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Regulation of human ZNF687, a gene associated with Paget's disease of bone. Int J Biochem Cell Biol 2023; 154:106332. [PMID: 36372390 DOI: 10.1016/j.biocel.2022.106332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Mutations in Zinc finger 687 (ZNF687) were associated with Paget's disease of bone (PDB), a disease characterized by increased bone resorption and excessive bone formation. It was suggested that ZNF687 plays a role in bone differentiation and development. However, the mechanisms involved in ZNF687 regulation remain unknown. This study aimed to obtain novel knowledge regarding ZNF687 transcriptional and epigenetic regulation. Through in silico analysis, we hypothesized three ZNF687 promoter regions located upstream exon 1 A, 1B, and 1 C and denominated promoter regions 1, 2, and 3, respectively. Their functionality was confirmed by luciferase activity assays and positive/negative regulatory regions were identified using promoter deletions constructs. In silico analysis revealed a high density of CpG islands in these promoter regions and in vitro methylation suppressed promoters' activity. Using bioinformatic approaches, bone-associated transcription factor binding sites containing CpG dinucleotides were identified, including those for NFκB, PU.1, DLX5, and SOX9. By co-transfection in HEK293 and hFOB cells, we found that DLX5 specifically activated ZNF687 promoter region 1, and its methylation impaired DLX5-driven promoter stimulation. NFκB repressed and activated promoter regions 1 and 2, respectively, and these activities were affected by methylation. PU.1 induced ZNF687 promoter region 1 which was affected by methylation. SOX9 differentially regulated ZNF687 promoters in HEK293 and hFOB cells that were impaired after methylation. In conclusion, this study provides novel insights into ZNF687 regulation by demonstrating that NFκB, PU.1, DLX5, and SOX9 are regulators of ZNF687 promoters, and DNA methylation influences their activity. The contribution of the dysregulation of these mechanisms in PDB should be further elucidated.
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Kumar R, Ali SA, Singh SK, Bhushan V, Mathur M, Jamwal S, Mohanty AK, Kaushik JK, Kumar S. Antimicrobial Peptides in Farm Animals: An Updated Review on Its Diversity, Function, Modes of Action and Therapeutic Prospects. Vet Sci 2020; 7:vetsci7040206. [PMID: 33352919 PMCID: PMC7766339 DOI: 10.3390/vetsci7040206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial peptides (AMPs) are the arsenals of the innate host defense system, exhibiting evolutionarily conserved characteristics that are present in practically all forms of life. Recent years have witnessed the emergence of antibiotic-resistant bacteria compounded with a slow discovery rate for new antibiotics that have necessitated scientific efforts to search for alternatives to antibiotics. Research on the identification of AMPs has generated very encouraging evidence that they curb infectious pathologies and are also useful as novel biologics to function as immunotherapeutic agents. Being innate, they exhibit the least cytotoxicity to the host and exerts a wide spectrum of biological activity including low resistance among microbes and increased wound healing actions. Notably, in veterinary science, the constant practice of massive doses of antibiotics with inappropriate withdrawal programs led to a high risk of livestock-associated antimicrobial resistance. Therefore, the world faces tremendous pressure for designing and devising strategies to mitigate the use of antibiotics in animals and keep it safe for posterity. In this review, we illustrate the diversity of farm animal-specific AMPs, and their biochemical foundations, mode of action, and prospective application in clinics. Subsequently, we present the data for their systematic classification under the major and minor groups, antipathogenic action, and allied bioactivities in the host. Finally, we address the limitations of their clinical implementation and envision areas for further advancement.
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Cathelicidins: family of antimicrobial peptides. A review. Mol Biol Rep 2012; 39:10957-70. [PMID: 23065264 PMCID: PMC3487008 DOI: 10.1007/s11033-012-1997-x] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Accepted: 10/01/2012] [Indexed: 11/29/2022]
Abstract
Cathelicidins are small, cationic, antimicrobial peptides found in humans and other species, including farm animals (cattle, horses, pigs, sheep, goats, chickens, rabbits and in some species of fish). These proteolytically activated peptides are part of the innate immune system of many vertebrates. These peptides show a broad spectrum of antimicrobial activity against bacteria, enveloped viruses and fungi. Apart from exerting direct antimicrobial effects, cathelicidins can also trigger specific defense responses in the host. Their roles in various pathophysiological conditions have been studied in mice and humans, but there are limited information about their expression sites and activities in livestock. The aim of the present review is to summarize current information about these antimicrobial peptides in farm animals, highlighting peptide expression sites, activities, and future applications for human and veterinary medicine.
