• Liu, H. et al. Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss. Nat. Med. 25, 95–102 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Ishizuka, J. J. et al. Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade. Nature 565, 43–48 (2019).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Mehdipour, P. et al. Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency. Nature 588, 169–173 (2020).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Gannon, H. S. et al. Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells. Nat. Commun. 9, 5450 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chen, R., Ishak, C. A. & De Carvalho, D. D. Endogenous retroelements and the viral mimicry response in cancer therapy and cellular homeostasis. Cancer Discov. 11, 2707–2725 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Loo Yau, H., Ettayebi, I. & De Carvalho, D. D. The cancer epigenome: exploiting its vulnerabilities for immunotherapy. Trends Cell Biol. 29, 31–43 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Heraud-Farlow, J. E., Chalk, A. M. & Walkley, C. R. Defining the functions of adenosine-to-inosine RNA editing through hematology. Curr. Opin. Hematol. 26, 241–248 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Eisenberg, E. & Levanon, E. Y. A-to-I RNA editing—immune protector and transcriptome diversifier. Nat. Rev. Genet. 19, 473–490 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Samuel, C. E. Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA-triggered innate immune responses. J. Biol. Chem. 294, 1710–1720 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Herbert, A. ALU non-B-DNA conformations, flipons, binary codes and evolution. R. Soc. Open Sci. 7, 200222 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chung, H. et al. Human ADAR1 prevents endogenous RNA from triggering translational shutdown. Cell 172, 811–824.e14 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • George, C. X., Ramaswami, G., Li, J. B. & Samuel, C. E. Editing of cellular self-RNAs by adenosine deaminase ADAR1 suppresses innate immune stress responses. J. Biol. Chem. 291, 6158–6168 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Liddicoat, B. J. et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Herbert, A. et al. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl Acad. Sci. USA 94, 8421–8426 (1997).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Herbert, A. Mendelian disease caused by variants affecting recognition of Z-DNA and Z-RNA by the Zα domain of the double-stranded RNA editing enzyme ADAR. Eur. J. Hum. Genet. 28, 114–117 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Zhang, T. et al. Influenza virus Z-RNAs induce ZBP1-mediated necroptosis. Cell 180, 1115–1129.e13 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hardin, C. C. et al. Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA antibodies. Biochemistry 26, 5191–5199 (1987).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Schade, M., Turner, C. J., Lowenhaupt, K., Rich, A. & Herbert, A. Structure–function analysis of the Z-DNA-binding domain Zα of dsRNA adenosine deaminase type I reveals similarity to the (α + β) family of helix–turn–helix proteins. EMBO J. 18, 470–479 (1999).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bazak, L., Levanon, E. Y. & Eisenberg, E. Genome-wide analysis of Alu editability. Nucleic Acids Res. 42, 6876–6884 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Nichols, P. J. et al. Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat. Commun. 12, 793 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Balasubramaniyam, T., Ishizuka, T., Xiao, C. D., Bao, H. L. & Xu, Y. 2′-O-Methyl-8-methylguanosine as a Z-form RNA stabilizer for structural and functional study of Z-RNA. Molecules 23, 2572–2579 (2018).

