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Kim J, Seo M, Lim Y, Kim J. START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402029. [PMID: 39075726 DOI: 10.1002/advs.202402029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/31/2024] [Indexed: 07/31/2024]
Abstract
Recognition of signaling molecules for coordinated regulation of target genes is a fundamental process for biological systems. Cells often rely on transcription factors to accomplish these intricate tasks, yet the subtle conformational changes of protein structures, coupled with the complexity of intertwined protein interaction networks, pose challenges for repurposing these for bioengineering applications. This study introduces a novel platform for ligand-responsive gene regulation, termed START (Synthetic Trans-Acting Riboswitch with Triggering RNA). Inspired by the bacterial ligand sensing system, riboswitch, and the synthetic gene regulator, toehold switch, the START platform enables the implementation of synthetic biosensors for various ligands. Rational sequence design with targeted domain optimization yields high-performance STARTs with a dynamic range up to 67.29-fold and a tunable ligand sensitivity, providing a simple and intuitive strategy for sensor engineering. The START platform also exhibits modularity and composability to allow flexible genetic circuit construction, enabling seamless implementation of OR, AND, and NOT Boolean logic gates for multiple ligand inputs. The START design principle is capable of broadening the suite of synthetic biosensors for diverse chemical and protein ligands, providing a novel riboregulator chassis for synthetic biology and bioengineering applications.
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Affiliation(s)
- Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Minchae Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Yelin Lim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
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2
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [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: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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3
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Li X, Tang P, Pang X, Song X, Xiong J, Yu L, Liu H, Pang C. The features analysis of hemoglobin expression on visual information transmission pathway in early stage of Alzheimer's disease. Sci Rep 2024; 14:15636. [PMID: 38972885 PMCID: PMC11228039 DOI: 10.1038/s41598-024-64099-0] [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: 03/06/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized primarily by cognitive impairment. The motivation of this paper is to explore the impact of the visual information transmission pathway (V-H pathway) on AD, and the following feature were observed: Hemoglobin expression on the V-H pathway becomes dysregulated as AD occurs so as to the pathway becomes dysfunctional. According to the feature, the following conclusion was proposed: As AD occurs, abnormal tau proteins penetrate bloodstream and arrive at the brain regions of the pathway. Then the tau proteins or other toxic substances attack hemoglobin molecules. Under the attack, hemoglobin expression becomes more dysregulated. The dysfunction of V-H pathway has an impact on early symptoms of AD, such as spatial recognition disorder and face recognition disorder.
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Affiliation(s)
- Xuehui Li
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Pan Tang
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xinping Pang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xianghu Song
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Jing Xiong
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Lei Yu
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Hui Liu
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Chaoyang Pang
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China.
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Jiang Y, Cai Y, Yang N, Gao S, Li Q, Pang Y, Su P. Molecular mechanisms of spinal cord injury repair across vertebrates: A comparative review. Eur J Neurosci 2024. [PMID: 38978308 DOI: 10.1111/ejn.16462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/09/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024]
Abstract
In humans and other adult mammals, axon regeneration is difficult in axotomized neurons. Therefore, spinal cord injury (SCI) is a devastating event that can lead to permanent loss of locomotor and sensory functions. Moreover, the molecular mechanisms of axon regeneration in vertebrates are not very well understood, and currently, no effective treatment is available for SCI. In striking contrast to adult mammals, many nonmammalian vertebrates such as reptiles, amphibians, bony fishes and lampreys can spontaneously resume locomotion even after complete SCI. In recent years, rapid progress in the development of next-generation sequencing technologies has offered valuable information on SCI. In this review, we aimed to provide a comparison of axon regeneration process across classical model organisms, focusing on crucial genes and signalling pathways that play significant roles in the regeneration of individually identifiable descending neurons after SCI. Considering the special evolutionary location and powerful regenerative ability of lamprey and zebrafish, they will be the key model organisms for ongoing studies on spinal cord regeneration. Detailed study of SCI in these model organisms will help in the elucidation of molecular mechanisms of neuron regeneration across species.
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Affiliation(s)
- Ying Jiang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yang Cai
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Ning Yang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Si Gao
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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5
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Wang M, Gao Y, Chen H, Cheng J, Wang G. Identification of core genes shared by ischemic stroke and myocardial infarction using an integrated approach. Medicine (Baltimore) 2024; 103:e38877. [PMID: 38968466 PMCID: PMC11224832 DOI: 10.1097/md.0000000000038877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Both ischemic stroke (IS) and myocardial infarction (MI) are caused by vascular occlusion that results in ischemia. While there may be similarities in their mechanisms, the potential relationship between these 2 diseases has not been comprehensively analyzed. Therefore, this study explored the commonalities in the pathogenesis of IS and MI. METHODS Datasets for IS (GSE58294, GSE16561) and MI (GSE60993, GSE61144) were downloaded from the Gene Expression Omnibus database. Transcriptome data from each of the 4 datasets were analyzed using bioinformatics, and the differentially expressed genes (DEGs) shared between IS and MI were identified and subsequently visualized using a Venn diagram. A protein-protein interaction (PPI) network was constructed using the Interacting Gene Retrieval Tool database, and identification of key core genes was performed using CytoHubba. Gene Ontology (GO) term annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the shared DEGs were conducted using prediction and network analysis methods, and the functions of the hub genes were determined using Metascape. RESULTS The analysis revealed 116 and 1321 DEGs in the IS and MI datasets, respectively. Of the 75 DEGs shared between IS and MI, 56 were upregulated and 19 were downregulated. Furthermore, 15 core genes - S100a12, Hp, Clec4d, Cd163, Mmp9, Ormdl3, Il2rb, Orm1, Irak3, Tlr5, Lrg1, Clec4e, Clec5a, Mcemp1, and Ly96 - were identified. GO enrichment analysis of the DEGs showed that they were mainly involved in the biological functions of neutrophil degranulation, neutrophil activation during immune response, and cytokine secretion. KEGG analysis showed enrichment in pathways pertaining to Salmonella infection, Legionellosis, and inflammatory bowel disease. Finally, the core gene-transcription factor, gene-microRNA, and small-molecule relationships were predicted. CONCLUSION These core genes may provide a novel theoretical basis for the diagnosis and treatment of IS and MI.
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Affiliation(s)
- Min Wang
- School of Clinical Medicine, Dali University, Dali, Yunnan, PR China
| | - Yuan Gao
- School of Clinical Medicine, Zhengzhou University, Zhengzhou, Henan, PR China
| | - Huaqiu Chen
- The First Hospital of Liangshan, Xichang, Sichuan, PR China
| | - Jianjie Cheng
- The First Affiliated Hospital of Dali University, Yunnan, PR China
| | - Guangming Wang
- School of Clinical Medicine, Dali University, Dali, Yunnan, PR China
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan, PR China
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6
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Ko DK, Brandizzi F. Dynamics of ER stress-induced gene regulation in plants. Nat Rev Genet 2024; 25:513-525. [PMID: 38499769 PMCID: PMC11186725 DOI: 10.1038/s41576-024-00710-4] [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] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
Endoplasmic reticulum (ER) stress is a potentially lethal condition that is induced by the abnormal accumulation of unfolded or misfolded secretory proteins in the ER. In eukaryotes, ER stress is managed by the unfolded protein response (UPR) through a tightly regulated, yet highly dynamic, reprogramming of gene transcription. Although the core principles of the UPR are similar across eukaryotes, unique features of the plant UPR reflect the adaptability of plants to their ever-changing environments and the need to balance the demands of growth and development with the response to environmental stressors. The past decades have seen notable progress in understanding the mechanisms underlying ER stress sensing and signalling transduction pathways, implicating the UPR in the effects of physiological and induced ER stress on plant growth and crop yield. Facilitated by sequencing technologies and advances in genetic and genomic resources, recent efforts have driven the discovery of transcriptional regulators and elucidated the mechanisms that mediate the dynamic and precise gene regulation in response to ER stress at the systems level.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
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7
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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8
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Nie XY, Menet JS. Circadian regulation of stereotypic chromatin conformations at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590818. [PMID: 38712031 PMCID: PMC11071494 DOI: 10.1101/2024.04.24.590818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cooperation between the circadian transcription factor (TF) CLOCK:BMAL1 and other TFs at cis-regulatory elements (CREs) is critical to daily rhythms of transcription. Yet, the modalities of this cooperation are unclear. Here, we analyzed the co-binding of multiple TFs on single DNA molecules in mouse liver using single molecule footprinting (SMF). We found that SMF reads clustered in stereotypic chromatin states that reflect distinguishable organization of TFs and nucleosomes, and that were remarkably conserved between all samples. DNA protection at CLOCK:BMAL1 binding motif (E-box) varied between CREs, from E-boxes being solely bound by CLOCK:BMAL1 to situations where other TFs competed with CLOCK:BMAL1 for E-box binding. SMF also uncovered CLOCK:BMAL1 cooperative binding at E-boxes separated by 250 bp, which structurally altered the CLOCK:BMAL1-DNA interface. Importantly, we discovered multiple nucleosomes with E-boxes at entry/exit sites that were removed upon CLOCK:BMAL1 DNA binding, thereby promoting the formation of open chromatin states that facilitate DNA binding of other TFs and that were associated with rhythmic transcription. These results demonstrate the utility of SMF for studying how CLOCK:BMAL1 and other TFs regulate stereotypical chromatin states at CREs to promote transcription.
