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Parra RG, Komives EA, Wolynes PG, Ferreiro DU. Frustration in physiology and molecular medicine. Mol Aspects Med 2025; 103:101362. [PMID: 40273505 DOI: 10.1016/j.mam.2025.101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 03/25/2025] [Accepted: 03/27/2025] [Indexed: 04/26/2025]
Abstract
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform these often amazing tasks, proteins must move and we must think of them as dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids. It is apparent however that, even when completely folded, not all conflicting interactions have been resolved so the structure remains 'locally frustrated'. Over the last decades it has become clearer that this local frustration is not just a random accident but plays an essential part of the inner workings of protein molecules. We will review here the physical origins of the frustration concept and review evidence that local frustration is important for protein physiology, protein-protein recognition, catalysis and allostery. Also, we highlight examples showing how alterations in the local frustration patterns can be linked to distinct pathologies. Finally we explore the extensions of the impact of frustration in higher order levels of organization of systems including gene regulatory networks and the neural networks of the brain.
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Affiliation(s)
- R Gonzalo Parra
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
| | - Diego U Ferreiro
- Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
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Parra RG, Komives EA, Wolynes PG, Ferreiro DU. Frustration In Physiology And Molecular Medicine. ARXIV 2025:arXiv:2502.03851v1. [PMID: 39975445 PMCID: PMC11838788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform these often amazing tasks, proteins must move and we must think of them as dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids. It is apparent however that, even when completely folded, not all conflicting interactions have been resolved so the structure remains 'locally frustrated'. Over the last decades it has become clearer that this local frustration is not just a random accident but plays an essential part of the inner workings of protein molecules. We will review here the physical origins of the frustration concept and review evidence that local frustration is important for protein physiology, protein-protein recognition, catalysis and allostery. Also, we highlight examples showing how alterations in the local frustration patterns can be linked to distinct pathologies. Finally we explore the extensions of the impact of frustration in higher order levels of organization of systems including gene regulatory networks and the neural networks of the brain.
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Affiliation(s)
- R. Gonzalo Parra
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Diego U. Ferreiro
- Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
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Tamburini B, Di Liberto D, Pratelli G, Rizzo C, Barbera LL, Lauricella M, Carlisi D, Maggio A, Palumbo Piccionello A, D’Anneo A, Caccamo N, Guggino G. Extra Virgin Olive Oil Polyphenol-Enriched Extracts Exert Antioxidant and Anti-Inflammatory Effects on Peripheral Blood Mononuclear Cells from Rheumatoid Arthritis Patients. Antioxidants (Basel) 2025; 14:171. [PMID: 40002358 PMCID: PMC11851824 DOI: 10.3390/antiox14020171] [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: 01/15/2025] [Revised: 01/28/2025] [Accepted: 01/28/2025] [Indexed: 02/27/2025] Open
Abstract
Rheumatoid arthritis (RA) is a long-term systemic autoimmune disorder that causes joint inflammation, swelling, pain, bone erosion, and deformities. Recent findings emphasize the anti-inflammatory and antioxidant properties of bioactive natural compounds, such as polyphenols extracted from plants and fruits, and their possible synergistic effect when used in combination with current therapies to improve the prognosis and symptoms of inflammatory rheumatic diseases. Here, we report that Sicilian extra virgin olive oil polyphenol-enriched extracts (PE-EVOOs) reduce intracellular reactive oxygen species (ROS) and pro-inflammatory cytokines, such as tumor necrosis factor-α (TNF-α) and interleukin-1 β (IL-1β), in peripheral mononuclear cells (PBMCs) obtained from both RA patients and healthy subjects (HSs) treated with lipopolysaccharides (LPS) as a control. HPLC-ESI-MS analysis highlighted that PE-EVOOs are rich in different polyphenolic compounds responsible for many of the observed biological effects. At molecular levels, Western blotting analyses revealed that PE-EVOO treatment is associated with the downregulation of the phosphorylated and active form of the inflammatory transcription factor NF-κB and the pro-inflammatory enzyme cyclooxygenase 2 (COX2). In addition, PE-EVOOs upregulated the transcription factor Nrf2 and its target antioxidant enzyme catalase and manganese superoxide dismutase (MnSOD). Collectively, these results suggest a possible use of PE-EVOOs as potential adjuvants for the treatment of RA.
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Affiliation(s)
- Bartolo Tamburini
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Section of Immunology, University of Palermo, 90127 Palermo, Italy; (B.T.); (N.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Rheumatology Section, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (C.R.); (L.L.B.); (G.G.)
| | - Diana Di Liberto
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Section of Biochemistry, University of Palermo, 90127 Palermo, Italy; (D.D.L.); (G.P.); (D.C.)
| | - Giovanni Pratelli
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Section of Biochemistry, University of Palermo, 90127 Palermo, Italy; (D.D.L.); (G.P.); (D.C.)
| | - Chiara Rizzo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Rheumatology Section, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (C.R.); (L.L.B.); (G.G.)
| | - Lidia La Barbera
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Rheumatology Section, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (C.R.); (L.L.B.); (G.G.)
| | - Marianna Lauricella
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Section of Biochemistry, University of Palermo, 90127 Palermo, Italy; (D.D.L.); (G.P.); (D.C.)
| | - Daniela Carlisi
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Section of Biochemistry, University of Palermo, 90127 Palermo, Italy; (D.D.L.); (G.P.); (D.C.)
| | - Antonella Maggio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy; (A.M.); (A.P.P.)
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy; (A.M.); (A.P.P.)
| | - Antonella D’Anneo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), Laboratory of Biochemistry, University of Palermo, 90127 Palermo, Italy;
| | - Nadia Caccamo
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Section of Immunology, University of Palermo, 90127 Palermo, Italy; (B.T.); (N.C.)
| | - Giuliana Guggino
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, Rheumatology Section, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (C.R.); (L.L.B.); (G.G.)
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Enhanced Transcriptional Strength of HIV-1 Subtype C Minimizes Gene Expression Noise and Confers Stability to the Viral Latent State. J Virol 2023; 97:e0137622. [PMID: 36533949 PMCID: PMC9888270 DOI: 10.1128/jvi.01376-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Stochastic fluctuations in gene expression emanating from the HIV-1 long terminal repeat (LTR), amplified by the Tat positive feedback circuit, determine the choice between viral infection fates: active transcription (ON) or transcriptional silence (OFF). The emergence of several transcription factor binding site (TFBS) variant strains in HIV-1 subtype C (HIV-1C), especially those containing the duplication of the NF-κB motif, mandates the evaluation of the effect of enhanced transcriptional strength on gene expression noise and its influence on viral fate selection switch. Using a panel of subgenomic LTR-variant strains containing different copy numbers of the NF-κB motif (ranging from 0 to 4), we used flow cytometry, mRNA quantification, and pharmacological perturbations to demonstrate an inverse correlation between promoter strength and gene expression noise in Jurkat T cells and primary CD4+ T cells. The inverse correlation is consistent in clonal cell populations at constant intracellular concentrations of Tat and when NF-κB levels were regulated pharmacologically. Further, we show that strong LTRs containing at least two copies of the NF-κB motif in the enhancer establish a more stable latent state and demonstrate more rapid latency reversal than weak LTRs containing fewer motifs. We also demonstrate a cooperative binding of NF-κB to the motif cluster in HIV-1C LTRs containing two, three, or four NF-κB motifs (Hill coefficient [H] = 2.61, 3.56, and 3.75, respectively). The present work alludes to a possible evolution of the HIV-1C LTR toward gaining transcriptional strength associated with attenuated gene expression noise with implications for viral latency. IMPORTANCE Over the past two consecutive decades, HIV-1 subtype C (HIV-1C) has been undergoing directional evolution toward augmenting the transcriptional strength of the long terminal repeat (LTR) by adding more copies of the existing transcription factor binding site (TFBS) by sequence duplication. Additionally, the duplicated elements are genetically diverse, suggesting broader-range signal receptivity by variant LTRs. The HIV-1 promoter is inherently noisy, and the stochastic fluctuations in gene expression of variant LTRs may influence the active transcription (ON)/transcriptional silence (OFF) latency decisions. The evolving NF-κB motif variations of HIV-1C offer a powerful opportunity to examine how the transcriptional strength of the LTR might influence gene expression noise. Our work here shows that the augmented transcriptional strength of the HIV-1C LTR leads to concomitantly reduced gene expression noise, consequently leading to stabler latency maintenance and rapid latency reversal. The present work offers a novel lead toward appreciating the molecular mechanisms governing HIV-1 latency.
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Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem 2022; 298:102349. [PMID: 35934050 PMCID: PMC9440430 DOI: 10.1016/j.jbc.2022.102349] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Many transcription factors contain intrinsically disordered transcription activation domains (TADs), which mediate interactions with coactivators to activate transcription. Historically, DNA-binding domains and TADs have been considered as modular units, but recent studies have shown that TADs can influence DNA binding. Whether these results can be generalized to more TADs is not clear. Here, we biophysically characterized the NFκB p50/RelA heterodimer including the RelA TAD and investigated the TAD's influence on NFκB-DNA interactions. In solution, we show the RelA TAD is disordered but compact, with helical tendency in two regions that interact with coactivators. We determined that the presence of the TAD increased the stoichiometry of NFκB-DNA complexes containing promoter DNA sequences with tandem κB recognition motifs by promoting the binding of NFκB dimers in excess of the number of κB sites. In addition, we measured the binding affinity of p50/RelA for DNA containing tandem κB sites and single κB sites. While the presence of the TAD enhanced the binding affinity of p50/RelA for all κB sequences tested, it also increased the affinity for nonspecific DNA sequences by over 10-fold, leading to an overall decrease in specificity for κB DNA sequences. In contrast, previous studies have generally reported that TADs decrease DNA-binding affinity and increase sequence specificity. Our results reveal a novel function of the RelA TAD in promoting binding to nonconsensus DNA, which sheds light on previous observations of extensive nonconsensus DNA binding by NFκB in vivo in response to strong inflammatory signals.
