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Schultheis H, Bentsen M, Heger V, Looso M. Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data. Sci Rep 2024; 14:9275. [PMID: 38654130 DOI: 10.1038/s41598-024-59989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to dynamically adjust gene expression in response to environmental signals. Computational procedures like digital genomic footprinting on chromatin accessibility assays such as ATACseq can be used to identify bound TFs in a genome-wide scale. This method utilizes short regions of low accessibility signals due to steric hindrance of DNA bound proteins, called footprints (FPs), which are combined with motif databases for TF identification. However, while over 1600 TFs have been described in the human genome, only ~ 700 of these have a known binding motif. Thus, a substantial number of FPs without overlap to a known DNA motif are normally discarded from FP analysis. In addition, the FP method is restricted to organisms with a substantial number of known TF motifs. Here we present DENIS (DE Novo motIf diScovery), a framework to generate and systematically investigate the potential of de novo TF motif discovery from FPs. DENIS includes functionality (1) to isolate FPs without binding motifs, (2) to perform de novo motif generation and (3) to characterize novel motifs. Here, we show that the framework rediscovers artificially removed TF motifs, quantifies de novo motif usage during an early embryonic development example dataset, and is able to analyze and uncover TF activity in organisms lacking canonical motifs. The latter task is exemplified by an investigation of a scATAC-seq dataset in zebrafish which covers different cell types during hematopoiesis.
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Affiliation(s)
- Hendrik Schultheis
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vanessa Heger
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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2
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Zhao F, Guo X, Li X, Liu F, Fu Y, Sun X, Yang Z, Zhang Z, Qin Z. Identification and Expressional Analysis of Putative PRDI-BF1 and RIZ Homology Domain-Containing Transcription Factors in Mulinia lateralis. BIOLOGY 2023; 12:1059. [PMID: 37626944 PMCID: PMC10451705 DOI: 10.3390/biology12081059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Mollusca represents one of the ancient bilaterian groups with high morphological diversity, while the formation mechanisms of the precursors of all germ cells, primordial germ cells (PGCs), have not yet been clarified in mollusks. PRDI-BF1 and RIZ homology domain-containing proteins (PRDMs) are a group of transcriptional repressors, and PRDM1 (also known as BLIMP1) and PRDM14 have been reported to be essential for the formation of PGCs. In the present study, we performed a genome-wide retrieval in Mulinia lateralis and identified 11 putative PRDMs, all of which possessed an N-terminal PR domain. Expressional profiles revealed that all these prdm genes showed specifically high expression levels in the given stages, implying that all PRDMs played important roles during early development stages. Specifically, Ml-prdm1 was highly expressed at the gastrula stage, the key period when PGCs arise, and was specifically localized in the cytoplasm of two or three cells of blastula, gastrula, or trochophore larvae, matching the typical characteristics of PGCs. These results suggested that Ml-prdm1-positive cells may be PGCs and that Ml-prdm1 could be a candidate marker for tracing the formation of PGCs in M. lateralis. In addition, the expression profiles of Ml-prdm14 hinted that it may not be associated with PGCs of M. lateralis. The present study provides insights into the evolution of the PRDM family in mollusks and offers a better understanding of the formation of PGCs in mollusks.
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Affiliation(s)
- Feng Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaolin Guo
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Fang Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Yifan Fu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaohan Sun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zujing Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
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3
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Jurich C, Yang ZJ. High-throughput computational investigation of protein electrostatics and cavity for SAM-dependent methyltransferases. Protein Sci 2023; 32:e4690. [PMID: 37278582 PMCID: PMC10273352 DOI: 10.1002/pro.4690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/25/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
S-adenosyl methionine (SAM)-dependent methyl transferases (MTases) are a ubiquitous class of enzymes catalyzing dozens of essential life processes. Despite targeting a large space of substrates with diverse intrinsic reactivity, SAM MTases have similar catalytic efficiency. While understanding of MTase mechanism has grown tremendously through the integration of structural characterization, kinetic assays, and multiscale simulations, it remains elusive how these enzymes have evolved to fit the diverse chemical needs of their respective substrates. In this work, we performed a high-throughput molecular modeling analysis of 91 SAM MTases to better understand how their properties (i.e., electric field [EF] strength and active site volumes) help achieve similar catalytic efficiency toward substrates of different reactivity. We found that EF strengths have largely adjusted to make the target atom a better methyl acceptor. For MTases that target RNA/DNA and histone proteins, our results suggest that EF strength accommodates formal hybridization state and variation in cavity volume trends with diversity of substrate classes. Metal ions in SAM MTases contribute negatively to EF strength for methyl donation and enzyme scaffolds tend to offset these contributions.