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Affiliation(s)
- Xinyu Y. Nie
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX
| | - Jerome S. Menet
- Department of Biology, Center for Biological Clock Research, Texas A&M University, College Station, TX
- Interdisciplinary Program of Genetics, Texas A&M University, College Station, TX
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Ledesma-Dominguez L, Carbajal-Degante E, Moreno-Hagelsieb G, Perez-Rueda E. DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes. Sci Rep 2024; 14:9155. [PMID: 38644393 DOI: 10.1038/s41598-024-59487-5] [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: 09/13/2023] [Accepted: 04/11/2024] [Indexed: 04/23/2024] Open
Abstract
Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. In this work, we propose a hybrid model to identify transcription factors (TFs) among prokaryotic and eukaryotic protein sequences, named Deep Regulation (DeepReg) model. Two architectures were used in the DL model: a convolutional neural network (CNN), and a bidirectional long-short-term memory (BiLSTM). DeepReg reached a precision of 0.99, a recall of 0.97, and an F1-score of 0.98. The quality of our predictions, the bias-variance trade-off approach, and the characterization of new TF predictions were evaluated and compared against those produced by DeepTFactor, as well as against experimental data from three model organisms. Predictions based on our DLM tended to exhibit less variance and bias than those from DeepTFactor, thus increasing reliability and decreasing overfitting.
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Affiliation(s)
- Leonardo Ledesma-Dominguez
- Posgrado en Ciencia en Ingeniería de la Computación, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, 04510, Mexico City, México.
| | - Erik Carbajal-Degante
- Coordinación de Universidad Abierta y Educación Digital (CUAED), Universidad Nacional Autónoma de México, 04510, Mexico City, México
| | | | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica del Estado de Yucatán, Universidad Nacional Autónoma de México, Mérida, Yucatán, México.
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10
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Cisterna B, Malatesta M. Molecular and Structural Alterations of Skeletal Muscle Tissue Nuclei during Aging. Int J Mol Sci 2024; 25:1833. [PMID: 38339110 PMCID: PMC10855217 DOI: 10.3390/ijms25031833] [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: 12/27/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Aging is accompanied by a progressive loss of skeletal muscle mass and strength. The mechanisms underlying this phenomenon are certainly multifactorial and still remain to be fully elucidated. Changes in the cell nucleus structure and function have been considered among the possible contributing causes. This review offers an overview of the current knowledge on skeletal muscle nuclei in aging, focusing on the impairment of nuclear pathways potentially involved in age-related muscle decline. In skeletal muscle two types of cells are present: fiber cells, constituting the contractile muscle mass and containing hundreds of myonuclei, and the satellite cells, i.e., the myogenic mononuclear stem cells occurring at the periphery of the fibers and responsible for muscle growth and repair. Research conducted on different experimental models and with different methodological approaches demonstrated that both the myonuclei and satellite cell nuclei of aged skeletal muscles undergo several structural and molecular alterations, affecting chromatin organization, gene expression, and transcriptional and post-transcriptional activities. These alterations play a key role in the impairment of muscle fiber homeostasis and regeneration, thus contributing to the age-related decrease in skeletal muscle mass and function.
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Affiliation(s)
| | - Manuela Malatesta
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
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11
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Shi D, Feng W, Zi Z. Machine learning unveils RNA polymerase II binding as a predictor for SMAD2-dependent transcription dynamics in response to Actvin signalling. IET Syst Biol 2024; 18:14-22. [PMID: 38193845 PMCID: PMC10860719 DOI: 10.1049/syb2.12085] [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: 08/07/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 01/10/2024] Open
Abstract
The transforming growth factor-β (TGF-β) superfamily, including Nodal and Activin, plays a critical role in various cellular processes. Understanding the intricate regulation and gene expression dynamics of TGF-β signalling is of interest due to its diverse biological roles. A machine learning approach is used to predict gene expression patterns induced by Activin using features, such as histone modifications, RNA polymerase II binding, SMAD2-binding, and mRNA half-life. RNA sequencing and ChIP sequencing datasets were analysed and differentially expressed SMAD2-binding genes were identified. These genes were classified into activated and repressed categories based on their expression patterns. The predictive power of different features and combinations was evaluated using logistic regression models and their performances were assessed. Results showed that RNA polymerase II binding was the most informative feature for predicting the expression patterns of SMAD2-binding genes. The authors provide insights into the interplay between transcriptional regulation and Activin signalling and offers a computational framework for predicting gene expression patterns in response to cell signalling.
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Affiliation(s)
- Dan Shi
- Max Planck Institute for Molecular GeneticsOtto Warburg LaboratoryBerlinGermany
| | - Weihua Feng
- Zhengzhou Tobacco Research Institute of China National Tobacco CorporationZhengzhouChina
| | - Zhike Zi
- Max Planck Institute for Molecular GeneticsOtto Warburg LaboratoryBerlinGermany
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
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12
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Danielewski M, Rapak A, Kruszyńska A, Małodobra-Mazur M, Oleszkiewicz P, Dzimira S, Kucharska AZ, Słupski W, Matuszewska A, Nowak B, Szeląg A, Piórecki N, Zaleska-Dorobisz U, Sozański T. Cornelian Cherry ( Cornus mas L.) Fruit Extract Lowers SREBP-1c and C/EBPα in Liver and Alters Various PPAR-α, PPAR-γ, LXR-α Target Genes in Cholesterol-Rich Diet Rabbit Model. Int J Mol Sci 2024; 25:1199. [PMID: 38256272 PMCID: PMC10816641 DOI: 10.3390/ijms25021199] [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: 12/23/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Cornelian cherry (Cornus mas L.) fruits, abundant in iridoids and anthocyanins, are natural products with proven beneficial impacts on the functions of the cardiovascular system and the liver. This study aims to assess and compare whether and to what extent two different doses of resin-purified cornelian cherry extract (10 mg/kg b.w. or 50 mg/kg b.w.) applied in a cholesterol-rich diet rabbit model affect the levels of sterol regulatory element-binding protein 1c (SREBP-1c) and CCAAT/enhancer binding protein α (C/EBPα), and various liver X receptor-α (LXR-α), peroxisome proliferator-activated receptor-α (PPAR-α), and peroxisome proliferator-activated receptor-γ (PPAR-γ) target genes. Moreover, the aim is to evaluate the resistive index (RI) of common carotid arteries (CCAs) and aortas, and histopathological changes in CCAs. For this purpose, the levels of SREBP-1c, C/EBPα, ATP-binding cassette transporter A1 (ABCA1), ATP-binding cassette transporter G1 (ABCG1), fatty acid synthase (FAS), endothelial lipase (LIPG), carnitine palmitoyltransferase 1A (CPT1A), and adiponectin receptor 2 (AdipoR2) in liver tissue were measured. Also, the levels of lipoprotein lipase (LPL), visceral adipose tissue-derived serine protease inhibitor (Vaspin), and retinol-binding protein 4 (RBP4) in visceral adipose tissue were measured. The RI of CCAs and aortas, and histopathological changes in CCAs, were indicated. The oral administration of the cornelian cherry extract decreased the SREBP-1c and C/EBPα in both doses. The dose of 10 mg/kg b.w. increased ABCA1 and decreased FAS, CPT1A, and RBP4, and the dose of 50 mg/kg b.w. enhanced ABCG1 and AdipoR2. Mitigations in atheromatous changes in rabbits' CCAs were also observed. The obtained outcomes were compared to the results of our previous works. The beneficial results confirm that cornelian cherry fruit extract may constitute a potentially effective product in the prevention and treatment of obesity-related disorders.