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Brahmachary M, Schönbach C, Yang L, Huang E, Tan SL, Chowdhary R, Krishnan SPT, Lin CY, Hume DA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB. Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. BMC Bioinformatics 2006; 7 Suppl 5:S8. [PMID: 17254313 PMCID: PMC1764486 DOI: 10.1186/1471-2105-7-s5-s8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect the expression of AMP-coding genes (AMPcgs). For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized. RESULTS Based upon the RIKEN full-length cDNA and public sequence data derived from human, mouse and rat, we identified 178 candidate AMP transcripts derived from 61 genes belonging to 29 AMP families. However, only for 31 mouse genes belonging to 22 AMP families we were able to determine true orthologous relationships with 30 human and 15 rat sequences. We screened the promoter regions of AMPcgs in the three species for motifs by an ab initio motif finding method and analyzed the derived promoter characteristics. Promoter models were developed for alpha-defensins, penk and zap AMP families. The results suggest a core set of transcription factors (TFs) that regulate the transcription of AMPcg families in mouse, rat and human. The three most frequent core TFs groups include liver-, nervous system-specific and nuclear hormone receptors (NHRs). Out of 440 motifs analyzed, we found that three represent potentially novel TF-binding motifs enriched in promoters of AMPcgs, while the other four motifs appear to be species-specific. CONCLUSION Our large-scale computational analysis of promoters of 22 families of AMPcgs across three mammalian species suggests that their key transcriptional regulators are likely to be TFs of the liver-, nervous system-specific and NHR groups. The computationally inferred promoter elements and potential TF binding motifs provide a rich resource for targeted experimental validation of TF binding and signaling studies that aim at the regulation of mouse, rat or human AMPcgs.
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Affiliation(s)
- Manisha Brahmachary
- Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Christian Schönbach
- Immunoinformatics Research Team, Advanced Genome Information Technology Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Liang Yang
- Department of Obstetrics and Gynecology, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore
| | - Enli Huang
- Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
| | - Sin Lam Tan
- Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
- University of the Western Cape, South African National Bioinformatics Institute (SANBI), Private Bag X17, Bellville 7535, South Africa
| | - Rajesh Chowdhary
- Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
| | - SPT Krishnan
- Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
| | - Chin-Yo Lin
- Brigham Young University, Department of Microbiology and Molecular Biology, 753 WIDB, Provo, UT 84602, USA
| | - David A Hume
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Chikatoshi Kai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kawai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Piero Carninci
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshihide Hayashizaki
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Vladimir B Bajic
- University of the Western Cape, South African National Bioinformatics Institute (SANBI), Private Bag X17, Bellville 7535, South Africa
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Yang Z, Jean-Baptiste G, Khoury C, Greenwood MT. The mouse sphingomyelin synthase 1 (SMS1) gene is alternatively spliced to yield multiple transcripts and proteins. Gene 2005; 363:123-32. [PMID: 16226406 DOI: 10.1016/j.gene.2005.07.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Revised: 07/12/2005] [Accepted: 07/18/2005] [Indexed: 11/18/2022]
Abstract
Sphingomyelin synthase 1 (SMS1) is a recently identified 413-residue protein that plays a critical role in sphingolipid metabolism by catalyzing the conversion of ceramide and phosphatidylcholine to sphingomyelin and diacylglycerol (DAG). We have previously reported the isolation of a mouse SMS1 encoding cDNA that contains a unique 5' UTR sequence. Three other mouse SMS1 cDNAs that differed in their 5' and 3' non-coding sequences were present in GenBank. In order to ascertain the origin of the unique 5' and 3' UTR sequences, we analyzed the structure of the mouse SMS1 gene. Analysis of the four different SMS1 cDNA sequences and of the corresponding mouse genomic fragment revealed that the SMS1 gene consists of 16 exons that are alternatively spliced to produce 4 different mRNAs (SMS1alpha1, SMS1alpha2, SMS1beta and SMS1gamma) and 3 different proteins (SMS1alpha, SMS1beta and SMS1gamma). RT-PCR was used to demonstrate that all four SMS1 cDNAs represent expressed transcripts that show distinctly different tissue distributions. Transcripts for SMS1alpha1, SMS1alpha2 and SMS1beta were found to increase in response to the pro-apoptotic effects of TNF-alpha. Finally, using a yeast-based assay, we confirmed that SMS1alpha prevents the growth inhibitory effects of Bax but SMS1beta neither prevents nor enhances the effects of Bax or of SMS1alpha. Taken together these results demonstrate the complexity of SMS1 gene structure, expression and function.
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Affiliation(s)
- Zhao Yang
- Department of Anatomy and Cell Biology, Polypeptide Laboratory, McGill University, Montreal, Quebec, Canada H3A 2B2
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