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Affiliation(s)
| | - Zhongyue J. Yang
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Data Science InstituteVanderbilt UniversityNashvilleTennesseeUSA
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
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4
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Cornescu GM, Panaite TD, Untea AE, Varzaru I, Saracila M, Dumitru M, Vlaicu PA, Gavris T. Mitigation of heat stress effects on laying hens' performances, egg quality, and some blood parameters by adding dietary zinc-enriched yeasts, parsley, and their combination. Front Vet Sci 2023; 10:1202058. [PMID: 37397001 PMCID: PMC10310801 DOI: 10.3389/fvets.2023.1202058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/23/2023] [Indexed: 07/04/2023] Open
Abstract
Objective Finding natural, handy and efficient nutritional solutions to prevent and mitigate negative effects caused by environmental heat stress and to be applied to large-scale laying hen industry. Research design A 3-weeks trial was conducted on 128 laying hens TETRA-SL LL (50 weeks of age) housed in 8 cages/group, 4 laying hens/cage, 32 laying hens/group, under heat stress conditions (34±1°C). The basal diet on corn and soybean meal was formulated to be isocaloric and isonitrogenic. Compared to Control group diet (C), experimental groups E1 included 1% zinc-enriched yeast; E2 included 2% parsley and E3 included 1% zinc-enriched yeast combined with 2% parsley to minimize the heat stress effects. Methods The parsley and the zinc-enriched yeast were analysed for their chemical composition, total polyphenols, antioxidant capacity, minerals, vitamin E and incorporated into the ration structure. Production parameters, egg quality, biochemical and haematological profiles of blood samples were analysed during the trial. Results A statistically significant (p < 0.05) average egg weight was noticed on E2 and E3 compared to Control group, and also during the 1st week compared to the 2nd and the 3rd experimental weeks. Average daily feed intake values were highly significant (p < 0.001) on E3 group compared to C, E1, E2, and on the 2nd week compared to the 3rd experimental week (p < 0.021). Feed conversion rate was highly significant (p < 0.001) during the 2nd and the 3rd experimental weeks compared to the 1st week. The average daily egg production was highly significant (p < 0.001) within 1st week compared to the 2nd and 3rd weeks. A highly significant (p < 0.001) yolk coloration was noticed on E2 and E3 groups. The malondialdehyde (MDA) concentration decreased significantly (p < 0.05) to all experimental groups compared to Control group during the 14th and 28th days of storage. Conclusion These findings suggest that the two ingredients minimized the heat stress effects on production performance parameters with a demonstrated antioxidant capacity role by delaying the lipid peroxidation during different storage time periods.
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Affiliation(s)
- Gabriela Maria Cornescu
- Animal Nutrition Physiology Department, National Research and Development Institute for Biology and Animal Nutrition, Balotesti, Romania
| | - Tatiana Dumitra Panaite
- Animal Nutrition Physiology Department, National Research and Development Institute for Biology and Animal Nutrition, Balotesti, Romania
| | - Arabela Elena Untea
- Animal Nutrition Physiology Department, National Research and Development Institute for Biology and Animal Nutrition, Balotesti, Romania
| | - Iulia Varzaru
- Animal Nutrition Physiology Department, National Research and Development Institute for Biology and Animal Nutrition, Balotesti, Romania
| | - Mihaela Saracila
- Animal Nutrition Physiology Department, National Research and Development Institute for Biology and Animal Nutrition, Balotesti, Romania
| | - Mihaela Dumitru
- Animal Nutrition Physiology Department, National Research and Development Institute for Biology and Animal Nutrition, Balotesti, Romania
| | - Petru Alexandru Vlaicu
- Faculty of Animal Production Engineering and Management, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Teodor Gavris
- Faculty of Animal Production Engineering and Management, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
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5
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Billon V, Sanchez-Luque FJ, Rasmussen J, Bodea GO, Gerhardt DJ, Gerdes P, Cheetham SW, Schauer SN, Ajjikuttira P, Meyer TJ, Layman CE, Nevonen KA, Jansz N, Garcia-Perez JL, Richardson SR, Ewing AD, Carbone L, Faulkner GJ. Somatic retrotransposition in the developing rhesus macaque brain. Genome Res 2022; 32:1298-1314. [PMID: 35728967 PMCID: PMC9341517 DOI: 10.1101/gr.276451.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity are poorly defined and are virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether nonhuman primate L1s can similarly generate somatic insertions in the brain. Here we applied approximately 40× single-cell whole-genome sequencing (scWGS), as well as retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and PCR-validated a somatic L1 insertion that generated target site duplications, carried a short 5' transduction, and was present in ∼7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30 million years of human evolution.
