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Padash R, Ramazani S. Investigation of stability of adenine and its tautomers in RNA and DNA, and their interaction with Na+, K+, Mg2+, Ca2+ and Zn2+. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2
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Humphries JE, Deneckere LE. Characterization of a Toll-like receptor (TLR) signaling pathway in Biomphalaria glabrata and its potential regulation by NF-kappaB. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 86:118-129. [PMID: 29746981 DOI: 10.1016/j.dci.2018.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 05/16/2023]
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3
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Tomar N, Mishra A, Mrinal N, Jayaram B. Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw116. [PMID: 27515825 PMCID: PMC4980569 DOI: 10.1093/database/baw116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 07/13/2016] [Indexed: 11/13/2022]
Abstract
Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5′→3′, 3′ →5′ or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically. Database URL:http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm
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Affiliation(s)
- Navneet Tomar
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Delhi, India
| | - Nirotpal Mrinal
- Labaratory of Molecular Biology, South Asian University, New Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Delhi, India Department of Chemistry, Indian Institute of Technology-Delhi, Delhi
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Salazar G, Bellocchi C, Todoerti K, Saporiti F, Piacentini L, Scorza R, Colombo GI. Gene expression profiling reveals novel protective effects of Aminaphtone on ECV304 endothelial cells. Eur J Pharmacol 2016; 782:59-69. [PMID: 27083548 DOI: 10.1016/j.ejphar.2016.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 01/09/2023]
Abstract
Aminaphtone, a drug used in the treatment of chronic venous insufficiency (CVI), showed a remarkable role in the modulation of several vasoactive factors, like endothelin-1 and adhesion molecules. We analysed in vitro the effects of Aminaphtone on whole-genome gene expression and production of different inflammatory proteins. ECV-304 endothelial cells were stimulated with IL-1β 100U/ml in the presence or absence of Aminaphtone 6μg/ml. Gene expression profiles were compared at 1, 3, and 6h after stimulation by microarray. Supernatants of ECV-304 cultures were analysed at 3, 6, 12, and 24h by multiplex ELISA for production of several cytokine and chemokines. Microarrays showed a significant down-regulation at all times of a wide range of inflammatory genes. Aminaphtone appeared also able to modulate the regulation of immune response process (down-regulating cytokine biosynthesis, transcripts involved in lymphocyte differentiation and cell proliferation, and cytokine-cytokine receptor interaction) and to regulate genes engaged in homeostasis, secretion, body fluid levels, response to hypoxia, cell division, and cell-to-cell communication and signalling. Results were confirmed and extended analysing the secretome, which showed significant reduction of the release of 14 cytokines and chemokines. These effects are predicted to be mediated by interaction with different transcription factors. Aminaphtone was able to modulate the expression of inflammatory molecules relevant to the pathogenesis of several conditions in which the endothelial dysfunction is the main player and early event, like scleroderma, lung fibrosis, or atherosclerosis.
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Affiliation(s)
- Giulia Salazar
- Referral Centre for Systemic Autoimmune Diseases, University of Milan and Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.
| | - Chiara Bellocchi
- Referral Centre for Systemic Autoimmune Diseases, University of Milan and Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Katia Todoerti
- Laboratory of Preclinical and Translational Research, IRCCS-CROB, Referral Cancer Centre of Basilicata, Rionero in Vulture, Italy
| | - Federica Saporiti
- Laboratory of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Luca Piacentini
- Laboratory of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Raffaella Scorza
- Referral Centre for Systemic Autoimmune Diseases, University of Milan and Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Gualtiero I Colombo
- Laboratory of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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Humphries J, Harter B. Identification of nuclear factor kappaB (NF-κB) binding motifs in Biomphalaria glabrata. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 53:366-70. [PMID: 26277107 DOI: 10.1016/j.dci.2015.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 05/16/2023]
Abstract
Biomphalaria glabrata acts as the intermediate host to the parasite, Schistosoma mansoni, and for this reason, the immune system of B. glabrata has been researched extensively. Several studies have demonstrated that the transcriptome profile of B. glabrata changes following exposure to a variety of pathogens, yet very little is known regarding the regulation of gene expression in this species. Nuclear factor kappaB (NF-κB) homologues have recently been identified in B. glabrata but few functional studies have been carried out on this family of transcription factors. The aims of this study therefore were to identify NF-κB binding sites (κB motifs) in B. glabrata and examine them via functional assays. Two different κB motifs were predicted. Furthermore, the Rel homology domain (RHD) of a B. glabrata NF-κB was able to bind these κB motifs in EMSAs, as well as a vertebrate κB motif.
