua Padua, Italy
| | - Sanne Bergstrand-Poulsen
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Miriam Di Marco
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Mette Vistesen
- Cell Stress and Survival Unit and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Matteo Tiberti
- Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Matteo Lambrughi
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Marja Jäättelä
- Unit of Cell Death and Metabolism and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Tuula Kallunki
- Unit of Cell Death and Metabolism and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center Copenhagen, Denmark
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20
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Eguchi T, Prince T, Wegiel B, Calderwood SK. Role and Regulation of Myeloid Zinc Finger Protein 1 in Cancer. J Cell Biochem 2016; 116:2146-54. [PMID: 25903835 DOI: 10.1002/jcb.25203] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022]
Abstract
Myeloid zinc finger 1 (MZF1) belongs to the SCAN-Zinc Finger (SCAN-ZF) transcription factor family that has recently been implicated in a number of types of cancer. Although the initial studies concentrated on the role of MZF1 in myeloid differentiation and leukemia, the factor now appears to be involved in the etiology of major solid tumors such as lung, cervical, breast, and colorectal cancer. Here we discuss the regulation of MZF1 that mediated its recruitment and activation in cancer, concentrating on posttranslational modification by phosphorylation, and sumoylation, formation of promyelocytic leukemia nuclear bodies and its association with co-activators and co-repressors.
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Affiliation(s)
- Taka Eguchi
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Thomas Prince
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Barbara Wegiel
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
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21
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Naville M, Warren IA, Haftek-Terreau Z, Chalopin D, Brunet F, Levin P, Galiana D, Volff JN. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates. Clin Microbiol Infect 2016; 22:312-323. [PMID: 26899828 DOI: 10.1016/j.cmi.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/24/2022]
Abstract
Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage.
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Affiliation(s)
- M Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - I A Warren
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - Z Haftek-Terreau
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France; Department of Genetics, University of Georgia, Athens, GA, USA
| | - F Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - P Levin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Galiana
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - J-N Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France.
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22
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Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol Mol Biol Rev 2015; 78:278-303. [PMID: 24847023 DOI: 10.1128/mmbr.00049-13] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.
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Phylogenic analysis revealed an expanded C₂H₂-homeobox subfamily and expression profiles of C₂H₂ zinc finger gene family in Verticillium dahliae. Gene 2015; 562:169-79. [PMID: 25725127 DOI: 10.1016/j.gene.2015.02.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/23/2015] [Indexed: 01/26/2023]
Abstract
C2H2 zinc finger (CZF) proteins are a major class of transcription factors that play crucial roles in fungal growth, development, various stress responses, and virulence. Little genome-wide data is available regarding the roles of CZF proteins in Verticillium dahliae, a destructive pathogen that causes vascular wilt disease in more than 200 plant species. We identified a total of 79 typical CZF genes in V. dahliae. Comparative analysis revealed that four plant pathogenic fungi, V. dahliae, Fusarium oxysporum, Magnaporthe oryzae, and Botrytis cinerea, have comparable numbers of predicted CZF genes with similar characteristics. Phylogenetic analysis identified a C2H2-homeobox subfamily in V. dahliae containing seven genes with similar gene structures. V. dahliae and F. oxysporum (Hypocreomycetidae) have more genes of this subfamily than M. oryzae (Sordariomycetidae) and B. cinerea (Leotiomycetes). Furthermore, gene-expression analysis of the smoke tree wilt fungus V. dahliae strain XS11 using digital gene-expression profiling and RT-qPCR revealed that a number of CZF genes were differentially expressed during microsclerotia formation, nutritional starvation, and simulated in planta conditions. Furthermore, the expression profiles revealed that some CZF genes were overrepresented during multiple stages, indicating that they might play diverse roles. Our results provide useful information concerning the functions of CZF genes in microsclerotia formation, nutritional stress responses, and pathogenicity in V. dahliae, and form a basis for future functional studies of these genes.
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Llorens C, Bernet GP, Ramasamy S, Feschotte C, Moya A. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. Mob Genet Elements 2014; 2:205-210. [PMID: 23550032 PMCID: PMC3575427 DOI: 10.4161/mge.22914] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
SCAND3 and KRBA2 are two mammalian proteins originally described as “cellular-integrases” due to sharing of a similar DDE-type integrase domain whose origin and relationship with other recombinases remain unclear. Here we perform phylogenetic analyses of 341 integrase/transposase sequences to reveal that the integrase domain of SCAND3 and KRBA2 derives from the same clade of GINGER2, a superfamily of cut-and-paste transposons widely distributed in insects and other protostomes, but seemingly absent or extinct in vertebrates. Finally, we integrate the results of phylogenetic analyses to the taxonomic distribution of SCAND3 and KRBA2 and their transposon relatives to discuss some of the processes that promoted the emergence of these two chimeric genes during mammalian evolution.