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Affiliation(s)
- Hannah E R Baughman
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Dominic Narang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Wei Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Amalia C Villagrán Suárez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Joan Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Maxwell J Bachochin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tristan R Gunther
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
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Singh A, Martinez-Yamout MA, Wright PE, Dyson H. Structural and dynamic studies of DNA recognition by NF-κB p50 RHR homodimer using methyl NMR spectroscopy. Nucleic Acids Res 2022; 50:7147-7160. [PMID: 35748866 PMCID: PMC9262625 DOI: 10.1093/nar/gkac535] [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: 02/18/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Protein dynamics involving higher-energy sparsely populated conformational substates are frequently critical for protein function. This study describes the dynamics of the homodimer (p50)2 of the p50 Rel homology region (RHR) of the transcription factor NF-κB, using 13C relaxation dispersion experiments with specifically (13C, 1H)-labeled methyl groups of Ile (δ), Leu and Val. Free (p50)2 is highly dynamic in solution, showing μs-ms relaxation dispersion consistent with exchange between the ground state and higher energy substates. These fluctuations propagate from the DNA-binding loops through the core of the domain. The motions are damped in the presence of κB DNA, but the NMR spectra of the DNA complexes reveal multiple local conformations of the p50 RHR homodimer bound to certain κB DNA sequences. Varying the length and sequence of κB DNA revealed two factors that promote a single bound conformation for the complex: the length of the κB site in the duplex and a symmetrical sequence of guanine nucleotides at both ends of the recognition motif. The dynamic nature of the DNA-binding loops, together with the multiple bound conformations of p50 RHR with certain κB sites, is consistent with variations in the transcriptional activity of the p50 homodimer with different κB sequences.
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Affiliation(s)
- Amrinder Singh
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla CA 92037, USA
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Ghosh G, Wang VYF. Origin of the Functional Distinctiveness of NF-κB/p52. Front Cell Dev Biol 2021; 9:764164. [PMID: 34888310 PMCID: PMC8650618 DOI: 10.3389/fcell.2021.764164] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
The transcription regulators of the NF-κB family have emerged as a critical factor affecting the function of various adult tissues. The NF-κB family transcription factors are homo- and heterodimers made up of five monomers (p50, p52, RelA, cRel and RelB). The family is distinguished by sequence homology in their DNA binding and dimerization domains, which enables them to bind similar DNA response elements and participate in similar biological programs through transcriptional activation and repression of hundreds of genes. Even though the family members are closely related in terms of sequence and function, they all display distinct activities. In this review, we discuss the sequence characteristics, protein and DNA interactions, and pathogenic involvement of one member of family, NF-κB/p52, relative to that of other members. We pinpoint the small sequence variations within the conserved region that are mostly responsible for its distinct functional properties.
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Affiliation(s)
- Gourisankar Ghosh
- Department of Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
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Long X, Yang Z, Li Y, Sun Q, Li X, Kuang E. BRLF1-dependent viral and cellular transcriptomes and transcriptional regulation during EBV primary infection in B lymphoma cells. Genomics 2021; 113:2591-2604. [PMID: 34087421 DOI: 10.1016/j.ygeno.2021.05.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/17/2021] [Accepted: 05/30/2021] [Indexed: 12/11/2022]
Abstract
The immediate-early protein BRLF1 plays important roles in lytic infection of Epstein-Barr virus (EBV), in which it activates lytic viral transcription and replication. However, knowledge of the influence of BRLF1 on cellular gene expression and transcriptional reprogramming during the early lytic cycle remains limited. In the present study, deep RNA-sequencing analysis identified all differentially expressed genes (DEGs) and alternative splicing in B lymphoma cells subjected to wild-type and BRLF1-deficient EBV primary infection. The BRLF1-dependent cellular DEGs were annotated, and major differentially enriched pathways were related to DNA replication and transcription, immune and inflammatory responses, cytokine-receptor interactions and chemokine signaling and metabolic processes. Furthermore, analysis of BRLF1-binding proteins by mass spectrometry shows that BRLF1 binds to and cooperates with several transcription factors and components of the spliceosome and then influences both RNA polymerase II-dependent transcription and pre-mRNA splicing. The RTA-binding RRE motifs or specific motifs of unique cooperative transcription factors in viral and cellular DEG promoter regions indicate that BRLF1 employs different strategies for regulating viral and cellular transcription. Thus, our study characterized BRLF1-dependent cellular and viral transcriptional profile during primary infection and then revealed the comprehensive virus-cell interaction and alterations of transcription during EBV primary infection and lytic replication.
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Affiliation(s)
- Xubing Long
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Ziwei Yang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Yang Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Qinqin Sun
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Xiaojuan Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China.
| | - Ersheng Kuang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong 510080, China.
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Fazal N, Khawaja H, Naseer N, Khan AJ, Latief N. Daphne mucronata enhances cell proliferation and protects human adipose stem cells against monosodium iodoacetate induced oxidative stress in vitro. Adipocyte 2020; 9:495-508. [PMID: 32867575 PMCID: PMC7714443 DOI: 10.1080/21623945.2020.1812242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 01/01/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are being used to treat many diseases as they exhibit great regenerative potential. However, MSC's transplantation sometimes does not yield the maximum regenerative outcome as they are unable to survive in inflammatory conditions. Several approaches including preconditioning are used to improve the survival rate of mesenchymal stem cells. One such recently reported approach is preconditioning MSCs with plant extracts. The present study was designed to evaluate the effect of Daphne mucronata extract on stressed human adipose-derived mesenchymal stem cells (hADMSCs). Isolated hADMSCs were preconditioned with different concentrations of Daphne muconata extract and the protective, proliferative, antioxidant and anti-inflammatory effect was assessed through various assays and expression analysis of inflammatory markers regulated through NF-κB pathway. Results suggest that preconditioning hADMSCs with Daphne mucronata increased the cell viability, proliferative and protective potential of hADMSCs with a concomitant reduction in LDH, ROS and elevation in SOD activity. Moreover, both the ELISA and gene expression analysis demonstrated down regulations of inflammatory markers (IL1-β, TNF-α, p65, p50, MMP13) in Daphne mucronata preconditioned hADMSCs as compared to stress. This is the first study to report the use of MIA induced oxidative stress against hADMSC's and effect of Daphne mucronata on stressed hADMSCs. Results of these studies provided evidence that Daphne mucronata protects the hADMSCs during stress conditions by down regulating the inflammatory markers and hence increase the viability and proliferative potential of hADMSCs that is crucial for transplantation purposes.
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Affiliation(s)
- Numan Fazal
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hamzah Khawaja
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nadia Naseer
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Azim Jahangir Khan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Noreen Latief
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Nejatbakhsh Samimi L, Farhadi E, Tahmasebi MN, Jamshidi A, Sharafat Vaziri A, Mahmoudi M. NF-κB signaling in rheumatoid arthritis with focus on fibroblast-like synoviocytes. AUTOIMMUNITY HIGHLIGHTS 2020. [PMCID: PMC7414649 DOI: 10.1186/s13317-020-00135-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The nuclear factor-κB (NF-κB) signaling pathway regulates multiple processes in innate and adaptive immune cells. This pathway is involved in inflammation through the regulation of cytokines, chemokines, and adhesion molecules expression. The NF-κB transcription factor also participates in the survival, proliferation, and differentiation of cells. Therefore, deregulated NF-κB activation contributes to the pathogenesis of inflammatory diseases. Rheumatoid arthritis (RA) is classified as a heterogeneous and complex autoimmune inflammatory disease. Although different immune and non-immune cells contribute to the RA pathogenesis, fibroblast-like synoviocytes (FLSs) play a crucial role in disease progression. These cells are altered during the disease and produce inflammatory mediators, including inflammatory cytokines and matrix metalloproteinases, which result in joint and cartilage erosion. Among different cell signaling pathways, it seems that deregulated NF-κB activation is associated with the inflammatory picture of RA. NF-κB activation can also promote the proliferation of RA-FLSs as well as the inhibition of FLS apoptosis that results in hyperplasia in RA synovium. In this review, the role of NF-κB transcription factor in immune and non-immune cells (especially FLSs) that are involved in RA pathogenesis are discussed.