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Clifford J, Adami C. Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively. Phys Biol 2015; 12:056004. [PMID: 26331781 DOI: 10.1088/1478-3975/12/5/056004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each site's locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal-Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.
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Affiliation(s)
- Jacob Clifford
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA. BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
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Singh S, Donfack P, Srivastava SK, Singh DK, Materny A, Asthana BP, Mishra PC. Monitoring potential molecular interactions of adenine with other amino acids using Raman spectroscopy and DFT modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 149:647-655. [PMID: 25985129 DOI: 10.1016/j.saa.2015.04.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 06/04/2023]
Abstract
We report on the modes of inter-molecular interaction between adenine (Ade) and the amino acids: glycine (Gly), lysine (Lys) and arginine (Arg) using Raman spectroscopy of binary mixtures of adenine and each of the three amino acids at varying molar ratios in the spectral region 1550-550 cm(-1). We focused our attention on certain specific changes in the Raman bands of adenine arising due to its interaction with the amino acids. While the changes are less apparent in the Ade/Gly system, in the Ade/Lys or Ade/Arg systems, significant changes are observed, particularly in the Ade Raman bands that involve the amino group moiety and the N7 and N1 atoms of the purine ring. The ν(N1-C6), ν(N1-C2), δ(C8-H) and δ(N7-C8-N9) vibrations at 1486, 1332, 1253 and 948 cm(-1) show spectral changes on varying the Ade to amino acid molar ratio, the extent of variation being different for the three amino acids. This observation suggests a specific interaction mode between Ade and Lys or Arg, which is due to the hydrogen bonding. The measured spectral changes provide a clear indication that the interaction of Ade depends strongly on the structures of the amino acids, especially their side chains. Density functional theory (DFT) calculations were carried out to elucidate the most probable interaction modes of Ade with the different amino acids.
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Affiliation(s)
- Shweta Singh
- Laser and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India.
| | - P Donfack
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Sunil K Srivastava
- Department of Pure and Applied Physics, Guru Ghasidas University, Main Campus, Koni, Bilaspur 495009, India
| | - Dheeraj K Singh
- Department of Physics, Sogang University, Seoul 121-742, South Korea
| | - A Materny
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - B P Asthana
- Laser and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - P C Mishra
- Laser and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India
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Siggers T, Gilmore TD, Barron B, Penvose A. Characterizing the DNA binding site specificity of NF-κB with protein-binding microarrays (PBMs). Methods Mol Biol 2015; 1280:609-30. [PMID: 25736775 DOI: 10.1007/978-1-4939-2422-6_36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
NF-κB transcription factors control a wide array of important cellular and organismal processes in eukaryotes. All NF-κB transcription factors bind to DNA target sites as dimers. In vertebrates, there are five NF-κB subunits, p50, p52, RelA (p65), c-Rel, and RelB, that can form almost all combinations of homodimers and heterodimers, which recognize distinct, but overlapping, target sequences. In this chapter, we describe the use of protein-binding microarrays (PBMs), a high-throughput method to measure the binding of proteins to different DNA sequences. PBM datasets allow for sensitive comparisons of NF-κB dimer DNA-binding differences and can aid in the computational and experimental prediction of NF-κB target genes.
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Affiliation(s)
- Trevor Siggers
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA,
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Siggers T, Gordân R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res 2013; 42:2099-111. [PMID: 24243859 PMCID: PMC3936734 DOI: 10.1093/nar/gkt1112] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.
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Affiliation(s)
- Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J Biomol Struct Dyn 2013; 32:1670-85. [PMID: 23998351 DOI: 10.1080/07391102.2013.830579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5'-C5'-C4'-C3') are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein-nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein-DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.