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Grau JH, Poustka AJ, Meixner M, Plötner J. LTR retroelements are intrinsic components of transcriptional networks in frogs. BMC Genomics 2014; 15:626. [PMID: 25056159 PMCID: PMC4131045 DOI: 10.1186/1471-2164-15-626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/15/2014] [Indexed: 12/16/2022] Open
Abstract
Background LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology. Results Here we present a first comparative analysis of LTR REs for anuran amphibians based on a full depth coverage transcriptome of the European pool frog, Pelophylax lessonae, the genome of the African clawed frog, Silurana tropicalis (release v7.1), and additional transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, Retroviridae) in the genome of S. tropicalis and discovered transcripts of several of these elements in all RNA-seq datasets analyzed. Elements of the Ty3/Gypsy family were most active, especially Amn-san elements, which accounted for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue specific expression patterns, for example Hydra1.1 and MuERV-like elements in Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. In the course of embryonic development the spectrum of transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and SnRV like retroviruses were abundantly transcribed while during organogenesis transcripts of the XEN1 retroviruses became much more active. Conclusions The differential expression of LTR REs during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. Our results support the meanwhile widely accepted concept that retroelements are not simple “junk DNA” or “harmful genomic parasites” but essential components of the transcriptomic machinery in vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-626) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Horacio Grau
- Dahlem Center for Genome Research and Medical Systems Biology, Fabeckstraße 60-62, 14195 Berlin, Germany.
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Roles for Tbx3 in regulation of two-cell state and telomere elongation in mouse ES cells. Sci Rep 2013; 3:3492. [PMID: 24336466 PMCID: PMC3861804 DOI: 10.1038/srep03492] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/26/2013] [Indexed: 01/12/2023] Open
Abstract
Mouse embryonic stem (ES) cell cultures exhibit heterogeneity and recently are discovered to sporadically enter the 2-cell (2C)-embryo state, critical for ES potency. Zscan4 could mark the sporadic 2C-state of ES cells. However, factors that regulate the Zscan4+/2C state remain to be elucidated. We show that Tbx3 plays a novel role in regulation of Zscan4+/2C state. Tbx3 activates 2-cell genes including Zscan4 and Tcstv1/3, but not vise versa. Ectopic expression of Tbx3 results in telomere elongation, consistent with a role for Zscan4 in telomere lengthening. Mechanistically, Tbx3 decreases Dnmt3b and increases Tet2 protein levels, and reduces binding of Dnmt3b to subtelomeres, resulting in reduced DNA methylation and derepression of genes at subtelomeres, e.g. Zscan4. These data suggest that Tbx3 can activate Zscan4+/2C state by negative regulation of DNA methylation at repeated sequences, linking to telomere maintenance and self-renewal of ES cells.
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Structure of the SCAN domain of human paternally expressed gene 3 protein. PLoS One 2013; 8:e69538. [PMID: 23936039 PMCID: PMC3720700 DOI: 10.1371/journal.pone.0069538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/10/2013] [Indexed: 11/19/2022] Open
Abstract
Human paternally expressed gene 3 protein (PEG3) is a large multi-domain entity with diverse biological functions, including acting as a transcription factor. PEG3 contains twelve Cys2-His2 type zinc finger domains, extended regions of predicted disorder and at the N-terminus a SCAN domain. PEG3 has been identified as partner of the E3 ubiquitin-protein ligase Siah1, an association we sought to investigate. An efficient bacterial recombinant expression system of the human PEG3-SCAN domain was prepared and crystals appeared spontaneously when the protein was being concentrated after purification. The structure was determined at 1.95 Å resolution and reveals a polypeptide fold of five helices in an extended configuration. An extensive dimerization interface, using almost a quarter of the solvent accessible surface, and key salt bridge interactions explain the stability of the dimer. Comparison with other SCAN domains reveals a high degree of conservation involving residues that contribute to the dimer interface. The PEG3-SCAN domain appears to constitute an assembly block, enabling PEG3 homo- or heterodimerization to control gene expression in a combinatorial fashion.