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Affiliation(s)
- Maciej Danielewski
- Department of Pharmacology, Wroclaw Medical University, J. Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (W.S.); (A.M.); (B.N.); (A.S.)
| | - Andrzej Rapak
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (A.R.); (A.K.)
| | - Angelika Kruszyńska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (A.R.); (A.K.)
| | - Małgorzata Małodobra-Mazur
- Department of Forensic Medicine, Division of Molecular Techniques, Wroclaw Medical University, M. Sklodowskiej-Curie 52, 50-369 Wroclaw, Poland;
| | - Paweł Oleszkiewicz
- Department of Radiology and Imaging Diagnostics II, Lower Silesian Center of Oncology, Pulmonology and Hematology, Grabiszynska 105, 53-439 Wroclaw, Poland;
| | - Stanisław Dzimira
- Department of Pathology, Wroclaw University of Environmental and Life Sciences, C. K. Norwida 31, 50-375 Wroclaw, Poland;
| | - Alicja Z. Kucharska
- Department of Fruit, Vegetable, and Plant Nutraceutical Technology, Wroclaw University of Environmental and Life Sciences, J. Chelmonskiego 37, 51-630 Wroclaw, Poland;
| | - Wojciech Słupski
- Department of Pharmacology, Wroclaw Medical University, J. Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (W.S.); (A.M.); (B.N.); (A.S.)
| | - Agnieszka Matuszewska
- Department of Pharmacology, Wroclaw Medical University, J. Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (W.S.); (A.M.); (B.N.); (A.S.)
| | - Beata Nowak
- Department of Pharmacology, Wroclaw Medical University, J. Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (W.S.); (A.M.); (B.N.); (A.S.)
| | - Adam Szeląg
- Department of Pharmacology, Wroclaw Medical University, J. Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (W.S.); (A.M.); (B.N.); (A.S.)
| | - Narcyz Piórecki
- Bolestraszyce Arboretum and Institute of Physiography, Bolestraszyce 130, 37-722 Wyszatyce, Poland;
- Institute of Physical Culture Sciences, Medical College, University of Rzeszow, Cicha 2A, 35-326 Rzeszow, Poland
| | - Urszula Zaleska-Dorobisz
- Department of General and Pediatric Radiology, Wroclaw Medical University, M. Sklodowskiej-Curie 50/52, 50-369 Wroclaw, Poland;
| | - Tomasz Sozański
- Department of Preclinical Sciences, Pharmacology and Medical Diagnostics, Faculty of Medicine, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland;
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13
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Tyagi S, Tyagi S. Incidence of Prostate Cancer in Transgender Women Undergoing Androgen Deprivation Therapy: A Review. Indian J Endocrinol Metab 2023; 27:476-479. [PMID: 38371191 PMCID: PMC10871014 DOI: 10.4103/ijem.ijem_53_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/10/2023] [Accepted: 06/25/2023] [Indexed: 02/20/2024] Open
Abstract
Transwomen frequently undergo androgen deprivation therapy (ADT) incorporated with oestrogen, but they are still prone to the occurrence of prostatic cancer since the prostate remains intact. The probability of this clinical condition reduces as compared with the general male population. This study aimed to study the occurrence of prostatic malignancy under hormonal therapy such as ADT in transwomen. An extensive literature search was performed using online searches on transgender health, centring on the incidence, diagnosis, treatment and management of prostate cancer in transgender women. Original articles from 1975 to 2022 were searched using PubMed, Scopus, EMBASE, DOAJ and Cochrane databases. Physical, mental and communal deliberation of health development is the major constituent of trans-health. It exhibits a fivefold reduction in prostatic malignancies in transwomen undergoing hormonal therapy contrasted with the extensive male community of indistinguishable age.
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Affiliation(s)
- Saurabh Tyagi
- MBBS Student, Gautam Buddha Chikitsa Mahavidyalya, Dehradun, Uttarakhand, India
| | - Surbhi Tyagi
- Department of Biochemistry, Subharti Medical College, Meerut, Uttar Pradesh, India
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14
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Khan DMIO, Karmaus PWF, Bach A, Crawford RB, Kaminski NE. An in vitro model of human hematopoiesis identifies a regulatory role for the aryl hydrocarbon receptor. Blood Adv 2023; 7:6253-6265. [PMID: 37477592 PMCID: PMC10589788 DOI: 10.1182/bloodadvances.2023010169] [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: 03/13/2023] [Revised: 06/22/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
In vitro models to study simultaneous development of different human immune cells and hematopoietic lineages are lacking. We identified and characterized, using single-cell methods, an in vitro stromal cell-free culture system of human hematopoietic stem and progenitor cell (HSPC) differentiation that allows concurrent development of multiple immune cell lineages. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor influencing many biological processes in diverse cell types. Using this in vitro model, we found that AHR activation by the highly specific AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin, drives differentiation of human umbilical cord blood-derived CD34+ HSPCs toward monocytes and granulocytes with a significant decrease in lymphoid and megakaryocyte lineage specification that may lead to reduced immune competence. To our knowledge, we also discovered for the first time, using single-cell modalities, that AHR activation decreased the expression of BCL11A and IRF8 in progenitor cells, which are critical genes involved in hematopoietic lineage specification processes at both transcriptomic and protein levels. Our in vitro model of hematopoiesis, coupled with single-cell tools, therefore allows for a better understanding of the role played by AHR in modulating hematopoietic differentiation.
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Affiliation(s)
- D M Isha Olive Khan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
| | - Peer W. F. Karmaus
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
- National Institute of Environmental Health Sciences, Durham, NC
| | - Anthony Bach
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
| | - Robert B. Crawford
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
| | - Norbert E. Kaminski
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI
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15
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Hong YK, Nakamoto M, Matsusaki M. Engineering metabolic cycle-inspired hydrogels with enzyme-fueled programmable transient volume changes. J Mater Chem B 2023; 11:8136-8141. [PMID: 37565488 DOI: 10.1039/d3tb00638g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
An enzyme-fueled transient volume phase transition (TVPT) of hydrogels under out-of-equilibrium conditions is reported. The approach takes inspiration from the metabolic cycle, comprising nutrient intake and anabolism/catabolism followed by waste excretion. The incorporation of methacrylic acid and acrylated trypsin in a polymeric hydrogel allowed the TVPT of the gel to be fueled by lysozyme. With the intake of lysozyme as fuel, the construction/destruction of electrostatic cross-linkages induced transient shrinkage/swelling of the gel accompanied by the depletion of lysozyme activity. The system's transient response could be flexibly programmed by adjusting not only the fuel concentration but the chemical composition of materials. The lysozyme-fueled TVPT of the gel could be exploited to transient changes in the mechanical properties of the gel. Our work opens a route toward a new class of stimuli-responsive hydrogels for biomedical applications.
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Affiliation(s)
- Young Kyoung Hong
- School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiko Nakamoto
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Michiya Matsusaki
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
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16
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Xu W, Li X. Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver. BIOLOGY 2023; 12:1107. [PMID: 37626993 PMCID: PMC10452108 DOI: 10.3390/biology12081107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Cell autonomous circadian oscillation is present in central and various peripheral tissues. The intrinsic tissue clock and various extrinsic cues drive gene expression rhythms. Transcription regulation is thought to be the main driving force for gene rhythms. However, how transcription rhythms arise remains to be fully characterized due to the fact that transcription is regulated at multiple steps. In particular, Pol II recruitment, pause release, and premature transcription termination are critical regulatory steps that determine the status of Pol II pausing and transcription output near the transcription start site (TSS) of the promoter. Recently, we showed that Pol II pausing exhibits genome-wide changes during daily transcription in mouse liver. In this article, we review historical as well as recent findings on the regulation of transcription rhythms by the circadian clock and other transcription factors, and the potential limitations of those results in explaining rhythmic transcription at the TSS. We then discuss our results on the genome-wide characteristics of daily changes in Pol II pausing, the possible regulatory mechanisms involved, and their relevance to future research on circadian transcription regulation.