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Yang JH, Chen WT, Lee MC, Fang WH, Hsu YJ, Chin-Lin, Chen HC, Chang HL, Chen CF, Tu MY, Kuo CW, Lin YH, Hsiao PJ, Su SL. Investigation of the variants at the binding site of inflammatory transcription factor NF-κB in patients with end-stage renal disease. BMC Nephrol 2019; 20:300. [PMID: 31382928 PMCID: PMC6683452 DOI: 10.1186/s12882-019-1471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background A chronic inflammatory state is a prominent feature in patients with end-stage renal disease (ESRD). Nuclear factor-kappa B (NF-κB) is a transcription factor that regulates the expression of genes involved in inflammation. Some genetic studies have demonstrated that the NF-κB genetic mutation could cause kidney injury and kidney disease progression. However, the association of a gene polymorphism in the transcription factor binding site of NF-κB with kidney disease is not clear. Methods We used the Taiwan Biobank database, the University of California, Santa Cruz, reference genome, and a chromatin immunoprecipitation sequencing database to find single nucleotide polymorphisms (SNPs) at potential binding sites of NF-κB. In addition, we performed a case–control study and genotyped 847 patients with ESRD and 846 healthy controls at Tri-Service General Hospital from 2015 to 2016. Furthermore, we used the ChIP assay to identify the binding activity of different genotypes and used Luciferase reporter assay to examine the function of the rs9395890 polymorphism. Result The results of biometric screening in the databases revealed 15 SNPs with the potential binding site of NF-κB. Genotype distributions of rs9395890 were significantly different in ESRD cases and healthy controls (P = 0.049). The ChIP assay revealed an approximately 1.49-fold enrichment of NF-κB of the variant type TT when compared to that of the wild-type GG in rs9395890 (P = 0.027; TT = 3.20 ± 0.16, GT = 2.81 ± 0.20, GG = 1.71 ± 0.18). The luciferase reporter assay showed that the NF-κB binding site activity in T allele was slightly higher than that in G allele, though it is not significant. Conclusions Our findings indicate that rs9395890 is associated with susceptibility to ESRD in Taiwan population. Electronic supplementary material The online version of this article (10.1186/s12882-019-1471-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jia-Hwa Yang
- School of Public Health and Graduate institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 114, Taiwan, Republic of China.,Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan, Republic of China
| | - Wei-Teing Chen
- Division of Chest Medicine, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan, Republic of China.,Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Meng-Chang Lee
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Wen-Hui Fang
- Department of Family and Community Medicine, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Yu-Juei Hsu
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Chin-Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsiang-Cheng Chen
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsueh-Lu Chang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chien-Fu Chen
- Department of Orthopedics, Taichung Armed Forces General Hospital, Taichung, Taiwan, Republic of China
| | - Min-Yu Tu
- Department of Orthopedics, Kaohsiung Armed Forces General Hospital, Gangshan Branch, Kaohsiung, Taiwan, Republic of China
| | - Chien-Wei Kuo
- Division of Nephrology Dialysis, Shih-Kang Clinic, New Taipei City, Taiwan, Republic of China
| | - Yuan-Hau Lin
- Division of Nephrology Dialysis, Yuan-Lin Clinic, Taipei, Taiwan, Republic of China
| | - Po-Jen Hsiao
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei City, Taiwan, Republic of China. .,Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan City, Taiwan, Republic of China. .,Big Data Research Center, Fu-Jen Catholic University, Taipei, Taiwan, Republic of China. .,Department of Life Sciences, National Central University, Taoyuan City, Taiwan, Republic of China.
| | - Sui-Lung Su
- School of Public Health and Graduate institute of Life Sciences, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 114, Taiwan, Republic of China. .,School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China.
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12
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Wu J, Wang Q, Dai W, Wang W, Yue M, Wang J. Massive GGAAs in genomic repetitive sequences serve as a nuclear reservoir of NF-κB. J Genet Genomics 2018; 45:193-203. [PMID: 29748061 DOI: 10.1016/j.jgg.2018.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/01/2022]
Abstract
Nuclear factor κB (NF-κB) is a DNA-binding transcription factor. Characterizing its genomic binding sites is crucial for understanding its gene regulatory function and mechanism in cells. This study characterized the binding sites of NF-κB RelA/p65 in the tumor neurosis factor-α (TNFα) stimulated HeLa cells by a precise chromatin immunoprecipitation-sequencing (ChIP-seq). The results revealed that NF-κB binds nontraditional motifs (nt-motifs) containing conserved GGAA quadruplet. Moreover, nt-motifs mainly distribute in the peaks nearby centromeres that contain a larger number of repetitive elements such as satellite, simple repeats and short interspersed nuclear elements (SINEs). This intracellular binding pattern was then confirmed by the in vitro detection, indicating that NF-κB dimers can bind the nontraditional κB (nt-κB) sites with low affinity. However, this binding hardly activates transcription. This study thus deduced that NF-κB binding nt-motifs may realize functions other than gene regulation as NF-κB binding traditional motifs (t-motifs). To testify the deduction, many ChIP-seq data of other cell lines were then analyzed. The results indicate that NF-κB binding nt-motifs is also widely present in other cells. The ChIP-seq data analysis also revealed that nt-motifs more widely distribute in the peaks with low-fold enrichment. Importantly, it was also found that NF-κB binding nt-motifs is mainly present in the resting cells, whereas NF-κB binding t-motifs is mainly present in the stimulated cells. Astonishingly, no known function was enriched by the gene annotation of nt-motif peaks. Based on these results, this study proposed that the nt-κB sites that extensively distribute in larger numbers of repeat elements function as a nuclear reservoir of NF-κB. The nuclear NF-κB proteins stored at nt-κB sites in the resting cells may be recruited to the t-κB sites for regulating its target genes upon stimulation.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Qiao Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Wei Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210002, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
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13
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Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins. Nat Commun 2017; 8:1537. [PMID: 29146913 PMCID: PMC5691083 DOI: 10.1038/s41467-017-00859-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/01/2017] [Indexed: 01/17/2023] Open
Abstract
Macroautophagy can regulate cell signalling and tumorigenesis via elusive molecular mechanisms. We establish a RAS mutant cancer cell model where the autophagy gene ATG5 is dispensable in A549 cells in vitro, yet promotes tumorigenesis in mice. ATG5 represses transcriptional activation by the TGFβ-SMAD gene regulatory pathway. However, autophagy does not terminate cytosolic signal transduction by TGFβ. Instead, we use proteomics to identify selective degradation of the signalling scaffold TRAF3. TRAF3 autophagy is driven by RAS and results in activation of the NF-κB family member RELB. We show that RELB represses TGFβ target promoters independently of DNA binding at NF-κB recognition sequences, instead binding with SMAD family member(s) at SMAD-response elements. Thus, autophagy antagonises TGFβ gene expression. Finally, autophagy-deficient A549 cells regain tumorigenicity upon SMAD4 knockdown. Thus, at least in this setting, a physiologic function for autophagic regulation of gene expression is tumour growth. Macroautophagy can regulate cell signalling and tumorigenesis but the molecular mechanisms are unclear. Here the authors show selective degradation of the signalling scaffold TRAF3 by autophagy and consequent activation of the NF-κB family member RELB regulate gene expression via antagonism of SMAD proteins.
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14
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Primate lentiviruses use at least three alternative strategies to suppress NF-κB-mediated immune activation. PLoS Pathog 2017; 13:e1006598. [PMID: 28859166 PMCID: PMC5597281 DOI: 10.1371/journal.ppat.1006598] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/13/2017] [Accepted: 08/22/2017] [Indexed: 01/02/2023] Open
Abstract
Primate lentiviruses have evolved sophisticated strategies to suppress the immune response of their host species. For example, HIV-2 and most simian immunodeficiency viruses (SIVs) use their accessory protein Nef to prevent T cell activation and antiviral gene expression by downmodulating the T cell receptor CD3. This Nef function was lost in HIV-1 and other vpu-encoding viruses suggesting that the acquisition of Vpu-mediated NF-κB inhibition reduced the selection pressure for inhibition of T cell activation by Nef. To obtain further insights into the modulation of NF-κB activity by primate lentiviral accessory factors, we analyzed 32 Vpr proteins from a large panel of divergent primate lentiviruses. We found that those of SIVcol and SIVolc infecting Colobinae monkeys showed the highest efficacy in suppressing NF-κB activation. Vpr-mediated inhibition of NF-κB resulted in decreased IFNβ promoter activity and suppressed type I IFN induction in virally infected primary cells. Interestingly, SIVcol and SIVolc differ from all other primate lentiviruses investigated by the lack of both, a vpu gene and efficient Nef-mediated downmodulation of CD3. Thus, primate lentiviruses have evolved at least three alternative strategies to inhibit NF-κB-dependent immune activation. Functional analyses showed that the inhibitory activity of SIVolc and SIVcol Vprs is independent of DCAF1 and the induction of cell cycle arrest. While both Vprs target the IKK complex or a factor further downstream in the NF-κB signaling cascade, only SIVolc Vpr stabilizes IκBα and inhibits p65 phosphorylation. Notably, only de-novo synthesized but not virion-associated Vpr suppressed the activation of NF-κB, thus enabling NF-κB-dependent initiation of viral gene transcription during early stages of the replication cycle, while minimizing antiviral gene expression at later stages. Our findings highlight the key role of NF-κB in antiviral immunity and demonstrate that primate lentiviruses follow distinct evolutionary paths to modulate NF-κB-dependent expression of viral and antiviral genes. The cellular transcription factor NF-κB plays a complex role in the lentiviral replication cycle. On the one hand, activation of NF-κB is required for efficient transcription of viral genes and reactivation of latent proviruses. On the other hand, NF-κB is also a key driver of antiviral gene expression, immune activation and progression to AIDS. As a result, primate lentiviruses tightly regulate the activation of NF-κB throughout their replication cycle to enable transcription of viral genes while minimizing antiviral gene expression. Here, we show that human and simian immunodeficiency viruses have evolved at least three alternative strategies to suppress NF-κB-dependent immune activation: HIV-2 and most SIVs prevent T cell activation via Nef-mediated downmodulation of CD3. In comparison, HIV-1 and its vpu-containing SIV precursors inhibit NF-κB activation via their accessory protein Vpu and lost the CD3 downmodulation function of Nef. Finally, SIVcol and SIVolc, infecting mantled guerezas and olive colobus monkeys, respectively, utilize Vpr. Our findings emphasize the key role of NF-κB as inducer of antiretroviral immune responses and add to the accumulating evidence that lentiviral accessory proteins target innate signaling cascades by sophisticated mechanisms to evade restriction.