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Affiliation(s)
- Victor Billon
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Francisco J Sanchez-Luque
- GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
- Institute of Parasitology and Biomedicine "Lopez-Neyra"-Spanish National Research Council, PTS Granada 18016, Spain
| | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Gabriela O Bodea
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Stephanie N Schauer
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Thomas J Meyer
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Cora E Layman
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Natasha Jansz
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Jose L Garcia-Perez
- GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Lucia Carbone
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
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6
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Vaghari-Tabari M, Jafari-Gharabaghlou D, Sadeghsoltani F, Hassanpour P, Qujeq D, Rashtchizadeh N, Ghorbanihaghjo A. Zinc and Selenium in Inflammatory Bowel Disease: Trace Elements with Key Roles? Biol Trace Elem Res 2021; 199:3190-3204. [PMID: 33098076 DOI: 10.1007/s12011-020-02444-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory condition that may emerge at a young age and often lasts for life. It often goes through phases of recurrence and remission and has a devastating effect on quality of life. The exact etiology of the disease is still unclear, but it appears that an inappropriate immune response to intestinal flora bacteria in people with a genetic predisposition may cause the disease. Managing inflammatory bowel disease is still a serious challenge. Oxidative stress and free radicals appear to be involved in the pathogenesis of this disease, and a number of studies have suggested the use of antioxidants as a therapeutic approach. The antioxidant and anti-inflammatory properties of some trace elements have led some of the research to focus on studying these trace elements in inflammatory bowel disease. Zinc and selenium are among the most important trace elements that have significant anti-inflammatory and antioxidant properties. Some studies have shown the importance of these trace elements in inflammatory bowel disease. In this review, we have attempted to provide a comprehensive overview of the findings of these studies and to gather current knowledge about the association of these trace elements with the inflammatory process and inflammatory bowel disease.
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Affiliation(s)
- Mostafa Vaghari-Tabari
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Davoud Jafari-Gharabaghlou
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Sadeghsoltani
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Hassanpour
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Nadereh Rashtchizadeh
- Connective Tissue Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Amir Ghorbanihaghjo
- Biotechnology Research Center, Tabriz University of Medical Sciences, P.O. Box 14711, Tabriz, 5166614711, Iran.
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7
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Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res 2021; 31:1663-1679. [PMID: 34426512 PMCID: PMC8415381 DOI: 10.1101/gr.275472.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Antibodies offer a powerful means to interrogate specific proteins in a complex milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive chromatin proteins. However, these reagents have not been widely field-tested. We therefore performed a screen to test their ability to enrich genomic regions via chromatin immunoprecipitation (ChIP) and a variety of orthogonal assays. Eight hundred eighty-seven unique antibodies against 681 unique human transcription factors (TFs) were assayed by ultra-high-resolution ChIP-exo/seq, generating approximately 1200 ChIP-exo data sets, primarily in a single pass in one cell type (K562). Subsets of PCRP mAbs were further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and protein binding microarray (PBM) experiments. About 5% of the tested antibodies displayed high-confidence target (i.e., cognate antigen) enrichment across at least one assay and are strong candidates for additional validation. An additional 34% produced ChIP-exo data that were distinct from background and thus warrant further testing. The remaining 61% were not substantially different from background, and likely require consideration of a much broader survey of cell types and/or assay optimizations. We show and discuss the metrics and challenges to antibody validation in chromatin-based assays.
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Affiliation(s)
- William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Luca Mariani
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | - Thomas R Blanda
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Prashant K Kuntala
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kylie Bocklund
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Joshua Mairose
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah N Dweikat
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Katelyn Mistretta
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Matthew J Rossi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Daniela James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Zibo Zhao
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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8
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Yang WT, Chen M, Xu R, Zheng PS. PRDM4 inhibits cell proliferation and tumorigenesis by inactivating the PI3K/AKT signaling pathway through targeting of PTEN in cervical carcinoma. Oncogene 2021; 40:3318-3330. [PMID: 33846573 PMCID: PMC8102194 DOI: 10.1038/s41388-021-01765-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/27/2021] [Accepted: 03/22/2021] [Indexed: 02/01/2023]
Abstract
PR domain zinc finger protein 4 (PRDM4) is a transcription factor that plays key roles in stem cell self-renewal and tumorigenesis. However, its biological role and exact mechanism in cervical cancer remain unknown. Here, both immunohistochemistry (IHC) and Western blot assays demonstrated that the expression of PRDM4 in cervical cancer tissues was much lower than that in the normal cervix. A xenograft assay showed that PRDM4 overexpression in the cervical cancer cell lines SiHa and HeLa dramatically inhibited cell proliferation and tumorigenic potential in vivo. Conversely, the silencing of PRDM4 promoted cervical cancer cell proliferation and tumorigenic potential. Mechanistically, PRDM4 induced cell cycle arrest at the transition from G0/G1 phase to S phase by upregulating p27 and p21 expression and downregulating Cyclin D1 and CDK4 expression. Furthermore, the PI3K/AKT signaling pathway was inactivated in PRDM4-overexpressing cells, which decreased the levels of p-AKT and upregulated the expression of PTEN, an inhibitor of the PI3K/AKT signaling pathway, at both the transcriptional and translational levels. Dual-luciferase reporter assays and qChIP assays confirmed that PRDM4 transactivated the expression of PTEN by binding to two specific regions in the PTEN promoter. Furthermore, PTEN silencing or a PTEN inhibitor rescued the cell defects induced by PRDM4 overexpression. Therefore, our data suggest that PRDM4 inhibits cell proliferation and tumorigenesis by downregulating the activity of the PI3K/AKT signaling pathway by directly transactivating PTEN expression in cervical cancer.