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Affiliation(s)
- Mariia Yu Zhitnikova
- a O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine , Acad. Proskura Street, 12, Kharkiv , 61085 , Ukraine
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Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PLoS Genet 2013; 9:e1003195. [PMID: 23326246 PMCID: PMC3542182 DOI: 10.1371/journal.pgen.1003195] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 11/08/2012] [Indexed: 12/20/2022] Open
Abstract
The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP) from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ∼50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites. The Drosophila homeodomain protein Tinman was the first transcription factor found to control the development and differentiation of the heart in any species. In spite of that, our knowledge of the number, identities, and mode of regulation of the downstream target genes of Tinman that are necessary to exert its cardiogenic functions is still very incomplete. To address these issues, we have performed a genome-wide analysis of DNA regions associated with Tinman-binding in embryos and the genes linked to them. The combined data from our in-depth in vivo assays of sequence elements with high Tinman occupancy allow the following general conclusions: (1) The majority of such sequences are active as regulatory elements (called enhancers) in mesodermal tissues that include Tinman-expressing cells. (2) The enhancers active in the heart progenitor cells and the heart generally are dependent on tinman gene activity, whereas those active in non-cardiac mesoderm are often bound neutrally by Tinman. (3) Tinman binding motifs in most cases are essential for cardiac enhancer activity, but in some cases they can be functionally-redundant with those of other cardiogenic factors. (4) Tinman-occupied cardiac enhancers are enriched for a newly discovered binding motif for an unknown factor that is functional in vivo.
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Xing Y, Zhou F, Wang J. Subset of genes targeted by transcription factor NF-κB in TNFα-stimulated human HeLa cells. Funct Integr Genomics 2012; 13:143-54. [DOI: 10.1007/s10142-012-0305-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 11/28/2022]
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Pradeep ANR, Anitha J, Awasthi AK, Babu MA, Geetha MN, Arun HK, Chandrashekhar S, Rao GC, Vijayaprakash NB. Activation of autophagic programmed cell death and innate immune gene expression reveals immuno-competence of integumental epithelium in Bombyx mori infected by a dipteran parasitoid. Cell Tissue Res 2012; 352:371-85. [PMID: 23161099 DOI: 10.1007/s00441-012-1520-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/27/2012] [Indexed: 01/22/2023]
Abstract
In insects, the integument forms the primary barrier between the environment and internal milieu, but cellular and immune responses of the integumental epithelium to infection by micro- and macro-parasites are mostly unknown. We elucidated cellular and immune responses of the epithelium induced through infection by a dipteran endoparasitoid, Exorista bombycis in the economically important silkworm Bombyx mori. Degradative autophagic vacuoles, lamella-like bodies, a network of cytoplasmic channels with cellular cargo, and an RER network that opened to vacuoles were observed sequentially with increase in age after infection. This temporal sequence culminated in apoptosis, accompanied by the upregulation of the caspase gene and fragmentation of DNA. The infection significantly enhanced the tyrosine level and phenol oxidase activity in the integument. Proteomic analysis revealed enhanced expression of innate immunity components of toll and melanization pathways, cytokines, signaling molecules, chaperones, and proteolytic enzymes demonstrating diverse host responses. qPCR analysis revealed the upregulation of spatzle, BmToll, and NF kappa B transcription factors Dorsal and BmRel. NF kappa B inhibitor cactus showed diminished expression when Dorsal and BmRel were upregulated, revealing a negative correlation (R = (-)0.612). During melanization, prophenol oxidase 2 was expressed, a novel finding in integumental epithelium. The integument showed a low level of melanin metabolism and localized melanism in order to prevent the spreading of cytotoxic quinones. The gene-encoding proteolytic enzyme, beta-N-acetylglucosaminidase, was activated at 24 h post-infection, whereas chitinase, was activated at 96 h post-infection; however, most of the immune genes enhanced their expression in the early stages of infection. Thus the integument contributes to humoral immune responses that enhance resistance against macroparasite invasion.
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Affiliation(s)
- Appukuttan Nair R Pradeep
- Proteomics Division, Seribiotech Research Laboratory, CSB-Kodathi Campus, Bangalore, Karnataka, India.
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