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15
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Zhao J, Li D, Seo J, Allen AS, Gordân R. Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2017; 10229:336-352. [PMID: 28691125 DOI: 10.1007/978-3-319-56970-3_21] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many recent studies have emphasized the importance of genetic variants and mutations in cancer and other complex human diseases. The overwhelming majority of these variants occur in non-coding portions of the genome, where they can have a functional impact by disrupting regulatory interactions between transcription factors (TFs) and DNA. Here, we present a method for assessing the impact of non-coding mutations on TF-DNA interactions, based on regression models of DNA-binding specificity trained on high-throughput in vitro data. We use ordinary least squares (OLS) to estimate the parameters of the binding model for each TF, and we show that our predictions of TF-binding changes due to DNA mutations correlate well with measured changes in gene expression. In addition, by leveraging distributional results associated with OLS estimation, for each predicted change in TF binding we also compute a normalized score (z-score) and a significance value (p-value) reflecting our confidence that the mutation affects TF binding. We use this approach to analyze a large set of pathogenic non-coding variants, and we show that these variants lead to significant differences in TF binding between alleles, compared to a control set of common variants. Thus, our results indicate that there is a strong regulatory component to the pathogenic non-coding variants identified thus far.
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Affiliation(s)
- Jingkang Zhao
- Center for Genomic and Computational Biology, Duke University, Durham NC 27708, USA.,Program in Computational Biology and Bioinformatics, Duke University, Durham NC 27708, USA
| | - Dongshunyi Li
- Department of Biostatistics and Bioinformatics, Duke University, Durham NC 27708, USA
| | - Jungkyun Seo
- Program in Computational Biology and Bioinformatics, Duke University, Durham NC 27708, USA
| | - Andrew S Allen
- Center for Genomic and Computational Biology, Duke University, Durham NC 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University, Durham NC 27708, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University, Durham NC 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University, Durham NC 27708, USA.,Department of Computer Science, Duke University, Durham NC 27708, USA
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16
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Sharma V, Monti P, Fronza G, Inga A. Human transcription factors in yeast: the fruitful examples of P53 and NF-кB. FEMS Yeast Res 2016; 16:fow083. [PMID: 27683095 DOI: 10.1093/femsyr/fow083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2016] [Indexed: 12/31/2022] Open
Abstract
The observation that human transcription factors (TFs) can function when expressed in yeast cells has stimulated the development of various functional assays to investigate (i) the role of binding site sequences (herein referred to as response elements, REs) in transactivation specificity, (ii) the impact of polymorphic nucleotide variants on transactivation potential, (iii) the functional consequences of mutations in TFs and (iv) the impact of cofactors or small molecules. These approaches have found applications in basic as well as applied research, including the identification and the characterisation of mutant TF alleles from clinical samples. The ease of genome editing of yeast cells and the availability of regulated systems for ectopic protein expression enabled the development of quantitative reporter systems, integrated at a chosen chromosomal locus in isogenic yeast strains that differ only at the level of a specific RE targeted by a TF or for the expression of distinct TF alleles. In many cases, these assays were proven predictive of results in higher eukaryotes. The potential to work in small volume formats and the availability of yeast strains with modified chemical uptake have enhanced the scalability of these approaches. Next to well-established one-, two-, three-hybrid assays, the functional assays with non-chimeric human TFs enrich the palette of opportunities for functional characterisation. We review ∼25 years of research on human sequence-specific TFs expressed in yeast, with an emphasis on the P53 and NF-кB family of proteins, highlighting outcomes, advantages, challenges and limitations of these heterologous assays.
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Affiliation(s)
- Vasundhara Sharma
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
| | - Paola Monti
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Gilberto Fronza
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Alberto Inga
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
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17
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Sharma V, Jordan JJ, Ciribilli Y, Resnick MA, Bisio A, Inga A. Quantitative Analysis of NF-κB Transactivation Specificity Using a Yeast-Based Functional Assay. PLoS One 2015; 10:e0130170. [PMID: 26147604 PMCID: PMC4493129 DOI: 10.1371/journal.pone.0130170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/18/2015] [Indexed: 11/18/2022] Open
Abstract
The NF-κB transcription factor family plays a central role in innate immunity and inflammation processes and is frequently dysregulated in cancer. We developed an NF-κB functional assay in yeast to investigate the following issues: transactivation specificity of NF-κB proteins acting as homodimers or heterodimers; correlation between transactivation capacity and in vitro DNA binding measurements; impact of co-expressed interacting proteins or of small molecule inhibitors on NF-κB-dependent transactivation. Full-length p65 and p50 cDNAs were cloned into centromeric expression vectors under inducible GAL1 promoter in order to vary their expression levels. Since p50 lacks a transactivation domain (TAD), a chimeric construct containing the TAD derived from p65 was also generated (p50TAD) to address its binding and transactivation potential. The p50TAD and p65 had distinct transactivation specificities towards seventeen different κB response elements (κB-REs) where single nucleotide changes could greatly impact transactivation. For four κB-REs, results in yeast were predictive of transactivation potential measured in the human MCF7 cell lines treated with the NF-κB activator TNFα. Transactivation results in yeast correlated only partially with in vitro measured DNA binding affinities, suggesting that features other than strength of interaction with naked DNA affect transactivation, although factors such as chromatin context are kept constant in our isogenic yeast assay. The small molecules BAY11-7082 and ethyl-pyruvate as well as expressed IkBα protein acted as NF-κB inhibitors in yeast, more strongly towards p65. Thus, the yeast-based system can recapitulate NF-κB features found in human cells, thereby providing opportunities to address various NF-κB functions, interactions and chemical modulators.
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Affiliation(s)
- Vasundhara Sharma
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jennifer J. Jordan
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michael A. Resnick
- Chromosome Stability Group; National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
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18
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Andrilenas KK, Penvose A, Siggers T. Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics 2014; 14:17-29. [PMID: 25431149 DOI: 10.1093/bfgp/elu046] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Protein-DNA binding is central to specificity in gene regulation, and methods for characterizing transcription factor (TF)-DNA binding remain crucial to studies of regulatory specificity. High-throughput (HT) technologies have revolutionized our ability to characterize protein-DNA binding by significantly increasing the number of binding measurements that can be performed. Protein-binding microarrays (PBMs) are a robust and powerful HT platform for studying DNA-binding specificity of TFs. Analysis of PBM-determined DNA-binding profiles has provided new insight into the scope and mechanisms of TF binding diversity. In this review, we focus specifically on the PBM technique and discuss its application to the study of TF specificity, in particular, the binding diversity of TF homologs and multi-protein complexes.
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19
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Du W, Gao J, Wang T, Wang J. Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites. PLoS One 2014; 9:e101490. [PMID: 24992458 PMCID: PMC4081663 DOI: 10.1371/journal.pone.0101490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 06/09/2014] [Indexed: 11/18/2022] Open
Abstract
In this study, we established a single nucleotide mutation matrix (SNMM) model based on the relative binding affinities of NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants detected with the double-stranded DNA microarray. We evaluated this model by scoring different groups of 10-bp DNA sequences with this model and analyzing the correlations between the scores and the relative binding affinities detected with three wet experiments, including the electrophoresis mobility shift assay (EMSA), the protein-binding microarray (PBM) and the systematic evolution of ligands by exponential enrichment-sequencing (SELEX-Seq). The results revealed that the SNMM scores were strongly correlated with the detected binding affinities. We also scored the DNA sequences with other three models, including the principal coordinate (PC) model, the position weight matrix scoring algorithm (PWMSA) model and the Match model, and analyzed the correlations between the scores and the detected binding affinities. In comparison with these models, the SNMM model achieved reliable results. We finally determined 0.747 as the optimal threshold for predicting the NF-κB DNA-binding sites with the SNMM model. The SNMM model thus provides a new alternative model for scoring the relative binding affinities of NF-κB to the 10-bp DNA sequences and predicting the NF-κB DNA-binding sites.
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Affiliation(s)
- Wenxin Du
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Jing Gao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Tingting Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
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20
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Ramachandran S, Karp PH, Osterhaus SR, Jiang P, Wohlford-Lenane C, Lennox KA, Jacobi AM, Praekh K, Rose SD, Behlke MA, Xing Y, Welsh MJ, McCray PB. Post-transcriptional regulation of cystic fibrosis transmembrane conductance regulator expression and function by microRNAs. Am J Respir Cell Mol Biol 2014; 49:544-51. [PMID: 23646886 DOI: 10.1165/rcmb.2012-0430oc] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are increasingly recognized as important posttranscriptional regulators of gene expression, and changes in their actions can contribute to disease states. Little is understood regarding miRNA functions in the airway epithelium under normal or diseased conditions. We profiled miRNA expression in well-differentiated primary cultures of human cystic fibrosis (CF) and non-CF airway epithelia, and discovered that miR-509-3p and miR-494 concentrations were increased in CF epithelia. Human non-CF airway epithelia, transfected with the mimics of miR-509-3p or miR-494, showed decreased cystic fibrosis transmembrane conductance regulator (CFTR) expression, whereas their respective anti-miRs exerted the opposite effect. Interestingly, the two miRNAs acted cooperatively in regulating CFTR expression. Upon infecting non-CF airway epithelial cells with Staphylococcus aureus, or upon stimulating them with the proinflammatory cytokines TNF-α or IL-1β, we observed an increased expression of both miRNAs and a concurrent decrease in CFTR expression and function, suggesting that inflammatory mediators may regulate these miRNAs. Transfecting epithelia with anti-miRs for miR-509-3p and miR-494, or inhibiting NF-κB signaling before stimulating cells with TNFα or IL-1β, suppressed these responses, suggesting that the expression of both miRNAs was responsive to NF-κB signaling. Thus, miR-509-3p and miR-494 are dynamic regulators of CFTR abundance and function in normal, non-CF airway epithelia.