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Affiliation(s)
- Wen-Ting Yang
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of the People's Republic of China, Xi'an, Shaanxi, People's Republic of China
| | - Mei Chen
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Rui Xu
- Department of Internal Medicine One, Shaanxi Cancer Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Peng-Sheng Zheng
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of the People's Republic of China, Xi'an, Shaanxi, People's Republic of China.
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9
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Di Tullio F, Schwarz M, Zorgati H, Mzoughi S, Guccione E. The duality of PRDM proteins: epigenetic and structural perspectives. FEBS J 2021; 289:1256-1275. [PMID: 33774927 DOI: 10.1111/febs.15844] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/26/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
PRDF1 and RIZ1 homology domain containing (PRDMs) are a subfamily of Krüppel-like zinc finger proteins controlling key processes in metazoan development and in cancer. PRDMs exhibit unique dualities: (a) PR domain/ZNF arrays-their structure combines a SET-like domain known as a PR domain, typically found in methyltransferases, with a variable array of C2H2 zinc fingers (ZNF) characteristic of DNA-binding transcription factors; (b) transcriptional activators/repressors-their physiological function is context- and cell-dependent; mechanistically, some PRDMs have a PKMT activity and directly catalyze histone lysine methylation, while others are rather pseudomethyltransferases and act by recruiting transcriptional cofactors; (c) oncogenes/tumor suppressors-their pathological function depends on the specific PRDM isoform expressed during tumorigenesis. This duality is well known as the 'Yin and Yang' of PRDMs and involves a complex regulation of alternative splicing or alternative promoter usage, to generate full-length or PR-deficient isoforms with opposing functions in cancer. In conclusion, once their dualities are fully appreciated, PRDMs represent a promising class of targets in oncology by virtue of their widespread upregulation across multiple tumor types and their somatic dispensability, conferring a broad therapeutic window and limited toxic side effects. The recent discovery of a first-in-class compound able to inhibit PRDM9 activity has paved the way for the identification of further small molecular inhibitors able to counteract PRDM oncogenic activity.
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Affiliation(s)
- Federico Di Tullio
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan Schwarz
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Habiba Zorgati
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Mzoughi
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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10
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Abdel-Wahhab MA, Hassan MA, El-Nekeety AA, Abdel-Azeim SH, Hassan NS, Jaswir I, Salleh HM. Zinc loaded whey protein nanoparticles mitigate the oxidative stress and modulate antioxidative gene expression in testicular tissues in rats. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells 2020; 9:cells9122603. [PMID: 33291744 PMCID: PMC7761934 DOI: 10.3390/cells9122603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) (PR) homologous domain containing (PRDM) transcription factors are expressed in neuronal and stem cell systems, and they exert multiple functions in a spatiotemporal manner. Therefore, it is believed that PRDM factors cooperate with a number of protein partners to regulate a critical set of genes required for maintenance of stem cell self-renewal and differentiation through genetic and epigenetic mechanisms. In this review, we summarize recent findings about the expression of PRDM factors and function in stem cell and neuronal systems with a focus on cofactor-dependent regulation of PRDM3/16 and FOG1/2. We put special attention on summarizing the effects of the PRDM proteins interaction with chromatin modulators (NuRD complex and CtBPs) on the stem cell characteristic and neuronal differentiation. Although PRDM factors are known to possess intrinsic enzyme activity, our literature analysis suggests that cofactor-dependent regulation of PRDM3/16 and FOG1/2 is also one of the important mechanisms to orchestrate bidirectional target gene regulation. Therefore, determining stem cell and neuronal-specific cofactors will help better understanding of PRDM3/16 and FOG1/2-controlled stem cell maintenance and neuronal differentiation. Finally, we discuss the clinical aspect of these PRDM factors in different diseases including cancer. Overall, this review will help further sharpen our knowledge of the function of the PRDM3/16 and FOG1/2 with hopes to open new research fields related to these factors in stem cell biology and neuroscience.