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Razin SV, Borunova VV, Maksimenko OG, Kantidze OL. Cys2His2 zinc finger protein family: classification, functions, and major members. BIOCHEMISTRY (MOSCOW) 2013; 77:217-26. [PMID: 22803940 DOI: 10.1134/s0006297912030017] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cys2His2 (C2H2)-type zinc fingers are widespread DNA binding motifs in eukaryotic transcription factors. Zinc fingers are short protein motifs composed of two or three β-layers and one α-helix. Two cysteine and two histidine residues located in certain positions bind zinc to stabilize the structure. Four other amino acid residues localized in specific positions in the N-terminal region of the α-helix participate in DNA binding by interacting with hydrogen donors and acceptors exposed in the DNA major groove. The number of zinc fingers in a single protein can vary over a wide range, thus enabling variability of target DNA sequences. Besides DNA binding, zinc fingers can also provide protein-protein and RNA-protein interactions. For the most part, proteins containing the C2H2-type zinc fingers are trans regulators of gene expression that play an important role in cellular processes such as development, differentiation, and suppression of malignant cell transformation (oncosuppression).
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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Li J, Chen X, He J, Li M, Liu Y, Zi H, Hu Z, Zhang J. A yeast two‐hybrid screen identifies histone H2A.Z as a transcription factor ZNF24 interactor. J Cell Biochem 2012; 113:3411-8. [DOI: 10.1002/jcb.24217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jianzhong Li
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Xia Chen
- Cancer Institute, Second Military Medical University, Shanghai, China
| | - Jielu He
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Mengwen Li
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Ying Liu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Haiyang Zi
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Zhenlin Hu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Junping Zhang
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
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Genetic innovation in vertebrates: gypsy integrase genes and other genes derived from transposable elements. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:724519. [PMID: 22928150 PMCID: PMC3424704 DOI: 10.1155/2012/724519] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/15/2012] [Indexed: 01/08/2023]
Abstract
Due to their ability to drive DNA rearrangements and to serve as a source of new coding and regulatory sequences, transposable elements (TEs) are considered as powerful evolutionary agents within genomes. In this paper, we review the mechanism of molecular domestication, which corresponds to the formation of new genes derived from TE sequences. Many genes derived from retroelements and DNA transposons have been identified in mammals and other vertebrates, some of them fulfilling essential functions for the development and survival of their host organisms. We will particularly focus on the evolution and expression of Gypsy integrase (GIN) genes, which have been formed from ancient event(s) of molecular domestication and have evolved differentially in some vertebrate sublineages. What we describe here is probably only the tip of the evolutionary iceberg, and future genome analyses will certainly uncover new TE-derived genes and biological functions driving genetic innovation in vertebrates and other organisms.
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Liang Y, Huimei Hong F, Ganesan P, Jiang S, Jauch R, Stanton LW, Kolatkar PR. Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206. Nucleic Acids Res 2012; 40:8721-32. [PMID: 22735705 PMCID: PMC3458555 DOI: 10.1093/nar/gks611] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 Å crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN–Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN–Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development.
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Affiliation(s)
- Yu Liang
- Laboratory for Structural Biochemistry, Stem Cell and Developmental Biology, Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore
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Abstract
SCAN is a protein domain frequently found at the N termini of proteins encoded by mammalian tandem zinc finger (ZF) genes, whose structure is known to be similar to that of retroviral gag capsid domains and whose multimerization has been proposed as a model for retroviral assembly. We report that the SCAN domain is derived from the C-terminal portion of the gag capsid (CA) protein from the Gmr1-like family of Gypsy/Ty3-like retrotransposons. On the basis of sequence alignments and phylogenetic distributions, we show that the ancestral host SCAN domain (ESCAN for extended SCAN) was exapted from a full-length CA gene from a Gmr1-like retrotransposon at or near the root of the tetrapod animal branch. A truncated variant of ESCAN that corresponds to the annotated SCAN domain arose shortly thereafter and appears to be the only form extant in mammals. The Anolis lizard has a large number of tandem ZF genes with N-terminal ESCAN or SCAN domains. We predict DNA binding sites for all Anolis ESCAN-ZF and SCAN-ZF proteins and demonstrate several highly significant matches to Anolis Gmr1-like sequences, suggesting that at least some of these proteins target retroelements. SCAN is known to mediate protein dimerization, and the CA protein multimerizes to form the core retroviral and retrotransposon capsid structure. We speculate that the SCAN domain originally functioned to target host ZF proteins to retroelement capsids.
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Phan KD, Croteau LP, Kam JWK, Kania A, Cloutier JF, Butler SJ. Neogenin may functionally substitute for Dcc in chicken. PLoS One 2011; 6:e22072. [PMID: 21779375 PMCID: PMC3133656 DOI: 10.1371/journal.pone.0022072] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/14/2011] [Indexed: 11/22/2022] Open
Abstract
Dcc is the key receptor that mediates attractive responses of axonal growth cones to netrins, a family of axon guidance cues used throughout evolution. However, a Dcc homolog has not yet been identified in the chicken genome, raising the possibility that Dcc is not present in avians. Here we show that the closely related family member neogenin may functionally substitute for Dcc in the developing chicken spinal cord. The expression pattern of chicken neogenin in the developing spinal cord is a composite of the distribution patterns of both rodent Dcc and neogenin. Moreover, whereas the loss of mouse neogenin has no effect on the trajectory of commissural axons, removing chicken neogenin by RNA interference results in a phenotype similar to the functional inactivation of Dcc in mouse. Taken together, these data suggest that the chick neogenin is functionally equivalent to rodent Dcc.