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Affiliation(s)
| | - Xiaodong Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China;
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17
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Al-Hawary SIS, Pallathadka H, Hjazi A, Zhumanov ZE, Alazbjee AAA, Imad S, Alsalamy A, Hussien BM, Jaafer NS, Mahmoudi R. ETS transcription factor ELK3 in human cancers: An emerging therapeutic target. Pathol Res Pract 2023; 248:154728. [PMID: 37542863 DOI: 10.1016/j.prp.2023.154728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
Cancer is a genetic and complex disorder, resulting from several events associated with onset, development, and metastasis. Tumor suppressors and oncogenes are among the main regulators of tumor progression, contributing to various cancer-related behaviors like cell proliferation, invasion, migration, epithelial-mesenchymal transition (EMT), cell cycle, and apoptosis. Transcription factors (TFs) could act as tumor suppressors or oncogenes in cancer progression. E-twenty-six/E26 (ETS) family of TFs have a winged helix-turn-helix (HLH) motif, which interacted with specific DNA regions with high levels of purines and GGA core. ETS proteins act as transcriptional repressors or activators to modulate the expression of target genes. ETS transcription factor ELK3 (ELK3), as a type of ETS protein, was shown to enhance in various cancers, suggesting that it may have an oncogenic role. These studies indicated that ELK3 promoted invasion, migration, cell cycle, proliferation, and EMT, and suppressed cell apoptosis. In addition, these studies demonstrated that ELK3 could be a promising diagnostic and prognostic biomarker in human cancer. Moreover, accumulating data proved that ELK3 could be a novel chemoresistance mediator in human cancer. Here, we aimed to explore the overall change of ELK3 and its underlying molecular mechanism in human cancers. Moreover, we aimed to investigate the potential role of ELK3 as a prognostic and diagnostic biomarker as well as its capability as a chemoresistance mediator in cancer.
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Affiliation(s)
| | | | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ziyadulla Eshmamatovich Zhumanov
- Department of Pathological Anatomy, With a Section-biopsy Course, Samarkand State Medical Institute, Amir Temur Street 18, Samarkand, Uzbekistan; Department of Scientific Affairs, Tashkent State Dental Institute, Makhtumkuli Street 103, Tashkent 100047, Uzbekistan
| | | | - Shad Imad
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Noor Sadiq Jaafer
- Department of Medical Laboratory Technologies, Al Rafidain University College, Bagdad, Iraq
| | - Reza Mahmoudi
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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18
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Tognon M, Giugno R, Pinello L. A survey on algorithms to characterize transcription factor binding sites. Brief Bioinform 2023; 24:bbad156. [PMID: 37099664 PMCID: PMC10422928 DOI: 10.1093/bib/bbad156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023] Open
Abstract
Transcription factors (TFs) are key regulatory proteins that control the transcriptional rate of cells by binding short DNA sequences called transcription factor binding sites (TFBS) or motifs. Identifying and characterizing TFBS is fundamental to understanding the regulatory mechanisms governing the transcriptional state of cells. During the last decades, several experimental methods have been developed to recover DNA sequences containing TFBS. In parallel, computational methods have been proposed to discover and identify TFBS motifs based on these DNA sequences. This is one of the most widely investigated problems in bioinformatics and is referred to as the motif discovery problem. In this manuscript, we review classical and novel experimental and computational methods developed to discover and characterize TFBS motifs in DNA sequences, highlighting their advantages and drawbacks. We also discuss open challenges and future perspectives that could fill the remaining gaps in the field.
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Affiliation(s)
- Manuel Tognon
- Computer Science Department, University of Verona, Verona, Italy
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rosalba Giugno
- Computer Science Department, University of Verona, Verona, Italy
| | - Luca Pinello
- Molecular Pathology Unit, Center for Computational and Integrative Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
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19
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Sui Z, Zhang Y, Zhang Z, Wang C, Li X, Xing F, Chu M. Analysis of Lin28B Promoter Activity and Screening of Related Transcription Factors in Dolang Sheep. Genes (Basel) 2023; 14:genes14051049. [PMID: 37239408 DOI: 10.3390/genes14051049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The Lin28B gene is involved in the initiation of puberty, but its regulatory mechanisms remain unclear. Therefore, in this study, we aimed to study the regulatory mechanism of the Lin28B promoter by cloning the Lin28B proximal promoter for bioinformatic analysis. Next, a series of deletion vectors were constructed based on the bioinformatic analysis results for dual-fluorescein activity detection. The transcriptional regulation mechanism of the Lin28B promoter region was analyzed by detecting mutations in transcription factor-binding sites and overexpression of transcription factors. The dual-luciferase assay showed that the Lin28B promoter region -837 to -338 bp had the highest transcriptional activity, and the transcriptional activity of the Lin28B transcriptional regulatory region decreased significantly after Egr1 and SP1 mutations. Overexpression of the Egr1 transcription factor significantly enhanced the transcription of Lin28B, and the results indicated that Egr1 and SP1 play important roles in regulating Lin28B. These results provide a theoretical basis for further research on the transcriptional regulation of sheep Lin28B during puberty initiation.
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Affiliation(s)
- Zhiyuan Sui
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar 843300, China
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Yongjie Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar 843300, China
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Zhishuai Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar 843300, China
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Chenguang Wang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar 843300, China
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Xiaojun Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar 843300, China
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Feng Xing
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar 843300, China
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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20
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Sui Z, Zhang Z, Zhang Y, Zhang J, Li Q, Xing F. Analysis of Methylation and mRNA Expression of Lin28B Gene Promoter Region in the Hypothalamus of Dolang Sheep During Pubertal Initiation. DNA Cell Biol 2023; 42:130-139. [PMID: 36809059 DOI: 10.1089/dna.2022.0281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Lin28B plays an important role in puberty initiation in sheep. This study aimed to discuss the correlation between different growth periods and the methylation status of cytosine-guanine dinucleotide (CpG) islands in the promoter region of the Lin28B gene in the Dolang sheep's hypothalamus. In this study, the sequence of the Lin28B gene promoter region in Dolang sheep was obtained by cloning and sequencing, and methyl groups of the CpG island of the Lin28B gene promoter in the hypothalamus were detected by bisulfite sequencing PCR during the three periods of prepuberty, adolescence, and postpuberty in Dolang sheep. Lin28B expression in the Dolang sheep's hypothalamus was detected by fluorescence quantitative PCR at three stages: prepuberty, puberty, and postpuberty. In this experiment, the 2993-bp Lin28B promoter region was obtained, and it was predicted that there was a CpG island containing 15 transcription factor binding sites and 12 CpG sites, which may play a role in gene expression regulation. Overall, methylation levels increased from prepuberty to postpuberty, while Lin28B expression levels decreased, indicating that Lin28B expression was negatively correlated with promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG5, CpG7, and CpG9 between pre- and postpuberty (p < 0.05). Our data show that Lin28B expression is increased by demethylation of promoter CpG islands, with CpG5, CpG7, and CpG9 implicated as critical regulatory sites.
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Affiliation(s)
- Zhiyuan Sui
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Zhishuai Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Yongjie Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Jihu Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Qingjin Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Feng Xing
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
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21
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Kuo TL, Cheng KH, Chen LT, Hung WC. ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance. iScience 2023; 26:105881. [PMID: 36654862 PMCID: PMC9840936 DOI: 10.1016/j.isci.2022.105881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
ARID1A is a tumor suppressor gene mutated in 7-10% of pancreatic cancer patients. However, its function in pancreas development and endocrine regulation is unclear. We generated mice that lack Arid1a expression in the pancreas. Our results showed that deletion of the Arid1a gene in mice caused a reduction in islet numbers and insulin production, both of which are associated with diabetes mellitus (DM) phenotype. RNA sequencing of isolated islets confirmed DM gene signature and decrease of developmental lineage genes. We identified neurogenin3, a transcription factor that controls endocrine fate specification, is a direct target of Aird1a. Gene set enrichment analysis indicated the enhancement of histone deacetylase (HDAC) pathway after Arid1a depletion and a clinically approved HDAC inhibitor showed therapeutic benefit by suppressing disease onset. Our data suggest that Arid1a is required for the development of pancreatic islets by regulating Ngn3+-mediated transcriptional program and is important in maintaining endocrine function.
