Epigenetic Control of Gene Expression by Bacterial Virulence Factors: Comparison
Please note this is a comparison between Version 2 by Rita Xu and Version 1 by Lea Denzer.

There are several levels to influence the expression of eukaryotic genes. A first level of interference is changing of the DNA’s structure on the chromatin level. Epigenetic modulation enables remodelling of the chromatin to transfer heterochromatin into euchromatin allowing transcription or vice versa. In addition, the affinity of promotors and other regulatory DNA sequences for RNA polymerases and transcription factors (TFs) can be influenced by cytosine or adenine methylation. Only a minor portion (fewer than 2%) of genes is transcribed into mRNAs, instead the majority is transferred into so called non-coding RNAs (ncRNAs). Certain long ncRNAs (lncRNAs) are also involved in epigenetic regulations. Epigenetic mechanisms are used for manipulation of gene expression in the course of several cellular processes. Here, we give an overview on the epigenetic control of gene expression by bacterial virulence factors during host cell infection.

  • epigenetics
  • gene expression
  • bacteria
  • virulence factor
  • histone modification
  • DNA methylation
  • lncRNA
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References

  1. Tony Kouzarides; Chromatin Modifications and Their Function. Cell 2007, 128, 693-705, 10.1016/j.cell.2007.02.005.
  2. Diana C Hargreaves; Gerald R. Crabtree; ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Research 2011, 21, 396-420, 10.1038/cr.2011.32.
  3. Karolin Luger; Armin W. Mäder; Robin K. Richmond; David F. Sargent; Timothy J. Richmond; Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997, 389, 251-260, 10.1038/38444.
  4. Elias Cornejo; Philipp Schlaermann; Shaeri Mukherjee; How to rewire the host cell: A home improvement guide for intracellular bacteria. Journal of Cell Biology 2017, 216, 3931-3948, 10.1083/jcb.201701095.
  5. Hélène Bierne; Pascale Cossart; When bacteria target the nucleus: the emerging family of nucleomodulins. Cellular Microbiology 2012, 14, 622-633, 10.1111/j.1462-5822.2012.01758.x.
  6. J. C. Van Wolfswinkel; Rene F Ketting; The role of small non-coding RNAs in genome stability and chromatin organization. Journal of Cell Science 2010, 123, 1825-1839, 10.1242/jcs.061713.
  7. Benjamin Lee; Louis C. Mahadevan; Stability of histone modifications across mammalian genomes: Implications for ‘epigenetic’ marking. Journal of Cellular Biochemistry 2009, 108, 22-34, 10.1002/jcb.22250.
  8. Stuart L. Schreiber; Bradley E. Bernstein; Signaling network model of chromatin. Cell 2002, 111, 771-778, 10.1016/s0092-8674(02)01196-0.
  9. Edwin Smith; Ali Shilatifard; The Chromatin Signaling Pathway: Diverse Mechanisms of Recruitment of Histone-Modifying Enzymes and Varied Biological Outcomes. Molecular Cell 2010, 40, 689-701, 10.1016/j.molcel.2010.11.031.
  10. Thomas R. Cech; Joan A. Steitz; The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones. Cell 2014, 157, 77-94, 10.1016/j.cell.2014.03.008.
  11. Thomas Mikeska; Jeffrey M Craig; DNA Methylation Biomarkers: Cancer and Beyond. Genes 2014, 5, 821-864, 10.3390/genes5030821.
  12. Aleksander M Grabiec; Paul-Peter Tak; Kris A Reedquist; Targeting histone deacetylase activity in rheumatoid arthritis and asthma as prototypes of inflammatory disease: should we keep our HATs on?. Arthritis Research & Therapy 2008, 10, 226, 10.1186/ar2489.
  13. Zimu Zhang; Rongxin Zhang; Epigenetics in autoimmune diseases: Pathogenesis and prospects for therapy. Autoimmunity Reviews 2015, 14, 854-863, 10.1016/j.autrev.2015.05.008.