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Affiliation(s)
- Keith Dai Phan
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | | | - Joseph Wai Keung Kam
- Montreal Neurological Institute, McGill University, Montréal, Québec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Artur Kania
- Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Departments of Anatomy and Cell Biology and Biology, McGill University, Montréal, Québec, Canada
| | - Jean-François Cloutier
- Montreal Neurological Institute, McGill University, Montréal, Québec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Samantha Joanna Butler
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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Kahns S, Losson R, Nielsen AL. Nizp1 zinc finger protein localization is determined by SCAN-domain inclusion regulated through alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:539-45. [DOI: 10.1016/j.bbagrm.2010.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 05/21/2010] [Accepted: 06/01/2010] [Indexed: 12/22/2022]
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Li J, Chen X, Liu Y, Ding L, Qiu L, Hu Z, Zhang J. The transcriptional repression of platelet-derived growth factor receptor-β by the zinc finger transcription factor ZNF24. Biochem Biophys Res Commun 2010; 397:318-22. [DOI: 10.1016/j.bbrc.2010.05.110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 05/24/2010] [Indexed: 11/16/2022]
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Howng SYB, Avila RL, Emery B, Traka M, Lin W, Watkins T, Cook S, Bronson R, Davisson M, Barres BA, Popko B. ZFP191 is required by oligodendrocytes for CNS myelination. Genes Dev 2010; 24:301-11. [PMID: 20080941 DOI: 10.1101/gad.1864510] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The controlling factors that prompt mature oligodendrocytes to myelinate axons are largely undetermined. In this study, we used a forward genetics approach to identify a mutant mouse strain characterized by the absence of CNS myelin despite the presence of abundant numbers of late-stage, process-extending oligodendrocytes. Through linkage mapping and complementation testing, we identified the mutation as a single nucleotide insertion in the gene encoding zinc finger protein 191 (Zfp191), which is a widely expressed, nuclear-localized protein that belongs to a family whose members contain both DNA-binding zinc finger domains and protein-protein-interacting SCAN domains. Zfp191 mutants express an array of myelin-related genes at significantly reduced levels, and our in vitro and in vivo data indicate that mutant ZFP191 acts in a cell-autonomous fashion to disrupt oligodendrocyte function. Therefore, this study demonstrates that ZFP191 is required for the myelinating function of differentiated oligodendrocytes.
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Affiliation(s)
- Shen Yi B Howng
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
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Affiliation(s)
- Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, Supérieure de Lyon, France.
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Li J, Chen X, Gong X, Liu Y, Feng H, Qiu L, Hu Z, Zhang J. A transcript profiling approach reveals the zinc finger transcription factor ZNF191 is a pleiotropic factor. BMC Genomics 2009; 10:241. [PMID: 19463170 PMCID: PMC2694838 DOI: 10.1186/1471-2164-10-241] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 05/22/2009] [Indexed: 12/12/2022] Open
Abstract
Background The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. Zfp191 is widely expressed during early embryogenesis and in adult organs. Moreover, Zfp191-/- embryos have been shown to be severely retarded in development and die approximately at embryonic day E7.5. ZNF191 can specifically interact with the widespread TCAT motif which constitutes the HUMTH01 microsatellite in the tyrosine hydroxylase (TH) gene. Allelic variations of HUMTH01 have been stated to have a quantitative silencing effect on TH gene expression and to correlate with quantitative and qualitative changes in the binding by ZNF191. In addition, ZNF191 displays a suppressive effect on the transcription; however, little downstream targets have identified. Results We searched for ZNF191 target genes by using a transient overexpression and knockdown strategy in the human embryo kidney (HEK293) cells. Microarray analyses identified 6094 genes modulated by overexpression of ZNF191 and 3332 genes regulated by knockdown of ZNF191, using a threshold of 1.2-fold. Several interested candidate genes, validated by real time RT-PCR, were correlated well with the array data. Interestingly, 1456 genes were identified in both transient overexpression and transient knockdown strategies. The GenMAPP and MappFinder software packages were further used for pathway analysis of these significantly altered genes. Several gene pathways were found to be involved in processes of the regulation of kinase activity, transcription, angiogenesis, brain development and response to DNA damage. Conclusion Our analysis reveals for the first time that ZNF191 is a pleiotropic factor that has a role in hematopoiesis, brain development and cancers.