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12
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Zinc citrate incorporation with whey protein nanoparticles alleviate the oxidative stress complication and modulate gene expression in the liver of rats. Food Chem Toxicol 2019; 125:439-451. [DOI: 10.1016/j.fct.2019.01.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
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13
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PI3Ka-Akt1-mediated Prdm4 induction in adipose tissue increases energy expenditure, inhibits weight gain, and improves insulin resistance in diet-induced obese mice. Cell Death Dis 2018; 9:876. [PMID: 30158592 PMCID: PMC6115456 DOI: 10.1038/s41419-018-0904-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 12/23/2022]
Abstract
Stimulation of white adipose tissue (WAT) browning is considered as a potential approach to treat obesity and metabolic diseases. Our previous studies have shown that phytochemical butein can stimulate WAT browning through induction of Prdm4 in adipocytes. Here, we investigated the effects of butein on diet-induced obesity and its underlying molecular mechanism. Treatment with butein prevented weight gains and improved metabolic profiles in diet-induced obese mice. Butein treatment groups also displayed higher body temperature, increased energy expenditure, and enhanced expression of thermogenic genes in adipose tissue. Butein also suppressed body weight gains and improved glucose and insulin tolerance in mice housed at thermoneutrality (30 °C). These effects were associated with adipose-selective induction of Prdm4, suggesting the role of Prdm4 in butein-mediated anti-obese effects. To directly assess the in vivo role of Prdm4, we generated aP2-Prdm4 transgenic mouse lines overexpressing Prdm4 in adipose tissues. Adipose-specific transgenic expression of Prdm4 recapitulated the butein’s actions in stimulating energy expenditure, cold tolerance, and thermogenic gene expression, resulting in prevention of obesity and improvement of metabolism. Mechanistically, direct inhibition of PI3Kα activity followed by selective suppression of its downstream Akt1 mirrored butein’s effect on Ucp1 expression and oxygen consumption. In addition, effects of butein were completely abolished in Akt1 KO mouse embryonic fibroblasts. Together, these studies demonstrate the role of butein in obesity and metabolic diseases, further highlighting that adipose PI3Kα–Akt1–Prdm4 axis is a regulator of energy expenditure.
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14
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Soussi A, Gargouri M, El Feki A. Effects of co-exposure to lead and zinc on redox status, kidney variables, and histopathology in adult albino rats. Toxicol Ind Health 2018; 34:469-480. [PMID: 29702030 DOI: 10.1177/0748233718770293] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lead (Pb) is a toxic metal that induces a wide range of biochemical and physiological effects in humans. Oxidative damage has been proposed as a possible mechanism involved in Pb toxicity. The current study was carried out to evaluate the antioxidant activities of zinc (Zn) supplement against lead acetate-induced kidney injury in rats. In this study, adults male rats were treated for 15 days with Pb (0.344 g/kg body weight (bw)) associated or not with Zn (10 mg/kg bw). Our study showed that supplementation with Zn prevented renal dysfunction as indicated by plasma biomarkers (urea, uric acid, creatinine, lactate dehydrogenase, and alkaline phosphatase levels) and oxidative stress-related parameters (thiobarbituric acid reactive substances, protein carbonyl, advanced oxidation protein product, superoxide dismutase, catalase, glutathione peroxidase, and vitamins (A, E)) in kidney tissue. The corrective effect of Zn on Pb-induced kidney nephrotoxicity recovered normal kidney histology. Overall, this study indicates that Zn alleviated the toxic effects of this heavy metal on renal tissue, suggesting its role as a potential antioxidant and nephroprotective agent.
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Affiliation(s)
- Ahlem Soussi
- Laboratory of Animal Ecophysiology, Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Manel Gargouri
- Laboratory of Animal Ecophysiology, Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Abdelfattah El Feki
- Laboratory of Animal Ecophysiology, Faculty of Sciences, University of Sfax, Sfax, Tunisia
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15
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Liu H, Dai X, Cao X, Yan H, Ji X, Zhang H, Shen S, Si Y, Zhang H, Chen J, Li L, Zhao JC, Yu J, Feng XH, Zhao B. PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression. EMBO Rep 2018; 19:embr.201745180. [PMID: 29669796 DOI: 10.15252/embr.201745180] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/17/2018] [Accepted: 03/23/2018] [Indexed: 12/12/2022] Open
Abstract
Yes-associated protein (YAP) is a transcriptional co-activator and a major effector of the Hippo pathway that promotes cell proliferation and stemness, while inhibiting apoptosis. YAP plays a central role in organ size control, and its deregulation strongly promotes cancer initiation and progression. However, the mechanisms by which YAP promotes cell invasion and metastasis are not fully understood. Here, we report that YAP induces leukocyte-specific integrin β2 (ITGB2) expression in cancer cells, thereby promoting cell invasion through the endothelium in a manner mimicking leukocytes. Through independent biochemical purification and a functional screen, we further identified PR/SET domain 4 (PRDM4) as a transcription factor interacting with the WW domains of YAP to mediate ITGB2 expression and cell invasion. Consistently, ITGB2 and PRDM4 mRNA levels are significantly increased in metastatic prostate cancer. In addition, PRDM4 contributes to YAP-induced tumorigenesis possibly via mediating the expression of other YAP target genes. Our results demonstrate that YAP promotes cell invasion by inducing leukocyte-specific integrin expression, and identify PRDM4 as a novel transcription factor for YAP targets.