  14. Farzam Vaziri; Samira Tarashi; Abolfazl Fateh; Seyed Davar Siadat; New insights of Helicobacter pylori host-pathogen interactions: The triangle of virulence factors, epigenetic modifications and non-coding RNAs. World Journal of Clinical Cases 2018, 6, 64-73, 10.12998/wjcc.v6.i5.64.
  15. Peter A. Jones; The Role of DNA Methylation in Mammalian Epigenetics. Science 2001, 293, 1068-1070, 10.1126/science.1063852.
  16. Yukie Yoda; Hideyuki Takeshima; Tohru Niwa; Jeong Goo Kim; Takayuki Ando; Ryoji Kushima; Toshiro Sugiyama; Hitoshi Katai; Hirokazu Noshiro; Toshikazu Ushijima; et al. Integrated analysis of cancer-related pathways affected by genetic and epigenetic alterations in gastric cancer. Gastric Cancer 2014, 18, 65-76, 10.1007/s10120-014-0348-0.
  17. Mélodie Duval; Pascale Cossart; Alice Lebreton; Mammalian microRNAs and long noncoding RNAs in the host-bacterial pathogen crosstalk. Seminars in Cell & Developmental Biology 2017, 65, 11-19, 10.1016/j.semcdb.2016.06.016.
  18. Saccani, S.; Pantano, S.; Natoli, G; p38-Dependent marking of inflammatory genes for increased NF-kappa B recruitment. Nat. Immunol. 2002, 3, 69–75.
  19. Melanie A. Hamon; Pascale Cossart; Histone Modifications and Chromatin Remodeling during Bacterial Infections. Cell Host & Microbe 2008, 4, 100-109, 10.1016/j.chom.2008.07.009.
  20. Melanie A. Hamon; Eric Batsché; Béatrice Régnault; To Nam Tham; Stéphanie Seveau; Christian Muchardt; Pascale Cossart; Histone modifications induced by a family of bacterial toxins. Proceedings of the National Academy of Sciences 2007, 104, 13467-13472, 10.1073/pnas.0702729104.
  21. Bernd Schmeck; Wiebke Beermann; Vincent Van Laak; Janine Zahlten; Bastian Opitz; Martin Witzenrath; Andreas C. Hocke; Trinad Chakraborty; Michael Kracht; Simone Rosseau; et al.Norbert SuttorpStefan Hippenstiel Intracellular bacteria differentially regulated endothelial cytokine release by MAPK-dependent histone modification. The Journal of Immunology 2005, 175, 2843-2850, 10.4049/jimmunol.175.5.2843.
  22. Bastian Opitz; Anja Püschel; Wiebke Beermann; Andreas C. Hocke; Stefanie Förster; Bernd Schmeck; Vincent Van Laak; Trinad Chakraborty; Norbert Suttorp; Stefan Hippenstiel; et al. Listeria monocytogenes activated p38 MAPK and induced IL-8 secretion in a nucleotide-binding oligomerization domain 1-dependent manner in endothelial cells.. The Journal of Immunology 2006, 176, 484-490, 10.4049/jimmunol.176.1.484.
  23. Arbibe, L.; Kim, D.W.; Batsche, E.; Pedron, T.; Mateescu, B.; Muchardt, C.; Parsot, C.; Sansonetti, P.J; An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses. Nat. Immunol. 2007, 8, 47–56.
  24. Damian F. Brennan; David Barford; Eliminylation: a post-translational modification catalyzed by phosphothreonine lyases. Trends in Biochemical Sciences 2009, 34, 108-114, 10.1016/j.tibs.2008.11.005.
  25. Daniel V. Zurawski; Karen L. Mumy; Christina S. Faherty; Beth A. McCormick; Anthony T. Maurelli; Shigella flexneritype III secretion system effectors OspB and OspF target the nucleus to downregulate the host inflammatory response via interactions with retinoblastoma protein. Molecular Microbiology 2009, 71, 350-368, 10.1111/j.1365-2958.2008.06524.x.
  26. Haig A. Eskandarian; Francis Impens; Marie-Anne Nahori; Guillaume Soubigou; Jean-Yves Coppée; Pascale Cossart; Melanie A. Hamon; A Role for SIRT2-Dependent Histone H3K18 Deacetylation in Bacterial Infection. Science 2013, 341, 1238858-1238858, 10.1126/science.1238858.