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21
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Liu H, Yang J, Yuan Y, Xia Z, Chen M, Xie L, Ma X, Wang J, Ouyang S, Wu Q, Yu F, Zhou X, Yang Y, Cao Y, Hu J, Yin B. Regulation of Mcl-1 by constitutive activation of NF-κB contributes to cell viability in human esophageal squamous cell carcinoma cells. BMC Cancer 2014; 14:98. [PMID: 24529193 PMCID: PMC3930545 DOI: 10.1186/1471-2407-14-98] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 02/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most lethal malignancies with a 5-year survival rate less than 15%. Understanding of the molecular mechanisms involved in the pathogenesis of ESCC becomes critical to develop more effective treatments. METHODS Mcl-1 expression was measured by reverse transcription (RT)-PCR and Western blotting. Human Mcl-1 promoter activity was evaluated by reporter gene assay. The interactions between DNA and transcription factors were confirmed by electrophoretic mobility shift assay (EMSA) in vitro and by chromatin immunoprecipitation (ChIP) assay in cells. RESULTS Four human ESCC cell lines, TE-1, Eca109, KYSE150 and KYSE510, are revealed increased levels of Mcl-1 mRNA and protein compare with HaCaT, an immortal non-tumorigenic cell line. Results of reporter gene assays demonstrate that human Mcl-1 promoter activity is decreased by mutation of kappaB binding site, specific NF-kappaB inhibitor Bay11-7082 or dominant inhibitory molecule DNMIkappaBalpha in TE-1 and KYSE150 cell lines. Mcl-1 protein level is also attenuated by Bay11-7082 treatment or co-transfection of DNMIkappaBalpha in TE-1 and KYSE150 cells. EMSA results indicate that NF-kappaB subunits p50 and p65 bind to human Mcl-1-kappaB probe in vitro. ChIP assay further confirm p50 and p65 directly bind to human Mcl-1 promoter in intact cells, by which regulates Mcl-1 expression and contributes to the viability of TE-1 cells. CONCLUSIONS Our data provided evidence that one of the mechanisms of Mcl-1 expression in human ESCC is regulated by the activation of NF-kappaB signaling. The newly identified mechanism might provide a scientific basis for developing effective approaches to treatment human ESCC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jianguo Hu
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Road, Changsha, Hunan 410011, China.
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22
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Eggeling R, Gohr A, Keilwagen J, Mohr M, Posch S, Smith AD, Grosse I. On the value of intra-motif dependencies of human insulator protein CTCF. PLoS One 2014; 9:e85629. [PMID: 24465627 PMCID: PMC3899044 DOI: 10.1371/journal.pone.0085629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/05/2013] [Indexed: 01/08/2023] Open
Abstract
The binding affinity of DNA-binding proteins such as transcription factors is mainly determined by the base composition of the corresponding binding site on the DNA strand. Most proteins do not bind only a single sequence, but rather a set of sequences, which may be modeled by a sequence motif. Algorithms for de novo motif discovery differ in their promoter models, learning approaches, and other aspects, but typically use the statistically simple position weight matrix model for the motif, which assumes statistical independence among all nucleotides. However, there is no clear justification for that assumption, leading to an ongoing debate about the importance of modeling dependencies between nucleotides within binding sites. In the past, modeling statistical dependencies within binding sites has been hampered by the problem of limited data. With the rise of high-throughput technologies such as ChIP-seq, this situation has now changed, making it possible to make use of statistical dependencies effectively. In this work, we investigate the presence of statistical dependencies in binding sites of the human enhancer-blocking insulator protein CTCF by using the recently developed model class of inhomogeneous parsimonious Markov models, which is capable of modeling complex dependencies while avoiding overfitting. These findings lead to a more detailed characterization of the CTCF binding motif, which is only poorly represented by independent nucleotide frequencies at several positions, predominantly at the 3' end.
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Affiliation(s)
- Ralf Eggeling
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
| | - André Gohr
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Michaela Mohr
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Stefan Posch
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States of America
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
- German Center of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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23
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Abbas AK, Le K, Pimmett VL, Bell DA, Cairns E, DeKoter RP. Negative regulation of the peptidylarginine deiminase type IV promoter by NF-κB in human myeloid cells. Gene 2014; 533:123-31. [DOI: 10.1016/j.gene.2013.09.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/26/2013] [Indexed: 01/01/2023]
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24
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An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example. PLoS One 2013; 8:e76109. [PMID: 24130762 PMCID: PMC3794954 DOI: 10.1371/journal.pone.0076109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/20/2013] [Indexed: 12/29/2022] Open
Abstract
SELEX-Seq is now the optimal high-throughput technique for characterizing DNA-binding specificities of transcription factors. In this study, we introduced an improved EMSA-based SELEX-Seq strategy with several advantages. The improvements of this strategy included: (1) using a FAM-labeled probe to track protein-DNA complex in polyacrylamide gel for rapidly recovering the protein-bound dsDNA without relying on traditional radioactive labeling or ethidium bromide staining; (2) monitoring the specificity of SELEX selection by detecting a positive and negative sequence doped into the input DNAs used in each round with PCR amplification; (3) using nested PCR to ensure the specificity of PCR amplification of the selected DNAs after each round; (4) using the nucleotides added at the 5′ end of the nested PCR primers as the split barcode to code DNAs from various rounds for multiplexing sequencing samples. The split barcode minimized selection times and thus greatly simplified the current SELEX-Seq procedure. The reliability of the strategy was demonstrated by performing a successful SELEX-Seq of a well-known transcription factor, NF-κB. Therefore, this study provided a useful SELEX-Seq strategy for characterizing DNA-binding specificities of transcription factors.
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Xing Y, Yang Y, Zhou F, Wang J. Characterization of genome-wide binding of NF-κB in TNFα-stimulated HeLa cells. Gene 2013; 526:142-9. [PMID: 23688556 DOI: 10.1016/j.gene.2013.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 04/28/2013] [Accepted: 05/01/2013] [Indexed: 01/06/2023]
Abstract
This study characterized the genome-wide binding of NF-κB RelA with ChIP-Seq and explored its effects on the gene transcription with DNA microarray. It was found that NF-κB showed several significant binding characteristics, including the inter- and intra-chromosomal differential high-fold enrichment binding, the dominant intronic binding to vast majority of target genes through multiple ChIP-seq peaks and κB sites, extensively binding to large number of genes in the human genome, and binding its target genes more broadly through noncanonical κB sites than canonical κB sites. These in vivo genome-wide binding characteristics exerted effects on the transcription of its direct target genes in genome, reflecting some important traits of this protein which acts as a stimulatory transcription factor involving in many biological processes and responding to various internal and external stimuli.
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Affiliation(s)
- Yujun Xing
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
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26
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Ryzhakov G, Teixeira A, Saliba D, Blazek K, Muta T, Ragoussis J, Udalova IA. Cross-species analysis reveals evolving and conserved features of the nuclear factor κB (NF-κB) proteins. J Biol Chem 2013; 288:11546-54. [PMID: 23508954 PMCID: PMC3630861 DOI: 10.1074/jbc.m113.451153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
NF-κB is a key regulator of immune gene expression in metazoans. It is currently unclear what changes occurred in NF-κB during animal evolution and what features remained conserved. To address this question, we compared the biochemical and functional properties of NF-κB proteins derived from human and the starlet sea anemone (Nematostella vectensis) in 1) a high-throughput assay of in vitro preferences for DNA sequences, 2) ChIP analysis of in vivo recruitment to the promoters of target genes, 3) a LUMIER-assisted examination of interactions with cofactors, and 4) a transactivation assay. We observed a remarkable evolutionary conservation of the DNA binding preferences of the animal NF-κB orthologs. We also show that NF-κB dimerization properties, nuclear localization signals, and binding to cytosolic IκBs are conserved. Surprisingly, the Bcl3-type nuclear IκB proteins functionally pair up only with NF-κB derived from their own species. The basis of the differential NF-κB recognition by IκB subfamilies is discussed.
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Affiliation(s)
- Grigory Ryzhakov
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, London W6 8LH, United Kingdom.
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Cyrne L, Oliveira-Marques V, Marinho HS, Antunes F. H2O2 in the Induction of NF-κB-Dependent Selective Gene Expression. Methods Enzymol 2013; 528:173-88. [DOI: 10.1016/b978-0-12-405881-1.00010-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Gu GM, Wang JK. [DNA-binding profiles of mammalian transcription factors]. YI CHUAN = HEREDITAS 2012; 34:950-68. [PMID: 22917900 DOI: 10.3724/sp.j.1005.2012.00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The differential gene expression is the molecular base of development and responses to stimuli of organisms. Transcription factors (TFs) play important regulatory roles in this kind of differential gene expression. Therefore, to elucidate how these TFs regulate the complex differential gene expression, it is necessary to identify all target genes of them and construct the gene transcription regulatory network controlled by them. DNA binding is a key step for TFs regulating gene transcription. Therefore, in order to identify their target genes, it is indispensable to identify all possible DNA sequences that can be recognized and bound by TFs at the molecular level of their interactions with DNA, i.e., construction of the DNA-binding profiles of TFs. In recent years, along with the development of DNA microarray and high-throughput DNA sequencing techniques, there appeared some revolutionary new techniques for constructing DNA-binding profiles of TFs, which greatly promotes studies in this field. These techniques include ChIP-chip and ChIP-Seq for constructing in vivo DNA-binding profiles of TFs, dsDNA microarray, SELEX-SAGE, Bind-n-Seq, MMP-SELEX, EMSA-Seq, and HiTS-FLIP for constructing in vitro DNA-binding profiles of TFs. This paper reviewed these techniques.
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Affiliation(s)
- Guang-Ming Gu
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China.
