A Multi-Omics Approach Reveals Features That Permit Robust and Widespread Regulation of IFN-Inducible Antiviral Effectors
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S. Raghav | W. Reith | F. Meissner | L. Nagy | J. Schoggins | T. Varga | S. Póliska | B. Daniel | G. Nagy | Matteo Pigni | C. Thelemann | M. Csumita | Lóránd Göczi | H. Mianesaz | L. Széles | K. Sen | H. Acha-Orbea | Attila Horváth | Bence Daniel | Gergely Nagy
[1] T. Decker,et al. Interferons reshape the 3D conformation and accessibility of macrophage chromatin , 2021, bioRxiv.
[2] N. Morgan,et al. An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells , 2020, Nature Communications.
[3] J. Shendure,et al. Towards a comprehensive catalogue of validated and target-linked human enhancers , 2020, Nature Reviews Genetics.
[4] W. Reith,et al. Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5′ and 3′ flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion , 2019, Nucleic acids research.
[5] J. Schoggins. Interferon-Stimulated Genes: What Do They All Do? , 2019, Annual review of virology.
[6] L. Ivashkiv,et al. Interferon target-gene expression and epigenomic signatures in health and disease , 2019, Nature Immunology.
[7] T. Decker,et al. A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription , 2019, Nature Communications.
[8] A. Ploss,et al. Decoding type I and III interferon signalling during viral infection , 2019, Nature Microbiology.
[9] A. Hoffmann,et al. Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions , 2019, Scientific Reports.
[10] K. Tretina,et al. Interferon-induced guanylate-binding proteins: Guardians of host defense in health and disease , 2019, The Journal of experimental medicine.
[11] Jason D. Buenrostro,et al. The cis-Regulatory Atlas of the Mouse Immune System , 2019, Cell.
[12] Sandy L. Klemm,et al. Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.
[13] C. Horvath,et al. Transcriptional and chromatin regulation in interferon and innate antiviral gene expression. , 2018, Cytokine & growth factor reviews.
[14] T. Decker,et al. Regulatory Networks Involving STATs, IRFs, and NFκB in Inflammation , 2018, Front. Immunol..
[15] K. Sakaguchi,et al. Interferon stimulation creates chromatin marks and establishes transcriptional memory , 2018, Proceedings of the National Academy of Sciences.
[16] D. Panne,et al. Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function , 2017, Proceedings of the National Academy of Sciences.
[17] Joshua B. Singer,et al. Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses , 2017, PLoS biology.
[18] Eugenia G. Giannopoulou,et al. Type I IFNs and TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation , 2017, Nature Immunology.
[19] M. Bulyk,et al. Transcription factor-DNA binding: beyond binding site motifs. , 2017, Current opinion in genetics & development.
[20] M. Peppelenbosch,et al. Transcriptional Regulation of Antiviral Interferon-Stimulated Genes , 2017, Trends in Microbiology.
[21] T. Decker,et al. Canonical and Non-Canonical Aspects of JAK–STAT Signaling: Lessons from Interferons for Cytokine Responses , 2017, Front. Immunol..
[22] Howard Y. Chang,et al. Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution , 2016, Nature Genetics.
[23] G. Cheng,et al. The Roles of Type I Interferon in Bacterial Infection. , 2016, Cell host & microbe.
[24] Chun Jimmie Ye,et al. Parsing the Interferon Transcriptional Network and Its Disease Associations , 2016, Cell.
[25] C. Glass,et al. Molecular control of activation and priming in macrophages , 2015, Nature Immunology.
[26] J. V. Falvo,et al. A Role for IFITM Proteins in Restriction of Mycobacterium tuberculosis Infection , 2015, Cell reports.
[27] M. Hersch,et al. TLR3-Mediated CD8+ Dendritic Cell Activation Is Coupled with Establishment of a Cell-Intrinsic Antiviral State , 2015, The Journal of Immunology.
[28] G. Stark,et al. Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex , 2015, Cell reports.
[29] Andrew C. Nelson,et al. Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation , 2015, PLoS genetics.