  27. Hélène Bierne; To Nam Tham; Eric Batsche; Anne Dumay; Morwenna Leguillou; Sophie Kernéis-Golsteyn; Béatrice Regnault; Jacob Seeler; Christian Muchardt; Jean Feunteun; et al.Pascale Cossart Human BAHD1 promotes heterochromatic gene silencing. Proceedings of the National Academy of Sciences 2009, 106, 13826-13831, 10.1073/pnas.0901259106.
  28. Paul Cotter; Faculty Opinions recommendation of A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response.. Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature 2011, 331, 1319–1321, 10.3410/f.9077956.9654054.
  29. Hélène Bierne; Renaud Pourpre; Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins. Toxins 2020, 12, 220, 10.3390/toxins12040220.
  30. Ting Li; Qiuhe Lu; Guolun Wang; Hao Xu; Huanwei Huang; Tao Cai; Biao Kan; Jianning Ge; Feng Shao; SET‐domain bacterial effectors target heterochromatin protein 1 to activate host rDNA transcription. EMBO reports 2013, 14, 733-740, 10.1038/embor.2013.86.
  31. Monica Rolando; Serena Sanulli; Christophe Rusniok; Laura Gomez-Valero; Clement Bertholet; Tobias Sahr; Raphaël Margueron; Carmen Buchrieser; Legionella pneumophila Effector RomA Uniquely Modifies Host Chromatin to Repress Gene Expression and Promote Intracellular Bacterial Replication. Cell Host & Microbe 2013, 13, 395-405, 10.1016/j.chom.2013.03.004.
  32. Mujtaba, S.; Winer, B.Y.; Jaganathan, A.; Patel, J.; Sgobba, M.; Schuch, R.; Gupta, Y.K.; Haider, S.; Wang, R.; Fischetti, V.A; et al. Anthrax SET protein: A potential virulence determinant that epigenetically represses NF-kappaB activation in infected macrophages. J. Biol. Chem. 2013, 288, 23458–23472.
  33. Imtiyaz Yaseen; Prabhjot Kaur; Vinay Kumar Nandicoori; Sanjeev Khosla; Mycobacteria modulate host epigenetic machinery by Rv1988 methylation of a non-tail arginine of histone H3. Nature Communications 2015, 6, 1–13, 10.1038/ncomms9922.
  34. Hongtao Li; Hao Xu; Yan Zhou; Jie Zhang; Chengzu Long; Shuqin Li; She Chen; Jian-Min Zhou; Feng Shao; The Phosphothreonine Lyase Activity of a Bacterial Type III Effector Family. Science 2007, 315, 1000-1003, 10.1126/science.1138960.
  35. Yongqun Zhu; Hongtao Li; Chengzu Long; Liyan Hu; Hao Xu; Liping Liu; She Chen; Da-Cheng Wang; Feng Shao; Structural Insights into the Enzymatic Mechanism of the Pathogenic MAPK Phosphothreonine Lyase. Molecular Cell 2007, 28, 899-913, 10.1016/j.molcel.2007.11.011.
  36. Leny Jose; Ranjit Ramachandran; Raghu Bhagavat; Roshna Lawrence Gomez; Aneesh Chandran; Sajith Raghunandanan; Ramakrishnapillai Vyomakesannair Omkumar; Nagasuma Chandra; Sathish Mundayoor; Ramakrishnan Ajay Kumar; et al. Hypothetical protein Rv3423.1 of Mycobacterium tuberculosis is a histone acetyltransferase. The FEBS Journal 2016, 283, 265-281, 10.1111/febs.13566.
  37. Song-Ze Ding; Wolfgang Fischer; Maria Kaparakis-Liaskos; George Liechti; D. Scott Merrell; Patrick A. Grant; Richard L. Ferrero; Sheila E. Crowe; Rainer Haas; Masanori Hatakeyama; et al.Joanna B. Goldberg Helicobacter pylori-Induced Histone Modification, Associated Gene Expression in Gastric Epithelial Cells, and Its Implication in Pathogenesis. PLOS ONE 2010, 5, e9875, 10.1371/journal.pone.0009875.