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Tan M, Yu D, Jin Y, Dou L, Li B, Wang Y, Yue J, Liang L. An information transmission model for transcription factor binding at regulatory DNA sites. Theor Biol Med Model 2012; 9:19. [PMID: 22672438 PMCID: PMC3442977 DOI: 10.1186/1742-4682-9-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 05/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Computational identification of transcription factor binding sites (TFBSs) is a rapid, cost-efficient way to locate unknown regulatory elements. With increased potential for high-throughput genome sequencing, the availability of accurate computational methods for TFBS prediction has never been as important as it currently is. To date, identifying TFBSs with high sensitivity and specificity is still an open challenge, necessitating the development of novel models for predicting transcription factor-binding regulatory DNA elements. RESULTS Based on the information theory, we propose a model for transcription factor binding of regulatory DNA sites. Our model incorporates position interdependencies in effective ways. The model computes the information transferred (TI) between the transcription factor and the TFBS during the binding process and uses TI as the criterion to determine whether the sequence motif is a possible TFBS. Based on this model, we developed a computational method to identify TFBSs. By theoretically proving and testing our model using both real and artificial data, we found that our model provides highly accurate predictive results. CONCLUSIONS In this study, we present a novel model for transcription factor binding regulatory DNA sites. The model can provide an increased ability to detect TFBSs.
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Affiliation(s)
- Mingfeng Tan
- Beijing Institute of Biotechnology, Beijing 100071, China
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Wee KB, Yio WK, Surana U, Chiam KH. Transcription factor oscillations induce differential gene expressions. Biophys J 2012; 102:2413-23. [PMID: 22713556 DOI: 10.1016/j.bpj.2012.04.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 01/04/2023] Open
Abstract
Intracellular protein levels of diverse transcription factors (TFs) vary periodically with time. However, the effects of TF oscillations on gene expression, the primary role of TFs, are poorly understood. In this study, we determined these effects by comparing gene expression levels induced in the presence and in the absence of TF oscillations under same mean intracellular protein level of TF. For all the nonlinear TF transcription kinetics studied, an oscillatory TF is predicted to induce gene expression levels that are distinct from a nonoscillatory TF. The conditions dictating whether TF oscillations induce either higher or lower average gene expression levels were elucidated. Subsequently, the predicted effects from an oscillatory TF, which follows sigmoid transcription kinetics, were applied to demonstrate how oscillatory dynamics provide a mechanism for differential target gene transactivation. Generally, the mean TF concentration at which oscillations occur relative to the promoter binding affinity of a target gene determines whether the gene is up- or downregulated whereas the oscillation amplitude amplifies the magnitude of the differential regulation. Notably, the predicted trends of differential gene expressions induced by oscillatory NF-κB and glucocorticoid receptor match the reported experimental observations. Furthermore, the biological function of p53 oscillations is predicted to prime the cell for death upon DNA damage via differential upregulation of apoptotic genes. Lastly, given N target genes, an oscillatory TF can generate between (N-1) and (2N-1) distinct patterns of differential transactivation. This study provides insights into the mechanism for TF oscillations to induce differential gene expressions, and underscores the importance of TF oscillations in biological regulations.
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Affiliation(s)
- Keng Boon Wee
- A∗STAR Institute of High Performance Computing, Connexis, Singapore.
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Chromatin immunoprecipitation analysis of NFκB transcriptional regulation by nuclear IκBα in human macrophages. Methods Mol Biol 2012; 809:121-34. [PMID: 22113272 DOI: 10.1007/978-1-61779-376-9_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transcription factor NFκB comprises a family of proteins that serve as crucial regulators of genes involved in host immune and inflammatory responses, cell survival, proliferation, and differentiation. Since transcription of NFκB-dependent genes is increased in numerous inflammatory disorders as well as in many types of cancer and leukemia, inhibition of NFκB-dependent transcription thus represents an important therapeutic target. We have previously shown that in human leukocytes, transcription of NFκB-dependent genes is inhibited by the nuclear translocation and accumulation of IκBα, which can be induced by an inhibitor of CRM1-dependent nuclear export, leptomycin B (LMB). In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the regulation of NFκB recruitment to NFκB-dependent promoters by nuclear IκBα induced by LMB. We show that in lipopolysaccharide (LPS)-stimulated human U-937 macrophages, recruitment of NFκB p65 and p50 proteins to NFκB-dependent promoters of IκBα and cIAP2 genes is suppressed by the LMB-induced nuclear IκBα. Even though in this study we use U-937 macrophages, this protocol should be readily adaptable to analyze the regulation of NFκB recruitment by nuclear IκBα also in other cell types.
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Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. Nat Immunol 2011; 13:95-102. [PMID: 22101729 PMCID: PMC3242931 DOI: 10.1038/ni.2151] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/26/2011] [Indexed: 12/14/2022]
Abstract
The unique DNA-binding properties of distinct NF-κB dimers influence the selective regulation of NF-κB target genes. To more thoroughly investigate these dimer-specific differences, we combined protein-binding microarrays and surface plasmon resonance to evaluate DNA sites recognized by eight different NF-κB dimers. We observed three distinct binding-specificity classes and clarified mechanisms by which dimers might regulate distinct sets of genes. We identified many new nontraditional NF-κB binding site (κB site) sequences and highlight the plasticity of NF-κB dimers in recognizing κB sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-κB target sites and uncover gene regulatory circuitry.
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Affiliation(s)
- Trevor Siggers
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Abraham B Chang
- Molecular Biology Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Ana Teixeira
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
| | - Daniel Wong
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
| | - Kevin J Williams
- Molecular Biology Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bilal Ahmed
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, Imperial College, London, UK
| | - Stephen T Smale
- Molecular Biology Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Antonaki A, Demetriades C, Polyzos A, Banos A, Vatsellas G, Lavigne MD, Apostolou E, Mantouvalou E, Papadopoulou D, Mosialos G, Thanos D. Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements. J Biol Chem 2011; 286:38768-38782. [PMID: 21896491 DOI: 10.1074/jbc.m111.234161] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The transcription factor NF-κB is a critical regulator of immune responses. To determine how NF-κB builds transcriptional control networks, we need to obtain a topographic map of the factor bound to the genome and correlate it with global gene expression. We used a ChIP cloning technique and identified novel NF-κB target genes in response to virus infection. We discovered that most of the NF-κB-bound genomic sites deviate from the consensus and are located away from conventional promoter regions. Remarkably, we identified a novel abundant NF-κB-binding site residing in specialized Alu-repetitive elements having the potential for long range transcription regulation, thus suggesting that in addition to its known role, NF-κB has a primate-specific function and a role in human evolution. By combining these data with global gene expression profiling of virus-infected cells, we found that most of the sites bound by NF-κB in the human genome do not correlate with changes in gene expression of the nearby genes and they do not appear to function in the context of synthetic promoters. These results demonstrate that repetitive elements interspersed in the human genome function as common target sites for transcription factors and may play an important role in expanding the repertoire of binding sites to engage new genes into regulatory networks.
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Affiliation(s)
- Athina Antonaki
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Constantinos Demetriades
- Department of Biology, Aristotle University of Thessaloniki, University Campus, Thessaloniki 54124, Greece
| | - Alexander Polyzos
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Aggelos Banos
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Giannis Vatsellas
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Matthieu D Lavigne
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Effie Apostolou
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Eva Mantouvalou
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - Deppie Papadopoulou
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece
| | - George Mosialos
- Department of Biology, Aristotle University of Thessaloniki, University Campus, Thessaloniki 54124, Greece.
| | - Dimitris Thanos
- Institute of Molecular Biology, Genetics and Biotechnology, Biomedical Research Foundation, Academy of Athens, 4 Soranou Efesiou Street, Athens 11527, Greece.
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Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk M, Angelov D, Dimitrov S, Udalova IA, Ragoussis J. Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol 2011; 12:R70. [PMID: 21801342 PMCID: PMC3218832 DOI: 10.1186/gb-2011-12-7-r70] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 07/11/2011] [Accepted: 07/29/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genetic studies have provided ample evidence of the influence of non-coding DNA polymorphisms on trait variance, particularly those occurring within transcription factor binding sites. Protein binding microarrays and other platforms that can map these sites with great precision have enhanced our understanding of how a single nucleotide polymorphism can alter binding potential within an in vitro setting, allowing for greater predictive capability of its effect on a transcription factor binding site. RESULTS We have used protein binding microarrays and electrophoretic mobility shift assay-sequencing (EMSA-Seq), a deep sequencing based method we developed to analyze nine distinct human NF-κB dimers. This family of transcription factors is one of the most extensively studied, but our understanding of its DNA binding preferences has been limited to the originally described consensus motif, GGRRNNYYCC. We highlight differences between NF-κB family members and also put under the spotlight non-canonical motifs that have so far received little attention. We utilize our data to interpret the binding of transcription factors between individuals across 1,405 genomic regions laden with single nucleotide polymorphisms. We also associated binding correlations made using our data with risk alleles of disease and demonstrate its utility as a tool for functional studies of single nucleotide polymorphisms in regulatory regions. CONCLUSIONS NF-κB dimers bind specifically to non-canonical motifs and these can be found within genomic regions in which a canonical motif is not evident. Binding affinity data generated with these different motifs can be used in conjunction with data from chromatin immunoprecipitation-sequencing (ChIP-Seq) to enable allele-specific analyses of expression and transcription factor-DNA interactions on a genome-wide scale.
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Affiliation(s)
- Daniel Wong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX37BN, UK
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Venkatesha SH, Berman BM, Moudgil KD. Herbal medicinal products target defined biochemical and molecular mediators of inflammatory autoimmune arthritis. Bioorg Med Chem 2011; 19:21-9. [PMID: 21115252 PMCID: PMC3020797 DOI: 10.1016/j.bmc.2010.10.053] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/18/2010] [Accepted: 10/25/2010] [Indexed: 11/18/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic debilitating disease characterized by synovial inflammation, damage to cartilage and bone, and deformities of the joints. Several drugs possessing anti-inflammatory and immunomodulatory properties are being used in the conventional (allopathic) system of medicine to treat RA. However, the long-term use of these drugs is associated with harmful side effects. Therefore, newer drugs with low or no toxicity for the treatment of RA are actively being sought. Interestingly, several herbs demonstrate anti-inflammatory and anti-arthritic activity. In this review, we describe the role of the major biochemical and molecular mediators in the pathogenesis of RA, and highlight the sites of action of herbal medicinal products that have anti-arthritic activity. With the rapidly increasing use of CAM products by patients with RA and other inflammation-related disorders, our review presents timely information validating the scientific rationale for the use of natural therapeutic products.