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Affiliation(s)
- Jianzhong Li
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, PR China.
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Gehring S, Sabo E, Martin MES, Dickson EM, Cheng CW, Gregory SH. Laser capture microdissection and genetic analysis of carbon-labeled Kupffer cells. World J Gastroenterol 2009; 15:1708-18. [PMID: 19360914 PMCID: PMC2668776 DOI: 10.3748/wjg.15.1708] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To develop a method of labeling and micro-dissecting mouse Kupffer cells within an extraordinarily short period of time using laser capture microdissection (LCM).
METHODS: Tissues are complex structures comprised of a heterogeneous population of interconnected cells. LCM offers a method of isolating a single cell type from specific regions of a tissue section. LCM is an essential approach used in conjunction with molecular analysis to study the functional interaction of cells in their native tissue environment. The process of labeling and acquiring cells by LCM prior to mRNA isolation can be elaborate, thereby subjecting the RNA to considerable degradation. Kupffer cell labeling is achieved by injecting India ink intravenously, thus circumventing the need for in vitro staining. The significance of this novel approach was validated using a cholestatic liver injury model.
RESULTS: mRNA extracted from the microdissected cell population displayed marked increases in colony-stimulating factor-1 receptor and Kupffer cell receptor message expression, which demonstrated Kupffer cell enrichment. Gene expression by Kupffer cells derived from bile-duct-ligated, versus sham-operated, mice was compared. Microarray analysis revealed a significant (2.5-fold, q value < 10) change in 493 genes. Based on this fold-change and a standardized PubMed search, 10 genes were identified that were relevant to the ability of Kupffer cells to suppress liver injury.
CONCLUSION: The methodology outlined herein provides an approach to isolating high quality RNA from Kupffer cells, without altering the tissue integrity.
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Thomas JH, Emerson RO. Evolution of C2H2-zinc finger genes revisited. BMC Evol Biol 2009; 9:51. [PMID: 19261184 PMCID: PMC2667407 DOI: 10.1186/1471-2148-9-51] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 03/04/2009] [Indexed: 11/20/2022] Open
Abstract
Background A recent study by Tadepally et al. describes the clustering of zinc finger (ZF) genes in the human genome and traces their evolutionary history among several placental mammals with complete or draft genome sequences. One of the main conclusions from the paper is that there is a dramatic rate of gene duplication and gene loss, including the surprising result that 118 human ZF genes are absent in chimpanzee. The authors also present evidence concerning the ancestral order in which the ZF-associated KRAB and SCAN domains were recruited to ZF proteins. Results Based on our analysis of two of the largest human ZF gene clusters, we find that nearly all of the human genes have plausible orthologs in chimpanzee. The one exception may be a result of the incomplete sequence coverage in the draft chimpanzee genome. The discrepancy in gene content analysis may result from the authors' dependence on the preliminary NCBI gene prediction set for chimpanzee, which appears to either fail to predict or to mispredict many chimpanzee ZF genes. Similar problems may affect the authors' interpretation of the more divergent dog, mouse, and rat ZF gene complements. In addition, we present evidence that the KRAB domain was recruited to ZF genes before the SCAN domain, rather than the reverse as the authors suggest. This discrepancy appears to result from the fact that the SCAN domain did indeed arise before the KRAB domain but is present only in non-ZF genes until a much later date. Conclusion When comparing gene content among species, especially when using draft genome assemblies, dependence on preliminary gene prediction sets can be seriously misleading. In such studies, genic sequences must be identified in a manner that is as independent as possible of prediction sets. In addition, we present evidence that provides a more parsimonious explanation for the large proportion of mammalian KRAB-ZF genes without a SCAN domain.
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Affiliation(s)
- James H Thomas
- Department of Genome Sciences, University of Washington, Seattle, 91895, USA.