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Affiliation(s)
- Huan Liu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoming Dai
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaolei Cao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huan Yan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyan Ji
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haitao Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuying Shen
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan Si
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hailong Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianfeng Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Li
- Institute of Aging Research, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jonathan C Zhao
- Department of Medicine-Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jindan Yu
- Department of Medicine-Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xin-Hua Feng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bin Zhao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
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16
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Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey. SCIENCE ADVANCES 2018; 4:eaaq0392. [PMID: 29740610 PMCID: PMC5938232 DOI: 10.1126/sciadv.aaq0392] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/14/2018] [Indexed: 06/01/2023]
Abstract
Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.
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Affiliation(s)
- Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah, Malaysia
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Andrew Waller
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Richard Newton
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Romain Paillot
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Neil Bryant
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Mark Vaudin
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France
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17
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NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming. Nat Cell Biol 2018. [PMID: 29531310 DOI: 10.1038/s41556-018-0047-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Somatic cell reprogramming by exogenous factors requires cooperation with transcriptional co-activators and co-repressors to effectively remodel the epigenetic environment. How this interplay is regulated remains poorly understood. Here, we demonstrate that NCoR/SMRT co-repressors bind to pluripotency loci to create a barrier to reprogramming with the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC), and consequently, suppressing NCoR/SMRT significantly enhances reprogramming efficiency and kinetics. The core epigenetic subunit of the NCoR/SMRT complex, histone deacetylase 3 (HDAC3), contributes to the effects of NCoR/SMRT by inducing histone deacetylation at pluripotency loci. Among the Yamanaka factors, recruitment of NCoR/SMRT-HDAC3 to genomic loci is mostly facilitated by c-MYC. Hence, we describe how c-MYC is beneficial for the early phase of reprogramming but deleterious later. Overall, we uncover a role for NCoR/SMRT co-repressors in reprogramming and propose a dual function for c-MYC in this process.
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18
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Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 2018; 356:356/6337/eaaj2239. [PMID: 28473536 DOI: 10.1126/science.aaj2239] [Citation(s) in RCA: 700] [Impact Index Per Article: 116.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
Abstract
The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.
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Affiliation(s)
- Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Ekaterina Morgunova
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Arttu Jolma
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Eevi Kaasinen
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Biswajyoti Sahu
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Syed Khund-Sayeed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA
| | - Pratyush K Das
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Teemu Kivioja
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Kashyap Dave
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Fan Zhong
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Kazuhiro R Nitta
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Minna Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Paul A Ginno
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Silvia Domcke
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Jian Yan
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Dirk Schübeler
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden. .,Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
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19
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Blimp-1/PRDM1 is a critical regulator of Type III Interferon responses in mammary epithelial cells. Sci Rep 2018; 8:237. [PMID: 29321612 PMCID: PMC5762727 DOI: 10.1038/s41598-017-18652-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/15/2017] [Indexed: 12/17/2022] Open
Abstract
The transcriptional repressor Blimp-1 originally cloned as a silencer of type I interferon (IFN)-β gene expression controls cell fate decisions in multiple tissue contexts. Conditional inactivation in the mammary gland was recently shown to disrupt epithelial cell architecture. Here we report that Blimp-1 regulates expression of viral defense, IFN signaling and MHC class I pathways, and directly targets the transcriptional activator Stat1. Blimp-1 functional loss in 3D cultures of mammary epithelial cells (MECs) results in accumulation of dsRNA and expression of type III IFN-λ. Cultures treated with IFN lambda similarly display defective lumen formation. These results demonstrate that type III IFN-λ profoundly influences the behavior of MECs and identify Blimp-1 as a critical regulator of IFN signaling cascades.