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Affiliation(s)
- Tzu-Lei Kuo
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Kuang-Hung Cheng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- Division of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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22
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Shaban HA. Nucleus-wide analysis of coherent RNA pol II movement in the context of chromatin dynamics in living cancer cells. Nucleus 2022; 13:313-318. [PMID: 36512483 PMCID: PMC9754109 DOI: 10.1080/19491034.2022.2157133] [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] [Indexed: 12/15/2022] Open
Abstract
Activation of transcription results in coordinated movement of chromatin over a range of micrometers. To investigate how transcriptional regulation affects the mobility of RNA Pol II molecules and whether this movement response depends on the coordinated movement of chromatin, we used our Dense Flow reConstruction and Correlation (DFCC) method. Using DFCC, we studies the nucleus-wide coherent movements of RNA Pol II in the context of DNA in humancancer cells. This study showed the dependance of coherent movements of RNA Pol II molecules (above 1 µm) on transcriptional activity. Here, we share the dataset of this study, includes nucleus-wide live imaging and analysis of DNA and RNA polymerase II in different transcription states, and the code for teh analysis. Our dataset may provide researchers interested in the long-range organization of chromatin in living cell images with the ability to link the structural genomic compartment to dynamic information. .
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Affiliation(s)
- Haitham A. Shaban
- Agora Cancer Research Center, Lausanne, Switzerland,Precision Oncology Center, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland,Spectroscopy Department, Physics Division, National Research Centre, Cairo, Egypt,CONTACT Haitham A. Shaban Precision Oncology Center, Department of Oncology, Lausanne University Hospital, Lausanne1005, Switzerland
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23
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Kim IB, Lee T, Lee J, Kim J, Lee S, Koh IG, Kim JH, An JY, Lee H, Kim WK, Ju YS, Cho Y, Yu SJ, Kim SA, Oh M, Han DW, Kim E, Choi JK, Yoo HJ, Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry 2022; 27:4680-4694. [PMID: 35840799 DOI: 10.1038/s41380-022-01697-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.
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Affiliation(s)
- Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, Hanyang University Guri Hospital, Guri, 11923, Republic of Korea
| | - Taeyeop Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea
| | - In Gyeong Koh
- Industry-University Cooperation Foundation, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05030, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongseong Cho
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, Eulji University, Daejeon, 13135, Republic of Korea
| | - Miae Oh
- Department of Psychiatry, Kyung Hee University Hospital, Seoul, 02447, Republic of Korea
| | - Dong Wook Han
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.,Organoid sciences, Ltd., Bundang-gu, Seongnam, 13488, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea. .,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Psychiatry, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Sovargen Co. Ltd., Daejeon, 34051, Republic of Korea.
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Ding X, Yu L, Chen L, Li Y, Zhang J, Sheng H, Ren Z, Li Y, Yu X, Jin S, Cao J. Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants. Cells 2022; 11:3045. [PMID: 36231007 PMCID: PMC9564188 DOI: 10.3390/cells11193045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous genome editing system. In addition, the emergence of Cas9 mutants, such as dCas9 (dead Cas9), which lost its endonuclease activity but maintains DNA recognition activity with the guide RNA, provides powerful genetic manipulation tools. In particular, combining the dCas9 protein and transcriptional activator to achieve specific regulation of gene expression has made important contributions to biotechnology in medical research as well as agriculture. CRISPR/dCas9 activation (CRISPRa) can increase the transcription of endogenous genes. Overexpression of foreign genes by traditional transgenic technology in plant cells is the routine method to verify gene function by elevating genes transcription. One of the main limitations of the overexpression is the vector capacity constraint that makes it difficult to express multiple genes using the typical Ti plasmid vectors from Agrobacterium. The CRISPRa system can overcome these limitations of the traditional gene overexpression method and achieve multiple gene activation by simply designating several guide RNAs in one vector. This review summarizes the latest progress based on the development of CRISPRa systems, including SunTag, dCas9-VPR, dCas9-TV, scRNA, SAM, and CRISPR-Act and their applications in plants. Furthermore, limitations, challenges of current CRISPRa systems and future prospective applications are also discussed.
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Affiliation(s)
- Xiao Ding
- Institute of Cotton, Shanxi Agricultural University, Yuncheng 044000, China
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Luo Chen
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujie Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinlun Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanyan Sheng
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengwei Ren
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunlong Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohan Yu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinglin Cao
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China
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Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.). Genes (Basel) 2022; 13:genes13101732. [PMID: 36292617 PMCID: PMC9602024 DOI: 10.3390/genes13101732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/21/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Drought is a major abiotic stressor that causes yield losses and limits the growing area for most crops. Soybeans are an important legume crop that is sensitive to water-deficit conditions and suffers heavy yield losses from drought stress. To improve drought-tolerant soybean cultivars through breeding, it is necessary to understand the mechanisms of drought tolerance in soybeans. In this study, we applied several transcriptome datasets obtained from soybean plants under drought stress in comparison to those grown under normal conditions to identify novel drought-responsive genes and their underlying molecular mechanisms. We found 2168 significant up/downregulated differentially expressed genes (DEGs) and 8 core modules using gene co-expression analysis to predict their biological roles in drought tolerance. Gene Ontology and KEGG analyses revealed key biological processes and metabolic pathways involved in drought tolerance, such as photosynthesis, glyceraldehyde-3-phosphate dehydrogenase and cytokinin dehydrogenase activity, and regulation of systemic acquired resistance. Genome-wide analysis of plants’ cis-acting regulatory elements (CREs) and transcription factors (TFs) was performed for all of the identified DEG promoters in soybeans. Furthermore, the PPI network analysis revealed significant hub genes and the main transcription factors regulating the expression of drought-responsive genes in each module. Among the four modules associated with responses to drought stress, the results indicated that GLYMA_04G209700, GLYMA_02G204700, GLYMA_06G030500, GLYMA_01G215400, and GLYMA_09G225400 have high degrees of interconnection and, thus, could be considered as potential candidates for improving drought tolerance in soybeans. Taken together, these findings could lead to a better understanding of the mechanisms underlying drought responses in soybeans, which may useful for engineering drought tolerance in plants.
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Dissanayaka Mudiyanselage SD, Ma J, Pechan T, Pechanova O, Liu B, Wang Y. A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription. PLoS Pathog 2022; 18:e1010850. [PMID: 36121876 PMCID: PMC9521916 DOI: 10.1371/journal.ppat.1010850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.
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Affiliation(s)
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Olga Pechanova
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Bin Liu
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
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27
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López-Jiménez E, González-Aguilera C. Role of Chromatin Replication in Transcriptional Plasticity, Cell Differentiation and Disease. Genes (Basel) 2022; 13:genes13061002. [PMID: 35741764 PMCID: PMC9222293 DOI: 10.3390/genes13061002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin organization is essential to maintain a correct regulation of gene expression and establish cell identity. However, during cell division, the replication of the genetic material produces a global disorganization of chromatin structure. In this paper, we describe the new scientific breakthroughs that have revealed the nature of the post-replicative chromatin and the mechanisms that facilitate its restoration. Moreover, we highlight the implications of these chromatin alterations in gene expression control and their impact on key biological processes, such as cell differentiation, cell reprogramming or human diseases linked to cell proliferation, such as cancer.
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Affiliation(s)
- Elena López-Jiménez
- Faculty of Medicine, National Heart and Lung Institute, Margaret Turner Warwick Centre for Fibrosing Lung Disease, Royal Brompton Campus, Imperial College London, London SW3 6LY, UK;
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence:
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28
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Qiu G, Deng Y. ZFP64 transcriptionally activates PD-1 and CTLA-4 and plays an oncogenic role in esophageal cancer. Biochem Biophys Res Commun 2022; 622:72-78. [DOI: 10.1016/j.bbrc.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/05/2022] [Indexed: 11/02/2022]
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29
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Ko DK, Brandizzi F. Transcriptional competition shapes proteotoxic ER stress resolution. NATURE PLANTS 2022; 8:481-490. [PMID: 35577961 PMCID: PMC9187302 DOI: 10.1038/s41477-022-01150-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Through dynamic activities of conserved master transcription factors (mTFs), the unfolded protein response (UPR) relieves proteostasis imbalance of the endoplasmic reticulum (ER), a condition known as ER stress1,2. Because dysregulated UPR is lethal, the competence for fate changes of the UPR mTFs must be tightly controlled3,4. However, the molecular mechanisms underlying regulatory dynamics of mTFs remain largely elusive. Here, we identified the abscisic acid-related regulator G-class bZIP TF2 (GBF2) and the cis-regulatory element G-box as regulatory components of the plant UPR led by the mTFs, bZIP28 and bZIP60. We demonstrate that, by competing with the mTFs at G-box, GBF2 represses UPR gene expression. Conversely, a gbf2 null mutation enhances UPR gene expression and suppresses the lethality of a bzip28 bzip60 mutant in unresolved ER stress. By demonstrating that GBF2 functions as a transcriptional repressor of the UPR, we address the long-standing challenge of identifying shared signalling components for a better understanding of the dynamic nature and complexity of stress biology. Furthermore, our results identify a new layer of UPR gene regulation hinged upon an antagonistic mTFs-GFB2 competition for proteostasis and cell fate determination.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
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30
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Biswas J, Li W, Singer RH, Coleman RA. Imaging Organization of RNA Processing within the Nucleus. Cold Spring Harb Perspect Biol 2021; 13:a039453. [PMID: 34127450 PMCID: PMC8635003 DOI: 10.1101/cshperspect.a039453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Within the nucleus, messenger RNA is generated and processed in a highly organized and regulated manner. Messenger RNA processing begins during transcription initiation and continues until the RNA is translated and degraded. Processes such as 5' capping, alternative splicing, and 3' end processing have been studied extensively with biochemical methods and more recently with single-molecule imaging approaches. In this review, we highlight how imaging has helped understand the highly dynamic process of RNA processing. We conclude with open questions and new technological developments that may further our understanding of RNA processing.