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Emerson RO, Thomas JH. Adaptive evolution in zinc finger transcription factors. PLoS Genet 2009; 5:e1000325. [PMID: 19119423 PMCID: PMC2604467 DOI: 10.1371/journal.pgen.1000325] [Citation(s) in RCA: 220] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 12/02/2008] [Indexed: 01/10/2023] Open
Abstract
The majority of human genes are conserved among mammals, but some gene families have undergone extensive expansion in particular lineages. Here, we present an evolutionary analysis of one such gene family, the poly–zinc-finger (poly-ZF) genes. The human genome encodes approximately 700 members of the poly-ZF family of putative transcriptional repressors, many of which have associated KRAB, SCAN, or BTB domains. Analysis of the gene family across the tree of life indicates that the gene family arose from a small ancestral group of eukaryotic zinc-finger transcription factors through many repeated gene duplications accompanied by functional divergence. The ancestral gene family has probably expanded independently in several lineages, including mammals and some fishes. Investigation of adaptive evolution among recent paralogs using dN/dS analysis indicates that a major component of the selective pressure acting on these genes has been positive selection to change their DNA-binding specificity. These results suggest that the poly-ZF genes are a major source of new transcriptional repression activity in humans and other primates. Gene families, arising by the repeated duplication and diversification of existing genes, are a pervasive feature of the genomes of higher organisms. In this study, we analyze the evolutionary history of one of the largest gene families in humans, the poly–zinc-finger genes. Each poly–zinc-finger gene is thought to act by regulating the expression levels of one or more other genes, but the ultimate function and purpose of most poly–zinc-finger genes is unknown. We have found that the poly–zinc-finger gene family has been growing rapidly in many lineages including the human lineage, and that evolution has favored the creation of new poly–zinc-finger genes that have different DNA targets than the genes from which they were derived. These results suggest that the emergence of new and different poly–zinc-finger genes has probably been important in the evolution of humans and many other animal species.
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Affiliation(s)
- Ryan O. Emerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - James H. Thomas
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Ding G, Lorenz P, Kreutzer M, Li Y, Thiesen HJ. SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res 2008; 37:D267-73. [PMID: 18974185 PMCID: PMC2686507 DOI: 10.1093/nar/gkn782] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
C2H2 zinc finger (C2H2-ZNF) genes are one of the largest and most complex gene super-families in metazoan genomes, with hundreds of members in the human and mouse genome. The ongoing investigation of this huge gene family requires computational support to catalog genotype phenotype comparisons of C2H2-ZNF genes between related species and finally to extend the worldwide knowledge on the evolution of C2H2-ZNF genes in general. Here, we systematically collected all the C2H2-ZNF genes in the human and mouse genome and constructed a database named SysZNF to deposit available datasets related to these genes. In the database, each C2H2-ZNF gene entry consists of physical location, gene model (including different transcript forms), Affymetrix gene expression probes, protein domain structures, homologs (and synteny between human and mouse), PubMed references as well as links to relevant public databases. The clustered organization of the C2H2-ZNF genes is highlighted. The database can be searched using text strings or sequence information. The data are also available for batch download from the web site. Moreover, the graphical gene model/protein view system, sequence retrieval system and some other tools embedded in SysZNF facilitate the research on the C2H2 type ZNF genes under an integrative view. The database can be accessed from the URL http://epgd.biosino.org/SysZNF.
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Affiliation(s)
- Guohui Ding
- Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
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43
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Noll L, Peterson FC, Hayes PL, Volkman BF, Sander T. Heterodimer formation of the myeloid zinc finger 1 SCAN domain and association with promyelocytic leukemia nuclear bodies. Leuk Res 2008; 32:1582-92. [PMID: 18472161 DOI: 10.1016/j.leukres.2008.03.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 03/03/2008] [Accepted: 03/15/2008] [Indexed: 01/07/2023]
Abstract
Myeloid zinc finger 1 (MZF1) is a transcription factor that plays an important role in blood cell development. Previous reports indicate MZF1 is an essential factor whose abnormal expression results in cancer. However, the molecular mechanisms by which MZF1 functions in development and contributes to cancer progression remain unknown. MZF1 is a member of the SCAN domain family of zinc finger proteins (SCAN-ZFP) that form dimers via their highly conserved SCAN motif. To better understand the molecular mechanism of MZF1 function, we sought to characterize the cellular localization pattern of MZF1 in the context of SCAN dimerization. Here we provide evidence that MZF1 is a constituent of promyelocytic leukemia nuclear bodies (PML-NBs) and that the SCAN domain is necessary for association with these intranuclear structures. In addition, the SCAN-ZFP member ZNF24 was identified as a novel heterodimeric partner of MZF1 that also associates with PML-NBs in a unique ring-type pattern. Finally, we provide support that MZF1 protein may be modified by SUMOylation, which provides further support for localization of MZF1 protein complexes to PML-NBs. Altogether, these data suggest that MZF1 is recruited to PML-NBs and that the SCAN domain may play an integral role in regulating the localization of heterodimeric protein complexes to these intranuclear structures.