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Affiliation(s)
- Shivaprasad H. Venkatesha
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Brian M. Berman
- Center for Integrative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Kamal D. Moudgil
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
- Division of Rheumatology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
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36
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Shlomai J. Redox control of protein-DNA interactions: from molecular mechanisms to significance in signal transduction, gene expression, and DNA replication. Antioxid Redox Signal 2010; 13:1429-76. [PMID: 20446770 DOI: 10.1089/ars.2009.3029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein-DNA interactions play a key role in the regulation of major cellular metabolic pathways, including gene expression, genome replication, and genomic stability. They are mediated through the interactions of regulatory proteins with their specific DNA-binding sites at promoters, enhancers, and replication origins in the genome. Redox signaling regulates these protein-DNA interactions using reactive oxygen species and reactive nitrogen species that interact with cysteine residues at target proteins and their regulators. This review describes the redox-mediated regulation of several master regulators of gene expression that control the induction and suppression of hundreds of genes in the genome, regulating multiple metabolic pathways, which are involved in cell growth, development, differentiation, and survival, as well as in the function of the immune system and cellular response to intracellular and extracellular stimuli. It also discusses the role of redox signaling in protein-DNA interactions that regulate DNA replication. Specificity of redox regulation is discussed, as well as the mechanisms providing several levels of redox-mediated regulation, from direct control of DNA-binding domains through the indirect control, mediated by release of negative regulators, regulation of redox-sensitive protein kinases, intracellular trafficking, and chromatin remodeling.
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Affiliation(s)
- Joseph Shlomai
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Tropical and Infectious Diseases, Institute for Medical Research Canada-Israel, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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Oeckinghaus A, Ghosh S. The NF-kappaB family of transcription factors and its regulation. Cold Spring Harb Perspect Biol 2010; 1:a000034. [PMID: 20066092 DOI: 10.1101/cshperspect.a000034] [Citation(s) in RCA: 2120] [Impact Index Per Article: 141.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear factor-kappaB (NF-kappaB) consists of a family of transcription factors that play critical roles in inflammation, immunity, cell proliferation, differentiation, and survival. Inducible NF-kappaB activation depends on phosphorylation-induced proteosomal degradation of the inhibitor of NF-kappaB proteins (IkappaBs), which retain inactive NF-kappaB dimers in the cytosol in unstimulated cells. The majority of the diverse signaling pathways that lead to NF-kappaB activation converge on the IkappaB kinase (IKK) complex, which is responsible for IkappaB phosphorylation and is essential for signal transduction to NF-kappaB. Additional regulation of NF-kappaB activity is achieved through various post-translational modifications of the core components of the NF-kappaB signaling pathways. In addition to cytosolic modifications of IKK and IkappaB proteins, as well as other pathway-specific mediators, the transcription factors are themselves extensively modified. Tremendous progress has been made over the last two decades in unraveling the elaborate regulatory networks that control the NF-kappaB response. This has made the NF-kappaB pathway a paradigm for understanding general principles of signal transduction and gene regulation.
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Affiliation(s)
- Andrea Oeckinghaus
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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38
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Natoli G. Control of NF-kappaB-dependent transcriptional responses by chromatin organization. Cold Spring Harb Perspect Biol 2010; 1:a000224. [PMID: 20066094 DOI: 10.1101/cshperspect.a000224] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A large number of genes have been positively selected and recruited to participate in various phases of the inflammatory response triggered by microbial stimuli. Because of the complexity of the response, the many phases in which it is deployed, and the many "flavors" in which it appears (depending on quality and intensity of the stimulus as well as the target organ), very elaborated mechanisms evolved to ensure that the expression of the induced genes is carefully and precisely organized so that each gene is expressed in response to specific stimuli and with kinetics and intensities that suit the peculiar function of its product(s). Data accumulated in recent years have strengthened the concept that chromatin is an essential substrate at which multiple signals are integrated to promote a correctly choreographed expression of the genes involved in inflammatory transcriptional responses. Although the current level of understanding of these mechanisms is far from complete, some concepts and ideas have resisted experimental challenges and now represent accepted paradigms that are the subject of this article.
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Affiliation(s)
- Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy.
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Oliveira-Marques V, Marinho HS, Cyrne L, Antunes F. Role of hydrogen peroxide in NF-kappaB activation: from inducer to modulator. Antioxid Redox Signal 2009; 11:2223-43. [PMID: 19496701 DOI: 10.1089/ars.2009.2601] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydrogen peroxide (H2O2) has been implicated in the regulation of the transcription factor NF-kappaB, a key regulator of the inflammatory process and adaptive immunity. However, no consensus exists regarding the regulatory role played by H2O2. We discuss how the experimental methodologies used to expose cells to H2O2 produce inconsistent results that are difficult to compare, and how the steady-state titration with H2O2 emerges as an adequate tool to overcome these problems. The redox targets of H2O2 in the NF-kappaB pathway--from the membrane to the post-translational modifications in both NF-kappaB and histones in the nucleus--are described. We also review how H2O2 acts as a specific regulator at the level of the single gene, and briefly discuss the implications of this regulation for human health in the context of kappaB polymorphisms. In conclusion, after near 30 years of research, H2O2 emerges not as an inducer of NF-kappaB, but as an agent able to modulate the activation of the NF-kappaB pathway by other agents. This modulation is generic at the level of the whole pathway but specific at the level of the single gene. Therefore, H2O2 is a fine-tuning regulator of NF-kappaB-dependent processes, as exemplified by its dual regulation of inflammation.
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Affiliation(s)
- Virgínia Oliveira-Marques
- Grupo de Bioquímica dos Oxidantes e Antioxidantes, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Oliveira-Marques V, Marinho HS, Cyrne L, Antunes F. Modulation of NF-kappaB-dependent gene expression by H2O2: a major role for a simple chemical process in a complex biological response. Antioxid Redox Signal 2009; 11:2043-53. [PMID: 19014314 DOI: 10.1089/ars.2008.2279] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We recently observed that H2O2 regulates inflammation via upexpression of a few NF-kappaB-dependent genes, while leaving expression of most NF-kappaB-dependent genes unaltered. Here we test the hypothesis that this differential gene expression depends on the apparent affinity of kappaB sites in the gene-promoter regions toward NF-kappaB. Accordingly, cells were transfected with three reporter plasmids containing kappaB sequences with different affinities for NF-kappaB. It was observed that the lower the affinity, the higher the range of TNF-alpha concentrations where H2O2 upregulated gene expression. Mathematical models reproduced the key experimental observations indicating that H2O2 upregulation ceased when NF-kappaB fully occupied the kappaB sites. In vivo, it is predicted that genes with high-affinity sites remain insensitive to H2O2, whereas genes with lower-affinity sites are upregulated by H2O2. In conclusion, a simple chemical mechanism is at the root of a complex biologic process such as differential gene expression caused by H2O2.
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Affiliation(s)
- Virgínia Oliveira-Marques
- Grupo de Bioquímica dos Oxidantes e Antioxidantes, Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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Gowrisankar S, Jegga AG. Regression based predictor for p53 transactivation. BMC Bioinformatics 2009; 10:215. [PMID: 19602281 PMCID: PMC2719629 DOI: 10.1186/1471-2105-10-215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 07/14/2009] [Indexed: 11/10/2022] Open
Abstract
Background The p53 protein is a master regulator that controls the transcription of many genes in various pathways in response to a variety of stress signals. The extent of this regulation depends in part on the binding affinity of p53 to its response elements (REs). Traditional profile scores for p53 based on position weight matrices (PWM) are only a weak indicator of binding affinity because the level of binding also depends on various other factors such as interaction between the nucleotides and, in case of p53-REs, the extent of the spacer between the dimers. Results In the current study we introduce a novel in-silico predictor for p53-RE transactivation capability based on a combination of multidimensional scaling and multinomial logistic regression. Experimentally validated known p53-REs along with their transactivation capabilities are used for training. Through cross-validation studies we show that our method outperforms other existing methods. To demonstrate the utility of this method we (a) rank putative p53-REs of target genes and target microRNAs based on the predicted transactivation capability and (b) study the implication of polymorphisms overlapping p53-RE on its transactivation capability. Conclusion Taking into account both nucleotide interactions and the spacer length of p53-RE, we have created a novel in-silico regression-based transactivation capability predictor for p53-REs and used it to analyze validated and novel p53-REs and to predict the impact of SNPs overlapping these elements.