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Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Weihan Li
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robert A Coleman
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. Int J Mol Sci 2021; 22:ijms222312855. [PMID: 34884664 PMCID: PMC8657788 DOI: 10.3390/ijms222312855] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 01/01/2023] Open
Abstract
The basic helix–loop–helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell’s fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.
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32
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Kemppainen M, Pardo A. Nucleus-directed fluorescent reporter system for promoter studies in the ectomycorrhizal fungus Laccaria bicolor. J Microbiol Methods 2021; 190:106341. [PMID: 34610385 DOI: 10.1016/j.mimet.2021.106341] [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: 08/09/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022]
Abstract
Currently ectomycorrhizal research suffers from a lack of molecular tools specifically adapted to study gene expression in fungal symbionts. Considering that, we designed pReNuK, a cloning vector for transcriptional promoter studies in the ectomycorrhizal basidiomycete Laccaria bicolor. The pReNuK vector offers the use of a nuclear localizing and chromatin incorporating histone H2B-mCherry fluorescent reporter protein and it is specifically optimized for efficient transgene expression in Laccaria. Moreover, pReNuK is designed to work in concert with Agrobacterium-mediated transformation under hygromycin B resistance selection. The functionality of the pReNuK reporter system was tested with the constitutive Laccaria glyceraldehyde 3-phosphate dehydrogenase gene promoter and further validated with the nitrogen source regulated nitrate reductase gene promoter. The expression of the nucleus-directed H2B-mCherry reporter is highly stable in time. Moreover, the transformation of Laccaria with pReNuK and the expression of the reporter do not have negative effects on the growth of the fungus. The pReNuK offers a novel tool for studying in vivo gene expression regulation in Laccaria, the leading fungal model for ectomycorrhizal research.
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Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina.
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, National University of Quilmes and CONICET, Bernal, Province of Buenos Aires, Argentina
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33
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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Rajput PS, Khan SR, Singh P, Chawla PA. Treatment of Small Cell Lung Cancer with Lurbinectedin: A Review. Anticancer Agents Med Chem 2021; 22:812-820. [PMID: 34229593 DOI: 10.2174/1871520621666210706150057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 05/15/2021] [Accepted: 05/23/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Lurbinectedin was approved on June 15, 2020 by Food and Drug Administration with a brand name ZEPZELCA as the first systematic approved therapy for patients having Small Cell Lung Cancer (SCLC). OBJECTIVES In this review, an attempt is made to summarize different aspects of Lurbinectedin, including the pathophysiology, chemistry, chemical synthesis, mechanism of action, adverse reactions, including pharmacokinetics of lurbinectedin. Special attention is given to various reported clinical trials of lurbinectedin. METHODS A comprehensive literature search was conducted in the relevant databases like ScienceDirect, PubMed, ResearchGate and Google Scholar to identify studies. Further upon a thorough study of these reports, significant findings/data were collected and compiled under suitable headings. Important findings related to clinical trials have been tabulated. CONCLUSION Lurbinectedin is known to act by inhibiting the active transcription of encoding genes, thereby bringing about the suppression of tumour related macrophages with an impact on tumour atmosphere. Lurbinectedin has emerged as a potential drug candidate for the treatment of small cell lung cancer (SCLC).
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Affiliation(s)
- Prince Singh Rajput
- Department of Pharmaceutical Analysis, ISF College of Pharmacy, G.T. Road, Moga-142 001, Punjab, India
| | - Sharib Raza Khan
- Department of Pharmaceutical Analysis, ISF College of Pharmacy, G.T. Road, Moga-142 001, Punjab, India
| | - Preeti Singh
- Department of Pharmaceutical Analysis, ISF College of Pharmacy, G.T. Road, Moga-142 001, Punjab, India
| | - Pooja A Chawla
- Department of Pharmaceutical Analysis, ISF College of Pharmacy, G.T. Road, Moga-142 001, Punjab, India
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35
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Popp AP, Hettich J, Gebhardt J. Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene. Nucleic Acids Res 2021; 49:6249-6266. [PMID: 34060631 PMCID: PMC8216454 DOI: 10.1093/nar/gkab443] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases a burst of transcripts before turning inactive again. While the basic course of transcription is well understood, it is unclear how binding of a TF affects the frequency, duration and size of a transcriptional burst. We systematically varied the residence time and concentration of a synthetic TF and characterized the transcription of a synthetic reporter gene by combining single molecule imaging, single molecule RNA-FISH, live transcript visualisation and analysis with a novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that TF binding solely affected burst frequency and variations in TF residence time had a stronger influence than variations in concentration. This enabled us to device a model of gene transcription, in which TF binding triggers multiple successive steps before the gene transits to the active state and actual mRNA synthesis is decoupled from TF presence. We quantified all transition times of the TF and the gene, including the TF search time and the delay between TF binding and the onset of transcription. Our quantitative measurements and analysis revealed detailed kinetic insight, which may serve as basis for a bottom-up understanding of gene regulation.
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Affiliation(s)
- Achim P Popp
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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36
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Danielewski M, Matuszewska A, Szeląg A, Sozański T. The Impact of Anthocyanins and Iridoids on Transcription Factors Crucial for Lipid and Cholesterol Homeostasis. Int J Mol Sci 2021; 22:6074. [PMID: 34199904 PMCID: PMC8200123 DOI: 10.3390/ijms22116074] [Citation(s) in RCA: 13] [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: 04/30/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022] Open
Abstract
Nutrition determines our health, both directly and indirectly. Consumed foods affect the functioning of individual organs as well as entire systems, e.g., the cardiovascular system. There are many different diets, but universal guidelines for proper nutrition are provided in the WHO healthy eating pyramid. According to the latest version, plant products should form the basis of our diet. Many groups of plant compounds with a beneficial effect on human health have been described. Such groups include anthocyanins and iridoids, for which it has been proven that their consumption may lead to, inter alia, antioxidant, cholesterol and lipid-lowering, anti-obesity and anti-diabetic effects. Transcription factors directly affect a number of parameters of cell functions and cellular metabolism. In the context of lipid and cholesterol metabolism, five particularly important transcription factors can be distinguished: liver X receptor (LXR), peroxisome proliferator-activated receptor-α (PPAR-α), peroxisome proliferator-activated receptor-γ (PPAR-γ), CCAAT/enhancer binding protein α (C/EBPα) and sterol regulatory element-binding protein 1c (SREBP-1c). Both anthocyanins and iridoids may alter the expression of these transcription factors. The aim of this review is to collect and systematize knowledge about the impact of anthocyanins and iridoids on transcription factors crucial for lipid and cholesterol homeostasis.
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Affiliation(s)
- Maciej Danielewski
- Department of Pharmacology, Wroclaw Medical University, Jana Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (A.M.); (A.S.); (T.S.)
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37
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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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38
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Ducker C, Shaw PE. Ubiquitin-Mediated Control of ETS Transcription Factors: Roles in Cancer and Development. Int J Mol Sci 2021; 22:5119. [PMID: 34066106 PMCID: PMC8151852 DOI: 10.3390/ijms22105119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Genome expansion, whole genome and gene duplication events during metazoan evolution produced an extensive family of ETS genes whose members express transcription factors with a conserved winged helix-turn-helix DNA-binding domain. Unravelling their biological roles has proved challenging with functional redundancy manifest in overlapping expression patterns, a common consensus DNA-binding motif and responsiveness to mitogen-activated protein kinase signalling. Key determinants of the cellular repertoire of ETS proteins are their stability and turnover, controlled largely by the actions of selective E3 ubiquitin ligases and deubiquitinases. Here we discuss the known relationships between ETS proteins and enzymes that determine their ubiquitin status, their integration with other developmental signal transduction pathways and how suppression of ETS protein ubiquitination contributes to the malignant cell phenotype in multiple cancers.