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Affiliation(s)
- LeAnne Noll
- Department of Surgery, Children's Research Institute Medical College of Wisconsin, Milwaukee, WI 53226, United States
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44
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ZNF397, a new class of interphase to early prophase-specific, SCAN-zinc-finger, mammalian centromere protein. Chromosoma 2008; 117:367-80. [PMID: 18369653 DOI: 10.1007/s00412-008-0155-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 02/14/2008] [Accepted: 02/28/2008] [Indexed: 01/15/2023]
Abstract
The centromere is a complex structure required for equal segregation of newly synthesised sister chromatids at mitosis. One of the significant objectives in centromere research is to determine the complete repertoire of protein components that constitute the kinetochore. Here, we identify a novel centromere protein using a centromere-positive autoimmune serum from a patient with watermelon stomach disease. Western blot and screening of a lambda phage expression library revealed a 60-kDa protein, ZNF397. This protein belongs to the classical Cys(2)His(2) group of the zinc-finger protein superfamily and contains two conserved domains: a leucine-rich SCAN domain and nine Cys(2)His(2) zinc fingers. Bioinformatic analysis shows that ZNF397 is conserved in placental mammals. Stable GFP:ZNF397-expressing human cells show co-localisation of ZNF397 with the constitutive centromere protein CENP-A during interphase and early prophase. Deletion and domain-swap constructs indicate that the SCAN domain is necessary but not sufficient for centromere localisation. Gene-knockout studies in mice using the mouse orthologue (Zfp397) reveal that ZNF397 is a non-essential protein. These properties define ZNF397 as a member of a new class of interphase to early prophase-specific and SCAN domain-containing mammalian centromere protein. The possible role of this protein in transcription at the centromere is discussed.
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45
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Brayer KJ, Segal DJ. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys 2008; 50:111-31. [PMID: 18253864 DOI: 10.1007/s12013-008-9008-5] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 12/28/2007] [Indexed: 11/28/2022]
Abstract
Cys2-His2 (C2H2) zinc finger domains (ZFs) were originally identified as DNA-binding domains, and uncharacterized domains are typically assumed to function in DNA binding. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. There are even examples of zinc fingers that support both DNA and protein interactions, which can be found in well-known DNA-binding proteins such as Sp1, Zif268, and Ying Yang 1 (YY1). C2H2 protein-protein interactions (PPIs) are proving to be more abundant than previously appreciated, more plastic than their DNA-binding counterparts, and more variable and complex in their interactions surfaces. Here we review the current knowledge of over 100 C2H2 zinc finger-mediated PPIs, focusing on what is known about the binding surface, contributions of individual fingers to the interaction, and function. An accurate understanding of zinc finger biology will likely require greater insights into the potential protein interaction capabilities of C2H2 ZFs.
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Affiliation(s)
- Kathryn J Brayer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
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46
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Luo K, Li J, Cui Y, Xu M, Yuan J, Tang W, Wan B, Yu L. Identification and characterization of the human SCAN domain zinc-finger gene ZNF449. Mol Biol Rep 2007; 33:51-7. [PMID: 16636917 DOI: 10.1007/s11033-005-3966-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2005] [Indexed: 10/24/2022]
Abstract
Zinc-finger proteins play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. In this study, we identified a gene encoding a zinc finger protein named ZNF449, which was isolated from human testis cDNA library and mapped to Xq26.3 by searching the UCSC genomic database. The ZNF449 cDNA consists of 4035 nucleotides and has a 518-amino acids open reading frame. The predicted protein contains a leucine-rich region (LER or SCAN domain) at the N-terminus. At the C-terminus of the protein, there are 7 C(2)H(2) (Cys2-His2) zinc-finger motifs. The expression pattern of ZNF449 showed that it was ubiquitously expressed in 18 human adult tissues. ZNF449 protein was located in the nucleus when overexpressed in cultured cells. These results indicate that ZNF449 is a member of the zinc-finger family and it may function as a transcription factor.
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Affiliation(s)
- Kuntian Luo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, 220 Handan Road, Shanghai, 200433, P. R. China
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47
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Li J, Chen X, Yang H, Wang S, Guo B, Yu L, Wang Z, Fu J. The zinc finger transcription factor 191 is required for early embryonic development and cell proliferation. Exp Cell Res 2006; 312:3990-8. [PMID: 17064688 DOI: 10.1016/j.yexcr.2006.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 08/19/2006] [Accepted: 08/23/2006] [Indexed: 11/20/2022]
Abstract
Human zinc finger protein 191 (ZNF191/ZNF24) was cloned and characterized as a SCAN family member, which shows 94% identity to its mouse homologue zinc finger protein 191 (Zfp191). ZNF191 can specifically interact with an intronic polymorphic TCAT repeat (HUMTH01) in the tyrosine hydroxylase (TH) gene. Allelic variations of HUMTH01 have been stated to have a quantitative silencing effect on TH gene expression and to correlate with quantitative and qualitative changes in the binding by ZNF191. Zfp191 is widely expressed during embryonic development and in multiple tissues and organs in adult. To investigate the functions of Zfp191 in vivo, we have used homologous recombination to generate mice that are deficient in Zfp191. Heterozygous Zfp191(+/-) mice are normal and fertile. Homozygous Zfp191(-/-) embryos are severely retarded in development and die at approximately 7.5 days post-fertilization. Unexpectedly, in Zfp191(-/-) and Zfp191(+/-) embryos, TH gene expression is not affected. Blastocyst outgrowth experiments and the RNA interference-mediated knockdown of ZNF191 in cultured cells revealed an essential role for Zfp191 in cell proliferation. In further agreement with this function, no viable Zfp191(-/-) cell lines were obtained by derivation of embryonic stem (ES) cells from blastocysts of Zfp191(+/-) intercrosses or by forced homogenotization of heterozygous ES cells at high concentrations of G418. These data show that Zfp191 is indispensable for early embryonic development and cell proliferation.