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Affiliation(s)
- Sivakumar Gowrisankar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM. OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. BMC Bioinformatics 2009; 10:208. [PMID: 19583839 PMCID: PMC2718928 DOI: 10.1186/1471-2105-10-208] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/07/2009] [Indexed: 12/29/2022] Open
Abstract
Background DNA sequence binding motifs for several important transcription factors happen to be self-overlapping. Many of the current regulatory site identification methods do not explicitly take into account the overlapping sites. Moreover, most methods use arbitrary thresholds and fail to provide a biophysical interpretation of statistical quantities. In addition, commonly used approaches do not include the location of a site with respect to the transcription start site (TSS) in an integrated probabilistic framework while identifying sites. Ignoring these features can lead to inaccurate predictions as well as incorrect design and interpretation of experimental results. Results We have developed a tool based on a Hidden Markov Model (HMM) that identifies binding location of transcription factors with preference for self-overlapping DNA motifs by combining the effects of their alternative binding modes. Interpreting HMM parameters as biophysical quantities, this method uses the occupancy probability of a transcription factor on a DNA sequence as the discriminant function, earning the algorithm the name OHMM: Occupancy via Hidden Markov Model. OHMM learns the classification threshold by training emission probabilities using unaligned sequences containing known sites and estimating transition probabilities to reflect site density in all promoters in a genome. While identifying sites, it adjusts parameters to model site density changing with the distance from the transcription start site. Moreover, it provides guidance for designing padding sequences in gel shift experiments. In the context of binding sites to transcription factor NF-κB, we find that the occupancy probability predicted by OHMM correlates well with the binding affinity in gel shift experiments. High evolutionary conservation scores and enrichment in experimentally verified regulated genes suggest that NF-κB binding sites predicted by our method are likely to be functional. Conclusion Our method deals specifically with identifying locations with multiple overlapping binding sites by computing the local occupancy of the transcription factor. Moreover, considering OHMM as a biophysical model allows us to learn the classification threshold in a principled manner. Another feature of OHMM is that we allow transition probabilities to change with location relative to the TSS. OHMM could be used to predict physical occupancy, and provides guidance for proper design of gel-shift experiments. Based upon our predictions, new insights into NF-κB function and regulation and possible new biological roles of NF-κB were uncovered.
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Affiliation(s)
- Amar Drawid
- BioMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ, USA.
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Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Handling Counterintuitive Results. J Mol Evol 2009; 68:654-64. [DOI: 10.1007/s00239-009-9238-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 03/30/2009] [Accepted: 04/15/2009] [Indexed: 01/26/2023]
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Mittler G, Butter F, Mann M. A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genes Dev 2009; 19:284-93. [PMID: 19015324 PMCID: PMC2652210 DOI: 10.1101/gr.081711.108] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 11/04/2008] [Indexed: 12/15/2022]
Abstract
Determining the underlying logic that governs the networks of gene expression in higher eukaryotes is an important task in the post-genome era. Sequence-specific transcription factors (TFs) that can read the genetic regulatory information and proteins that interpret the information provided by CpG methylation are crucial components of the system that controls the transcription of protein-coding genes by RNA polymerase II. We have previously described Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for the quantitative comparison of proteomes and the determination of protein-protein interactions. Here, we report a generic and scalable strategy to uncover such DNA protein interactions by SILAC that uses a fast and simple one-step affinity capture of TFs from crude nuclear extracts. Employing mutated or nonmethylated control oligonucleotides, specific TFs binding to their wild-type or methyl-CpG bait are distinguished from the vast excess of copurifying background proteins by their peptide isotope ratios that are determined by mass spectrometry. Our proof of principle screen identifies several proteins that have not been previously reported to be present on the fully methylated CpG island upstream of the human metastasis associated 1 family, member 2 gene promoter. The approach is robust, sensitive, and specific and offers the potential for high-throughput determination of TF binding profiles.
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Affiliation(s)
- Gerhard Mittler
- Center for Experimental Bioinformatics, University of Southern Denmark, DK-5230 Odense M, Denmark
- BIOSS—Center of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
| | - Falk Butter
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany
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Roman-Blas JA, Jimenez SA. Targeting NF-kappaB: a promising molecular therapy in inflammatory arthritis. Int Rev Immunol 2009; 27:351-74. [PMID: 18853343 DOI: 10.1080/08830180802295740] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The nuclear factor-kappa B family of transcription factors is intimately involved in the regulation of the inflammatory responses that play a fundamental role in the damage of articular tissues. Thus, many studies have examined the important contributions of components of the NF-kappaB signaling pathways to the pathogenesis of various rheumatic diseases and their pharmacologic modulation. Currently available therapeutic agents including nonsteroidal anti-inflammatory drugs, corticosteroids, nutraceuticals, and disease-modifying antirheumatic drugs, as well as novel specific small-molecule inhibitors have been employed. In addition, promising nucleic acid-based strategies have shown encouraging results. However, further research will be needed before NF-kappaB-aimed strategies become an effective therapy for inflammatory arthritis.
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Affiliation(s)
- Jorge A Roman-Blas
- Thomas Jefferson University, Jefferson Institute of Molecular Medicine, Philadelphia, Pennsylvania 19107, USA.
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Okamoto H, Cujec TP, Yamanaka H, Kamatani N. Molecular aspects of rheumatoid arthritis: role of transcription factors. FEBS J 2008; 275:4463-70. [PMID: 18662303 DOI: 10.1111/j.1742-4658.2008.06582.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rheumatoid arthritis is a multifactorial disease characterized by chronic inflammation of the joints. Both genetic and environmental factors are involved in the pathogenesis leading to joint destruction and ultimately disability. In the inflamed RA joint the synovium is highly infiltrated by CD4+ T cells, B cells and macrophages, and the intimal lining becomes hyperplastic owing to the increased number of macrophage-like and fibroblast-like synoviocytes. This hyperplastic intimal synovial lining forms an aggressive front, called pannus, which invades cartilage and bone structures, leading to the destruction and compromised function of affected joints. This process is mediated by a number of cytokines (tumor necrosis factor-alpha, interleukin-1, interleukin-6, interleukin-17 interferon-gamma, etc.), chemokines (monocyte chemoattractant protein-1, monocyte chemoattractant protein-4 CCL18, etc.), cell adhesion molecules (intercellular adhesion molecule-1, vascular cell adhesion molecule-1, etc.) and matrix metalloproteinases. Expression of these molecules is controlled at the transcription level and activation of a limited number of transcription factors is involved in this process.
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Affiliation(s)
- Hiroshi Okamoto
- Institute of Rheumatology, Tokyo Women's Medical University, Japan.
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Veprintsev DB, Fersht AR. Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA. Nucleic Acids Res 2008; 36:1589-98. [PMID: 18234719 PMCID: PMC2275157 DOI: 10.1093/nar/gkm1040] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 10/30/2007] [Accepted: 10/31/2007] [Indexed: 12/23/2022] Open
Abstract
The tumour suppressor p53 is a transcription factor that binds DNA in the vicinity of the genes it controls. The affinity of p53 for specific binding sites relative to other DNA sequences is an inherent driving force for specificity, all other things being equal. We measured the binding affinities of systematically mutated consensus p53 DNA-binding sequences using automated fluorescence anisotropy titrations. Based on measurements of the effects of every possible single base-pair substitution of a consensus sequence, we defined the DNA sequence with the highest affinity for full-length p53 and quantified the effects of deviation from it on the strength of protein-DNA interaction. The contributions of individual nucleotides were to a first approximation independent and additive. But, in some cases we observed significant deviations from additivity. Based on affinity data, we constructed a binding predictor that mirrored the existing p53 consensus sequence definition. We used it to search for high-affinity binding sites in the genome and to predict the effects of single-nucleotide polymorphisms in these sites. Although there was some correlation between the K(d) and biological function, the spread of the K(d)s by itself was not sufficient to explain the activation of different pathways by changes in p53 concentration alone.
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Gunewardena S, Zhang Z. A hybrid model for robust detection of transcription factor binding sites. ACTA ACUST UNITED AC 2008; 24:484-91. [PMID: 18184687 DOI: 10.1093/bioinformatics/btm629] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
MOTIVATION The short and degenerate nature of transcription factor (TF) binding sites contributes towards a low signal to noise ratio making it very difficult to separate them from their background. In order to tackle this problem one needs to look at ways of capturing the underlying biophysical properties that best discriminates TF binding sites from their background DNA. One such discriminatory property lies in the observed compositional differences in the nucleotide levels of TF binding sites and background DNA which are a result of processes such as purifying selection and selective preferences of TF binding sites for particular nucleotides or a combination of nucleotides over others. RESULTS In this article, we present a hybrid model, referred to as a MonoDi-nucleotide model for robustly detecting TF binding sites. It incorporates both mono- and dinucleotide statistics to optimally partition the base positions of an aligned set of TF binding sites (motif) into a non-redundant sequence of mono and/or dinucleotide segments that maximizes the odds ratio of the binding sites relative to their background DNA. We tested the MonoDi-nucleotide model on the benchmark dataset compiled by Tompa et al. (2005) for assessing computational tools that predict TF binding sites. The performance of the MonoDi-nucleotide model on this data set compares well to, and in many cases exceeds, the performance of existing tools. This is in part attributed to the significant role played by dinucleotides in discriminating TF binding sites from background DNA. AVAILABILITY A Matlab implementation of the MonoDi-nucleotide model can be found at http://www.utoronto.ca/zhanglab/MonoDi/.
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Affiliation(s)
- Sumedha Gunewardena
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto ON, Canada M5S 3E1, Canada.
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Natoli G, Chiocca S. Nuclear Ubiquitin Ligases, NF- B Degradation, and the Control of Inflammation. Sci Signal 2008; 1:pe1. [DOI: 10.1126/stke.11pe1] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Levitsky VG, Ignatieva EV, Ananko EA, Turnaev II, Merkulova TI, Kolchanov NA, Hodgman TC. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinformatics 2007; 8:481. [PMID: 18093302 PMCID: PMC2265442 DOI: 10.1186/1471-2105-8-481] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Accepted: 12/19/2007] [Indexed: 12/22/2022] Open
Abstract
Background Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered. Results To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-κB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies. To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA. Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced false positives at least at higher stringencies. Conclusion Based on this analysis, SiteGA adds substantial specificity even to optimized PWMs and may be considered for large-scale genome analysis. It adds to the range of techniques available for TFBS prediction, and EPD analysis has led to a list of genes which appear to be regulated by the above TFs.
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Affiliation(s)
- Victor G Levitsky
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.
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