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Affiliation(s)
- Charles Ducker
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Peter E. Shaw
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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39
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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40
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Yoon JY, Palukaitis P. Cucumber Mosaic Virus 1a Protein Interacts with the Tobacco SHE1 Transcription Factor and Partitions between the Nucleus and the Tonoplast Membrane. THE PLANT PATHOLOGY JOURNAL 2021; 37:182-193. [PMID: 33866760 PMCID: PMC8053847 DOI: 10.5423/ppj.ft.03.2021.0045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
The transcription factor SHE1 was identified as an interacting partner with the cucumber mosaic virus (CMV) 1a protein in the yeast two-hybrid system, by a pull-down assay, and via bimolecular fluorescent complementation. Using fluorescent-tagged proteins and confocal microscopy, the CMV 1a protein itself was found distributed predominantly between the nucleus and the tonoplast membrane, although it was also found in speckles in the cytoplasm. The SHE1 protein was localized in the nucleus, but in the presence of the CMV 1a protein was partitioned between the nucleus and the tonoplast membrane. SHE1 expression was induced by infection of tobacco with four tested viruses: CMV, tobacco mosaic virus, potato virus X and potato virus Y. Transgenic tobacco expressing the CMV 1a protein showed constitutive expression of SHE1, indicating that the CMV 1a protein may be responsible for its induction. However, previously, such plants also were shown to have less resistance to local and systemic movement of tobacco mosaic virus (TMV) expressing the green fluorescent protein, suggesting that the CMV 1a protein may act to prevent the function of the SHE1 protein. SHE1 is a member of the AP2/ERF class of transcription factors and is conserved in sequence in several Nicotiana species, although two clades of SHE1 could be discerned, including both different Nicotiana species and cultivars of tobacco, varying by the presence of particular insertions or deletions.
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Affiliation(s)
- Ju-Yeon Yoon
- Virology Unit, Division of Horticultural and Herbal Crop Environment, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women's University, Seoul 01797,
Korea
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41
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Sabari BR. Biomolecular Condensates and Gene Activation in Development and Disease. Dev Cell 2021; 55:84-96. [PMID: 33049213 DOI: 10.1016/j.devcel.2020.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 01/04/2023]
Abstract
Activating the right gene at the right time and place is essential for development. Emerging evidence suggests that this process is regulated by the mesoscale compartmentalization of the gene-control machinery, RNA polymerase II and its cofactors, within biomolecular condensates. Coupling gene activity to the reversible and dynamic process of condensate formation is proposed to enable the robust and precise changes in gene-regulatory programs during signaling and development. The macromolecular features that enable condensates and the regulatory pathways that control them are dysregulated in disease, highlighting their importance for normal physiology. In this review, we will discuss the role of condensates in gene activation; the multivalent features of protein, RNA, and DNA that enable reversible condensate formation; and how these processes are utilized in normal and disease biology. Understanding the regulation of condensates promises to provide novel insights into how organization of the gene-control machinery regulates development and disease.
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Affiliation(s)
- Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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42
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Zhou M, Li H, Wang X, Guan Y. Evidence of widespread, independent sequence signature for transcription factor cobinding. Genome Res 2021; 31:265-278. [PMID: 33303494 PMCID: PMC7849410 DOI: 10.1101/gr.267310.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/03/2020] [Indexed: 01/03/2023]
Abstract
Transcription factors (TFs) are the vocabulary that genomes use to regulate gene expression and phenotypes. The interactions among TFs enrich this vocabulary and orchestrate diverse biological processes. Although simple models identify open chromatin and the presence of TF motifs as the two major contributors to TF binding patterns, it remains elusive what contributes to the in vivo TF cobinding landscape. In this study, we developed a machine learning algorithm to explore the contributors of the cobinding patterns. The algorithm substantially outperforms the state-of-the-field models for TF cobinding prediction. Game theory-based feature importance analysis reveals that, for most of the TF pairs we studied, independent motif sequences contribute one or more of the two TFs under investigation to their cobinding patterns. Such independent motif sequences include, but are not limited to, transcription initiation-related proteins and known TF complexes. We found the motif sequence signatures and the TFs are rarely mutual, corroborating a hierarchical and directional organization of the regulatory network and refuting the possibility of artifacts caused by shared sequence similarity with the TFs under investigation. We modeled such regulatory language with directed graphs, which reveal shared, global factors that are related to many binding and cobinding patterns.
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Affiliation(s)
- Manqi Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hongyang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xueqing Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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43
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Rowland MA, Pilkiewicz KR, Mayo ML. Devil in the details: Mechanistic variations impact information transfer across models of transcriptional cascades. PLoS One 2021; 16:e0245094. [PMID: 33439904 PMCID: PMC7806174 DOI: 10.1371/journal.pone.0245094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/22/2020] [Indexed: 11/19/2022] Open
Abstract
The transcriptional network determines a cell’s internal state by regulating protein expression in response to changes in the local environment. Due to the interconnected nature of this network, information encoded in the abundance of various proteins will often propagate across chains of noisy intermediate signaling events. The data-processing inequality (DPI) leads us to expect that this intracellular game of “telephone” should degrade this type of signal, with longer chains losing successively more information to noise. However, a previous modeling effort predicted that because the steps of these signaling cascades do not truly represent independent stages of data processing, the limits of the DPI could seemingly be surpassed, and the amount of transmitted information could actually increase with chain length. What that work did not examine was whether this regime of growing information transmission was attainable by a signaling system constrained by the mechanistic details of more complex protein-binding kinetics. Here we address this knowledge gap through the lens of information theory by examining a model that explicitly accounts for the binding of each transcription factor to DNA. We analyze this model by comparing stochastic simulations of the fully nonlinear kinetics to simulations constrained by the linear response approximations that displayed a regime of growing information. Our simulations show that even when molecular binding is considered, there remains a regime wherein the transmitted information can grow with cascade length, but ends after a critical number of links determined by the kinetic parameter values. This inflection point marks where correlations decay in response to an oversaturation of binding sites, screening informative transcription factor fluctuations from further propagation down the chain where they eventually become indistinguishable from the surrounding levels of noise.
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Affiliation(s)
- Michael A. Rowland
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States of America
- * E-mail:
| | - Kevin R. Pilkiewicz
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States of America
| | - Michael L. Mayo
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States of America
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44
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Ko DK, Brandizzi F. A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:254-270. [PMID: 33098715 PMCID: PMC7942231 DOI: 10.1111/tpj.15044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 05/10/2023]
Abstract
Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis-regulatory elements (CREs) in ER stress-responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription-regulatory mechanisms in the stress responses and crop improvement.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
- Correspondence:
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45
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Lee JY, Mori C, Tokumoto M, Satoh M. Changes in DNA-binding activity of transcription factors in the kidney of mice exposed to cadmium. J Toxicol Sci 2021; 46:125-129. [PMID: 33642518 DOI: 10.2131/jts.46.125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cadmium (Cd) is a toxic heavy metal, long-term exposure to which causes renal damage associated with disruption in gene expression. Transcription factors whose activities were altered in the kidneys of mice exposed to Cd for 3 months were assessed using protein/DNA-binding assays. Female C57BL/6J mice were exposed to 300 ppm Cd in the diet for 3 months. Nuclear extracts of kidney were used for protein/DNA-binding assays. The concentration of Cd was approximately 100 ppm in mouse kidney, a level that did not induce renal toxicity. Among the 345 transcription factors evaluated, five transcription factors showed over a two-fold increase in their activities and 14 transcription factors showed a half-fold change in their activities after Cd exposure. These findings may provide new information about the causative transcription factors associated with Cd renal toxicity.