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20
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Li J, Qin Y, Zhang H. Identification of key miRNA-gene pairs in chronic lymphocytic leukemia through integrated analysis of mRNA and miRNA microarray. Oncol Lett 2017; 15:361-367. [PMID: 29285196 PMCID: PMC5738675 DOI: 10.3892/ol.2017.7287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/17/2017] [Indexed: 12/17/2022] Open
Abstract
The aim of the present study was to explore the miRNA-Gene regulatory mechanism in chronic lymphocytic leukemia (CLL), and identify new targets for the therapy of CLL. The miRNA expression dataset GSE62137 and mRNA expression dataset GSE22529 were downloaded from National Center of Biotechnology Information Gene Expression Omnibus database. In CLL samples compared with normal B cell samples, differentially expressed miRNAs (DEMs) were identified via the GEO2R instrument of GEO and differentially expressed genes (DEGs) were obtained via the limma package of R. Functional enrichment analysis of the DEGs was performed via the Database for Annotation, Visualization and Integrated Discovery. The targets of the DEMs were identified based on the miRNAWalk platform. The overlaps between the DEGs and the targets of the DEMs were selected, and the miRNA-Gene regulatory network was constructed based on the overlaps and the corresponding DEMs. A total of 63 DEMs and 504 DEGs were identified in CLL samples compared with normal B cell samples. Eleven enriched functional clusters of the DEGs were obtained. 405 miRNA-Gene regulatory pairs were identified. The miRNA-Gene regulatory pairs contained 351 target genes of the DEMs, including 9 overlaps with the DEGs. A miRNA-Gene regulatory network was constructed. Bioinformatics methods could help us develop a better understanding of the molecular mechanism of CLL. MiRNAs may play a critical role in regulating the process of CLL. They may affect CLL by regulating the processes of immunoreactivity and protein degradation. Genes such as Neurogenic Locus Notch Homolog Protein 2, PR/SET domain 4 and A-kinase anchoring protein 12 may be their regulating targets in CLL.
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Affiliation(s)
- Jie Li
- Department of Transfusion Medicine, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Yi Qin
- Institute of Medical Laboratory, Tianjin Medical University, Tianjin 300072, P.R. China
| | - Haiyan Zhang
- Department of Medical Record Management, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
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21
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Nelson AC, Mould AW, Bikoff EK, Robertson EJ. Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation. Sci Rep 2017; 7:6793. [PMID: 28754907 PMCID: PMC5533796 DOI: 10.1038/s41598-017-06859-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/19/2017] [Indexed: 12/18/2022] Open
Abstract
Trophoblast stem cells (TSCs) give rise to specialized cell types within the placenta. However, the regulatory mechanisms that guide trophoblast cell fate decisions during placenta development remain ill defined. Here we exploited ATAC-seq and transcriptional profiling strategies to describe dynamic changes in gene expression and chromatin accessibility during TSC differentiation. We detect significantly increased chromatin accessibility at key genes upregulated as TSCs exit from the stem cell state. However, downregulated gene expression is not simply due to the loss of chromatin accessibility in proximal regions. Additionally, transcriptional targets recognized by the zinc finger transcriptional repressor Prdm1/Blimp1, an essential regulator of placenta development, were identified in ChIP-seq experiments. Comparisons with previously reported ChIP-seq datasets for primordial germ cell-like cells and E18.5 small intestine, combined with functional annotation analysis revealed that Blimp1 has broadly shared as well as cell type-specific functional activities unique to the trophoblast lineage. Importantly, Blimp1 not only silences TSC gene expression but also prevents aberrant activation of divergent developmental programmes. Overall the present study provides new insights into the chromatin landscape and Blimp1-dependent regulatory networks governing trophoblast gene expression.
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Affiliation(s)
- Andrew C Nelson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.,School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Arne W Mould
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Elizabeth K Bikoff
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Elizabeth J Robertson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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Bashandy SAEM, Omara EAA, Ebaid H, Amin MM, Soliman MS. Role of zinc as an antioxidant and anti-inflammatory to relieve cadmium oxidative stress induced testicular damage in rats. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2016.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Tunbak H, Georgiou C, Guan C, Richardson WD, Chittka A. Zinc fingers 1, 2, 5 and 6 of transcriptional regulator, PRDM4, are required for its nuclear localisation. Biochem Biophys Res Commun 2016; 474:388-394. [PMID: 27125459 DOI: 10.1016/j.bbrc.2016.04.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 04/24/2016] [Indexed: 11/17/2022]
Abstract
PRDM4 is a member of the PRDM family of transcriptional regulators which control various aspects of cellular differentiation and proliferation. PRDM proteins exert their biological functions both in the cytosol and the nucleus of cells. All PRDM proteins are characterised by the presence of two distinct structural motifs, the PR/SET domain and the zinc finger (ZF) motifs. We previously observed that deletion of all six zinc fingers found in PRDM4 leads to its accumulation in the cytosol, whereas overexpressed full length PRDM4 is found predominantly in the nucleus. Here, we investigated the requirements for single zinc fingers in the nuclear localisation of PRDM4. We demonstrate that ZF's 1, 2, 5 and 6 contribute to the accumulation of PRDM4 in the nucleus. Their effect is additive as deleting either ZF1-2 or ZF 5-6 redistributes PRDM4 protein from being almost exclusively nuclear to cytosolic and nuclear. We investigated the potential mechanism of nuclear shuttling of PRDM4 via the importin α/β-mediated pathway and find that PRDM4 nuclear targeting is independent of α/β-mediated nuclear import.