[30] A. Visel,et al. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility , 2015, Epigenetics & Chromatin.
[31] G. Natoli,et al. A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages , 2015, Genes & development.
[32] C. Glass,et al. The selection and function of cell type-specific enhancers , 2015, Nature Reviews Molecular Cell Biology.
[33] Howard Y. Chang,et al. ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.
[34] Bin Zhang,et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations , 2014, Nucleic Acids Res..
[35] C. Rice,et al. Interferon-stimulated genes: a complex web of host defenses. , 2014, Annual review of immunology.
[36] J. Stender,et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. , 2013, Molecular cell.
[37] David A. Orlando,et al. Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.
[38] G. Bejerano,et al. Enhancers: five essential questions , 2013, Nature Reviews Genetics.
[39] G. Natoli,et al. Latent Enhancers Activated by Stimulation in Differentiated Cells , 2013, Cell.
[40] M. Diamond,et al. The broad-spectrum antiviral functions of IFIT and IFITM proteins , 2012, Nature Reviews Immunology.
[41] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[42] M. Mann,et al. Novel Murine Dendritic Cell Lines: A Powerful Auxiliary Tool for Dendritic Cell Research , 2012, Front. Immun..
[43] J. MacMicking. Interferon-inducible effector mechanisms in cell-autonomous immunity , 2012, Nature Reviews Immunology.
[44] S. Nutt,et al. Transcriptional programming of the dendritic cell network , 2012, Nature Reviews Immunology.
[45] K. Zhao,et al. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization , 2012, Cell Research.
[46] J. Ragoussis,et al. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding , 2011, Nature Immunology.
[47] C. Rice,et al. Interferon-stimulated genes and their antiviral effector functions , 2011, Current Opinion in Virology.
[48] Endre Barta,et al. Command line analysis of ChIP-seq results , 2011 .
[49] G. Kochs,et al. Transcription Factor Redundancy Ensures Induction of the Antiviral State* , 2010, The Journal of Biological Chemistry.
[50] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[51] Alexander J. Hartemink,et al. Finding regulatory DNA motifs using alignment-free evolutionary conservation information , 2010, Nucleic acids research.
[52] David J. Adams,et al. The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus , 2009, Cell.
[53] M. Mann,et al. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.
[54] Bryan R. G. Williams,et al. Interferon-inducible antiviral effectors , 2008, Nature Reviews Immunology.
[55] S. Goodbourn,et al. Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures. , 2008, The Journal of general virology.
[56] A. Pichlmair,et al. Innate recognition of viruses. , 2007, Immunity.
[57] A. Sher,et al. Cooperation of Toll-like receptor signals in innate immune defence , 2007, Nature Reviews Immunology.
[58] D. Haussler,et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.
[59] Tak W. Mak,et al. Integral role of IRF-5 in the gene induction programme activated by Toll-like receptors , 2005, Nature.
[60] E. Wagner,et al. AP-1: a double-edged sword in tumorigenesis , 2003, Nature Reviews Cancer.
[61] E. Kremmer,et al. Guanylate-binding protein-1 expression is selectively induced by inflammatory cytokines and is an activation marker of endothelial cells during inflammatory diseases. , 2002, The American journal of pathology.
[62] Govinda Rao,et al. IRF3 mediates a TLR3/TLR4-specific antiviral gene program. , 2002, Immunity.
[63] C. Horvath,et al. STAT proteins and transcriptional responses to extracellular signals. , 2000, Trends in biochemical sciences.
[64] T. Taniguchi,et al. Crystal structure of an IRF‐DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences , 1999, The EMBO journal.
[65] J. Darnell,et al. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. , 1994, Science.
[66] T. Taniguchi,et al. Recognition DNA sequences of interferon regulatory factor 1 (IRF-1) and IRF-2, regulators of cell growth and the interferon system , 1993, Molecular and cellular biology.
[67] Richard Taylor. Interpretation of the Correlation Coefficient: A Basic Review , 1990 .
[68] J E Darnell,et al. Interferon-induced nuclear factors that bind a shared promoter element correlate with positive and negative transcriptional control. , 1988, Genes & development.