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Affiliation(s)
- Jin-Yong Lee
- Laboratory of Pharmaceutical Health Sciences, School of Pharmacy, Aichi Gakuin Universityn
| | - Chikage Mori
- Laboratory of Pharmaceutical Health Sciences, School of Pharmacy, Aichi Gakuin Universityn
| | - Maki Tokumoto
- Laboratory of Pharmaceutical Health Sciences, School of Pharmacy, Aichi Gakuin Universityn
| | - Masahiko Satoh
- Laboratory of Pharmaceutical Health Sciences, School of Pharmacy, Aichi Gakuin Universityn
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46
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Grant PA, Winston F, Berger SL. The biochemical and genetic discovery of the SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194669. [PMID: 33338653 DOI: 10.1016/j.bbagrm.2020.194669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
One of the major advances in our understanding of gene regulation in eukaryotes was the discovery of factors that regulate transcription by controlling chromatin structure. Prominent among these discoveries was the demonstration that Gcn5 is a histone acetyltransferase, establishing a direct connection between transcriptional activation and histone acetylation. This breakthrough was soon followed by the purification of a protein complex that contains Gcn5, the SAGA complex. In this article, we review the early genetic and biochemical experiments that led to the discovery of SAGA and the elucidation of its multiple activities.
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Affiliation(s)
- Patrick A Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, United States of America
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States of America.
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Department of Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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47
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Duan C, Jiao J, Zheng J, Li D, Ning L, Xiang Y, Li G. Polyvalent Biotinylated Aptamer Scaffold for Rapid and Sensitive Detection of Tau Proteins. Anal Chem 2020; 92:15162-15168. [PMID: 33155796 DOI: 10.1021/acs.analchem.0c03643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biomimetic construction of artificial scaffolds has attracted increasing attention. However, the construction methods usually require redundant materials and procedures, which is inconvenient for further application. Herein, inspired by the polyvalent multifunctional structure in nature, we have designed a polyvalent biotinylated aptamer scaffold (PBAS) which can conduct analytical performance with high sensitivity and simplified procedures. To construct a PBAS, the aptamers are designed to hybridize with prepared linker probes to form polyvalent biotinylated scaffolds, which contain both multiple aptamers and signal labels. Therefore, multifunctional scaffolds can be constructed with high recognition and capture efficiency as well as significant signal amplification. Furthermore, the scaffold can be used for the assay of some disease marker proteins. By taking tau proteins as an example, the proposed aptasensor can exhibit excellent performance with a low detection limit of 153 pg mL-1 and a short assay time of 50 min, which is much better than most of the previous methods. By assays of tau proteins in both serum and artificial cerebro spinal fluid, the PBAS-based aptasensor can work well. Therefore, the scaffold may be expected to be a powerful analytical tool which may have wide applications in the detection of a variety of analytes.
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Affiliation(s)
- Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Jin Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Ji Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Limin Ning
- College of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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48
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Prados MB, Sica MP, Miranda S. Inflammatory conditions promote a switch of oligosaccharyltransferase (OST) catalytic subunit isoform expression. Arch Biochem Biophys 2020; 693:108538. [PMID: 32810478 DOI: 10.1016/j.abb.2020.108538] [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: 05/19/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Oligosaccharyltransferase (OST) complex catalyzes the N-glycosylation of nascent polypeptides in the endoplasmic reticulum. Glycoproteins are critical for normal cell-cell interactions, especially during an immune response. Abnormal glycosylation is an insignia of several inflammatory diseases. However, the mechanisms that regulate the differential N-glycosylation are not fully understood. The OST complex can be assembled with one out of two catalytic subunits, STT3A or STT3B, which have different enzymatic properties. In this work, we investigated the expression of STT3A and STT3B in several mouse models such as a crossbreeding of normal and abortion-prone mice and an intestinal inflammation model. These animals were either exposed or not to acoustic stress (acute or chronic). The expression of the isoforms was analysed by immunohistochemistry and protein immunoblot. Finally, we investigated the gene regulatory elements employing public databases. Results demonstrated that inflammation alters the balance between the expression of both isoforms in the affected tissues. In homoeostatic conditions, STT3A expression predominates over STT3B, especially in epithelial cells. This relation is reversed as a consequence of inflammation. An increase in STT3B activity was associated to the generation of mannose-rich N-glycans. Accordingly, this type of N-glycans were found to decorate diverse inflamed tissues. The STT3A and STT3B genes are differentially regulated, which could account for the differences in the expression levels observed here. Our results support the idea that these isoforms could play different roles in cellular physiology. This study opens the possibility of studying the STT3A/STT3B expression ratio as a biomarker in acute inflammation or chronic diseases.
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Affiliation(s)
- María Belén Prados
- Instituto Alberto C. Taquini de Investigaciones en Medicina Traslacional (IATIMET), Universidad de Buenos Aires. CONICET, Marcelo T. de Alvear 2270, C1122AAJ, Buenos Aires, Argentina.
| | - Mauricio Pablo Sica
- Instituto de Energía y Desarrollo Sustentable, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, CONICET, Av. E. Bustillo 9500, 8400 S. C. de Bariloche, Río Negro, Argentina; Instituto Balseiro, Universidad Nacional de Cuyo, Centro Atómico Bariloche, Av. E. Bustillo 9500, 8400 S. C. de Bariloche, Río Negro, Argentina.
| | - Silvia Miranda
- Instituto Alberto C. Taquini de Investigaciones en Medicina Traslacional (IATIMET), Universidad de Buenos Aires. CONICET, Marcelo T. de Alvear 2270, C1122AAJ, Buenos Aires, Argentina.
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49
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de Souza AF, de Paula MS, Lima RM, Silva MG, de Curcio JS, Pereira M, de Almeida Soares CM. The "Little Iron Waltz": The Ternary Response of Paracoccidioides spp. to Iron Deprivation. J Fungi (Basel) 2020; 6:E221. [PMID: 33053811 PMCID: PMC7712450 DOI: 10.3390/jof6040221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Paracoccidioides is a genus of thermodimorphic fungi that causes paracoccidioidomycosis. When in the host, the fungus undergoes several challenges, including iron deprivation imposed by nutritional immunity. In response to the iron deprivation triggered by the host, the fungus responds in a ternary manner using mechanisms of high affinity and specificity for the uptake of Fe, namely non-classical reductive iron uptake pathway, uptake of host iron proteins, and biosynthesis and uptake of siderophores. This triple response resembles the rhythmic structure of a waltz, which features three beats per compass. Using this connotation, we have constructed this review summarizing relevant findings in this area of study and pointing out new discoveries and perspectives that may contribute to the expansion of this "little iron waltz".
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Affiliation(s)
| | | | | | | | | | | | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia 74000-000, Brazil; (A.F.d.S.); (M.S.d.P.); (R.M.L.); (M.G.S.); (J.S.d.C.); (M.P.)
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50
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Aref R, Schüller HJ. Functional analysis of Cti6 core domain responsible for recruitment of epigenetic regulators Sin3, Cyc8 and Tup1. Curr Genet 2020; 66:1191-1203. [PMID: 32980916 PMCID: PMC7599196 DOI: 10.1007/s00294-020-01109-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 01/18/2023]
Abstract
Mapping of effective protein domains is a demanding stride to disclose the functional relationship between regulatory complexes. Domain analysis of protein interactions is requisite for understanding the pleiotropic responses of the respective partners. Cti6 is a multifunctional regulator for which we could show recruitment of co-repressors Sin3, Cyc8 and Tup1. However, the responsible core domain tethering Cti6 to these co-repressors is poorly understood. Here, we report the pivotal domain of Cti6 that is indispensable for co-repressor recruitment. We substantiated that amino acids 450–506 of Cti6 bind PAH2 of Sin3. To analyse this Cti6–Sin3 Interaction Domain (CSID) in more detail, selected amino acids within CSID were replaced by alanine. It is revealed that hydrophobic amino acids V467, L481 and L491 L492 L493 are important for Cti6–Sin3 binding. In addition to PAH2 of Sin3, CSID also binds to tetratricopeptide repeats (TPR) of Cyc8. Indeed, we could demonstrate Cti6 recruitment to promoters of genes, such as RNR3 and SMF3, containing iron-responsive elements (IRE). Importantly, Sin3 is also recruited to these promoters but only in the presence of functional Cti6. Our findings provide novel insights toward the critical interaction domain in the co-regulator Cti6, which is a component of regulatory complexes that are closely related to chromatin architecture and the epigenetic status of genes that are regulated by pleiotropic co-repressors.
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Affiliation(s)
- Rasha Aref
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Shoubra El-Khaymah, Cairo, 11241, Egypt.
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik Und Infektionsbiologie, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany.
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik Und Infektionsbiologie, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
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