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Affiliation(s)
- Hale Tunbak
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - Christiana Georgiou
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - Cui Guan
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - William David Richardson
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - Alexandra Chittka
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
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Han Y, Lin Q. [Research Progress of PR Domain Zinc Finger Protein 14]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2016; 19:93-7. [PMID: 26903163 PMCID: PMC6015138 DOI: 10.3779/j.issn.1009-3419.2016.02.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
正性调节区锌指蛋白14(PR domain zinc finger protein 14, PRDM14)是PRDM家族中的重要成员,PRDM14基因对维持细胞的完整性和控制细胞的分化、生长及凋亡起着关键作用,在原始生殖细胞的形成、干细胞全能性的维持和其他组织器官的形成中都发挥了重要作用。PRDM14具有1个PR结构域和6个锌指结构,PRDM14参与了组蛋白的去乙酰化及甲基化过程,通过启动子区甲基化水平的改变参与肿瘤的形成。PRDM14异常甲基化能够引起染色质结构、DNA构象及DNA与蛋白质作用方式的改变,使基因的转录和表达受抑制,这些改变引起了肿瘤的发生、发展及转移。本文根据国内外发表的相关文献对PRDM14的研究现状进行综述。
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Affiliation(s)
- Yudong Han
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
| | - Qiang Lin
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
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Mould AW, Morgan MAJ, Nelson AC, Bikoff EK, Robertson EJ. Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation. PLoS Genet 2015; 11:e1005375. [PMID: 26158850 PMCID: PMC4497732 DOI: 10.1371/journal.pgen.1005375] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/19/2015] [Indexed: 11/18/2022] Open
Abstract
The neonatal intestine is a very complex and dynamic organ that must rapidly adapt and remodel in response to a barrage of environmental stimuli during the first few postnatal weeks. Recent studies demonstrate that the zinc finger transcriptional repressor Blimp1/Prdm1 plays an essential role governing postnatal reprogramming of intestinal enterocytes during this period. Functional loss results in global changes in gene expression patterns, particularly in genes associated with metabolic function. Here we engineered a knock-in allele expressing an eGFP-tagged fusion protein under control of the endogenous regulatory elements and performed genome wide ChIP-seq analysis to identify direct Blimp1 targets and further elucidate the function of Blimp1 in intestinal development. Comparison with published human and mouse datasets revealed a highly conserved core set of genes including interferon-inducible promoters. Here we show that the interferon-inducible transcriptional activator Irf1 is constitutively expressed throughout fetal and postnatal intestinal epithelium development. ChIP-seq demonstrates closely overlapping Blimp1 and Irf1 peaks at key components of the MHC class I pathway in fetal enterocytes. The onset of MHC class I expression coincides with down-regulated Blimp1 expression during the suckling to weaning transition. Collectively, these experiments strongly suggest that in addition to regulating the enterocyte metabolic switch, Blimp1 functions as a gatekeeper in opposition to Irf1 to prevent premature activation of the MHC class I pathway in villus epithelium to maintain tolerance in the neonatal intestine. The transcriptional repressor Blimp1/Prdm1 plays a pivotal role in the metabolic switch that occurs in the small intestine during the suckling to weaning transition. Notably, expression profiling of perinatal Blimp1-deficient small intestine revealed premature activation of metabolic genes normally restricted to post-weaning enterocytes. To further elucidate the function of Blimp1 in intestinal development, we engineered a novel Blimp1-eGFP-fusion knock-in mouse strain to perform ChIP-seq analysis. In addition to identifying which metabolic genes are direct Blimp1 targets, ChIP-seq analysis revealed a highly conserved Blimp1/Irf-1 overlapping sites that function to control MHC class I antigen processing during acquisition of neonatal tolerance in the first weeks after birth during early colonization of the intestinal tract by commensal microorganisms. Moreover, immunohistochemical analysis of human fetal intestine suggests that a BLIMP1/IRF-1 axis may also function in human intestinal epithelium development.
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Affiliation(s)
- Arne W. Mould
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marc A. J. Morgan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Andrew C. Nelson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Elizabeth K. Bikoff
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail: (EKB); (EJR)
| | - Elizabeth J. Robertson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail: (EKB); (EJR)
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