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Affiliation(s)
- Jianzhong Li
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
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48
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Peterson FC, Hayes PL, Waltner JK, Heisner AK, Jensen DR, Sander TL, Volkman BF. Structure of the SCAN domain from the tumor suppressor protein MZF1. J Mol Biol 2006; 363:137-47. [PMID: 16950398 PMCID: PMC1941711 DOI: 10.1016/j.jmb.2006.07.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 07/27/2006] [Accepted: 07/27/2006] [Indexed: 10/24/2022]
Abstract
The SCAN domain mediates interactions between members of a subfamily of zinc-finger transcription factors and is found in more than 60 C2H2 zinc finger genes in the human genome, including the tumor suppressor gene myeloid zinc finger 1 (MZF1). Glutathione-S-transferase pull-down assays showed that the MZF1 SCAN domain self-associates, and a Kd value of 600 nM was measured by intrinsic tryptophan fluorescence polarization. The MZF1 structure determined by NMR spectroscopy revealed a domain-swapped dimer. Each monomer consists of five alpha helices in two subdomains connected by the alpha2-alpha3 loop. Residues from helix 3 of each monomer compose the core of the dimer interface, while the alpha1-alpha2 loop and helix 2 pack against helices 3 and 5 from the opposing monomer. Comprehensive sequence analysis is coupled with the first high-resolution structure of a SCAN dimer to provide an initial view of the recognition elements that govern dimerization for this large family of transcription factors.
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Affiliation(s)
- Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road Milwaukee, WI 53226, USA
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49
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Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res 2006; 16:669-77. [PMID: 16606702 PMCID: PMC1457042 DOI: 10.1101/gr.4842106] [Citation(s) in RCA: 241] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of segmental duplication, involving single genes or larger regions and including both tandem and distributed duplication events, have driven the expansion of this mammalian gene family. Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes not only identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change; at least 136 KRAB-ZNF coding genes are primate specific, including many recent duplicates. KRAB-ZNF genes are widely expressed and clustered genes are typically not coregulated, indicating that paralogs have evolved to fill roles in many different biological processes. To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets.
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Affiliation(s)
| | | | | | | | | | | | | | - Elbert Branscomb
- Microbial Systems Divisions, Biosciences, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Lisa Stubbs
- Genome Biology
- Corresponding author.E-mail ; fax (925) 422-2099
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50
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Carneiro FRG, Silva TCL, Alves AC, Haline-Vaz T, Gozzo FC, Zanchin NIT. Spectroscopic characterization of the tumor antigen NY-REN-21 and identification of heterodimer formation with SCAND1. Biochem Biophys Res Commun 2006; 343:260-8. [PMID: 16540086 DOI: 10.1016/j.bbrc.2006.02.140] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 02/23/2006] [Indexed: 11/23/2022]
Abstract
Human NY-REN-21 is a C2H2 type multi-finger protein, with a SCAN domain in the N-terminal region and a predicted coil central region. It represents a putative ortholog of mouse ZFP38, a transcriptional factor that recognizes a bipartite DNA motif and is unable to form homodimers. As shown in this work, NY-REN-21 contains a SCAN domain able to form homodimers and a central region that behaves as an intrinsically disordered protein. The SCAN domain is found in 71 human proteins and its ability to form homo- and heterodimers widens the number of genes that are regulated by this group of transcription factors. NY-REN-21 interaction with SCAND1 was identified using the yeast two-hybrid system and confirmed using recombinant proteins. SCAND1 is a truncated SCAN box protein, lacking the zinc finger region and the NY-REN-21/SCAND1 heterodimer is asymmetric concerning the DNA binding region. This result indicates that NY-REN-21 can function either as a homodimer or as a heterodimer with SCAND1.
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Affiliation(s)
- Flávia R G Carneiro
- Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, LNLS, Rua Giuseppe Maximo Scolfaro 10000, P.O. Box 6192, CEP 13084-971, Campinas SP, Brazil
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