    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Brown, B. A. 2nd, Lowenhaupt, K., Wilbert, C. M., Hanlon, E. B. & Rich, A. The Zα domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc. Natl Acad. Sci. USA 97, 13532–13536 (2000).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Kim, K. et al. Solution structure of the Zβ domain of human DNA-dependent activator of IFN-regulatory factors and its binding modes to B- and Z-DNAs. Proc. Natl Acad. Sci. USA 108, 6921–6926 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Peck, L. J., Nordheim, A., Rich, A. & Wang, J. C. Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc. Natl Acad. Sci. USA 79, 4560–4564 (1982).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chang, H. W. et al. Histone chaperone FACT and curaxins: effects on genome structure and function. J. Cancer Metastasis Treat. 5, 78 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Safina, A. et al. FACT is a sensor of DNA torsional stress in eukaryotic cells. Nucleic Acids Res. 45, 1925–1945 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sookdeo, A., Hepp, C. M., McClure, M. A. & Boissinot, S. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob. DNA 4, 3 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Beknazarov, N., Jin, S. & Poptsova, M. Deep learning approach for predicting functional Z-DNA regions using omics data. Sci Rep. 10, 19134 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bao, H. L. & Xu, Y. Observation of Z-DNA structure via the synthesis of oligonucleotide DNA containing 8-trifluoromethyl-2-deoxyguanosine. Curr. Protoc. 1, e28 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • Jeronimo, C., Watanabe, S., Kaplan, C. D., Peterson, C. L. & Robert, F. The histone chaperones FACT and Spt6 restrict H2A.Z from intragenic locations. Mol. Cell 58, 1113–1123 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Denli, A. M. et al. Primate-specific ORF0 contributes to retrotransposon-mediated diversity. Cell 163, 583–593 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Somers, K. et al. Potent antileukemic activity of curaxin CBL0137 against MLL-rearranged leukemia. Int. J. Cancer 146, 1902–1916 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Gasparian, A. V. et al. Curaxins: anticancer compounds that simultaneously suppress NF-κB and activate p53 by targeting FACT. Sci. Transl. Med. 3, 95ra74 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Carter, D. R. et al. Therapeutic targeting of the MYC signal by inhibition of histone chaperone FACT in neuroblastoma. Sci. Transl. Med. 7, 312ra176 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Koo, G. B. et al. Methylation-dependent loss of RIP3 expression in cancer represses programmed necrosis in response to chemotherapeutics. Cell Res. 25, 707–725 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Gabrilovich, D. I. & Nagaraj, S. Myeloid-derived suppressor cells as regulators of the immune system. Nat. Rev. Immunol. 9, 162–174 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Weiss, S. A., Wolchok, J. D. & Sznol, M. Immunotherapy of melanoma: facts and hopes. Clin. Cancer Res. 25, 5191–5201 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Wang, J. et al. UV-induced somatic mutations elicit a functional T cell response in the YUMMER1.7 mouse melanoma model. Pigment Cell Melanoma Res. 30, 428–435 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Nirschl, C. J. et al. IFNγ-dependent tissue-immune homeostasis is co-opted in the tumor microenvironment. Cell 170, 127–141.e15 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Benci, J. L. et al. Tumor interferon signaling regulates a multigenic resistance program to immune checkpoint blockade. Cell 167, 1540–1554.e12 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ishii, K. J. et al. TANK-binding kinase-1 delineates innate and adaptive immune responses to DNA vaccines. Nature 451, 725–729 (2008).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Chen, P. et al. Anti-CD70 immunocytokines for exploitation of interferon-γ-induced RIP1-dependent necrosis in renal cell carcinoma. PLoS ONE 8, e61446 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cancer Genome Atlas Network. Genomic classification of cutaneous melanoma. Cell 161, 1681–1696 (2015).

    Article 
    CAS 

    Google Scholar
     

  • Becht, E. et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 17, 218 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Gabitova-Cornell, L. et al. Cholesterol pathway inhibition induces TGF-β signaling to promote basal differentiation in pancreatic cancer. Cancer Cell 38, 567–583.e11 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Bachu, M. et al. A versatile mouse model of epitope-tagged histone H3.3 to study epigenome dynamics. J. Biol. Chem. 294, 1904–1914 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Roth, S. H., Levanon, E. Y. & Eisenberg, E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. Nat. Methods 16, 1131–1138 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res. 36, W70–W74 (2008).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Lo Giudice, C., Tangaro, M. A., Pesole, G. & Picardi, E. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. Nat. Protoc. 15, 1098–1131 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Kechin, A., Boyarskikh, U., Kel, A. & Filipenko, M. cutPrimers: a new tool for accurate cutting of primers from reads of targeted next generation sequencing. J. Comput. Biol. 24, 1138–1143 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Zhu, L. J. et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11, 237 (2010).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Penzkofer, T. et al. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res. 45, D68–D73 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ho, P. S., Ellison, M. J., Quigley, G. J. & Rich, A. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J. 5, 2737–2744 (1986).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Oki, S. et al. ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. EMBO Rep. 19, e46255 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Rosenberger, C. M. Characterization of innate responses to influenza virus infection in a novel lung type I epithelial cell model. J. Gen. Virol. 95, 350–362 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Brown, D. M., Fisher, T. L., Wei, C., Frelinger, J. G. & Lord, E. M. Tumours can act as adjuvants for humoral immunity. Immunology 102, 486–497 (2001).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rodriguez, D. A. Characterization of RIPK3-mediated phosphorylation of the activation loop of MLKL during necroptosis. Cell Death Differ. 23, 76–88 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     



  • Source link