  38. Meghan E. Pennini; Stéphanie Perrinet; Alice Dautry-Varsat; Agathe Subtil; Histone Methylation by NUE, a Novel Nuclear Effector of the Intracellular Pathogen Chlamydia trachomatis. PLOS Pathogens 2010, 6, e1000995, 10.1371/journal.ppat.1000995.
  39. Aneesh Chandran; Cecil Antony; Leny Jose; Sathish Mundayoor; Krishnamurthy Natarajan; Ramakrishnan Ajay Kumar; Mycobacterium tuberculosis Infection Induces HDAC1-Mediated Suppression of IL-12B Gene Expression in Macrophages. Frontiers in Microbiology 2015, 5, 98, 10.3389/fcimb.2015.00090.
  40. Yue Wang; Heather M Curry; Bruce S Zwilling; William P Lafuse; Mycobacteria inhibition of IFN-gamma induced HLA-DR gene expression by up-regulating histone deacetylation at the promoter region in human THP-1 monocytic cells. The Journal of Immunology 2005, 174, 5687–5694.
  41. Jose Carlos Garcia-Garcia; Nicole C. Barat; Sarah J. Trembley; J. Stephen Dumler; Epigenetic Silencing of Host Cell Defense Genes Enhances Intracellular Survival of the Rickettsial Pathogen Anaplasma phagocytophilum. PLOS Pathogens 2009, 5, e1000488, 10.1371/journal.ppat.1000488.
  42. Jose Carlos Garcia-Garcia; Kristen Rennoll-Bankert; Shaaretha Pelly; Aaron Milstone; J. Stephen Dumler; Silencing of Host Cell CYBB Gene Expression by the Nuclear Effector AnkA of the Intracellular Pathogen Anaplasma phagocytophilum. Infection and Immunity 2009, 77, 2385-2391, 10.1128/iai.00023-09.
  43. Kristen Rennoll-Bankert; J. Stephen Dumler; Lessons from Anaplasma phagocytophilum: Chromatin Remodeling by Bacterial Effectors. Infectious Disorders - Drug Targets 2012, 12, 380-387, 10.2174/187152612804142242.
  44. Kristen Rennoll-Bankert; Jose Carlos Garcia-Garcia; Sara H. Sinclair; J. Stephen Dumler; Chromatin-bound bacterial effector ankyrin A recruits histone deacetylase 1 and modifies host gene expression. Cellular Microbiology 2015, 17, 1640-1652, 10.1111/cmi.12461.
  45. Park, J.; Kim, K.J.; Choi, K.S.; Grab, D.J.; Dumler, J.S; Anaplasma phagocytophilum AnkA binds to granulocyte DNA and nuclear proteins. Cell. Microbiol. 2004, 6, 743–751.
  46. Dumler, J.S.; Sinclair, S.H.; Pappas-Brown, V.; Shetty, A.C; Genome-Wide Anaplasma phagocytophilum AnkA-DNA Interactions Are Enriched in Intergenic Regions and Gene Promoters and Correlate with Infection-Induced Differential Gene Expression. Front. Cell. Infect. Microbiol. 2016, 6, 97.
  47. Terumi Kohwi-Shigematsu; Terumi Kohwi-Shigematsu; Keiko Takahashi; Hunter W. Richards; Stephen Ayers; Hye-Jung Han; Shutao Cai; SATB1-mediated functional packaging of chromatin into loops. Methods 2012, 58, 243-254, 10.1016/j.ymeth.2012.06.019.
  48. Tian-Yun Wang; Zhong-Min Han; Yu-Rong Chai; Jun-He Zhang; A mini review of MAR-binding proteins. Molecular Biology Reports 2010, 37, 3553-3560, 10.1007/s11033-010-0003-8.
  49. Sergio A. Mojica; Kelley M. Hovis; Matthew B. Frieman; Bao Tran; Ru-Ching Hsia; Jacques Ravel; Clifton Jenkins-Houk; Katherine L. Wilson; Patrik M. Bavoil; SINC, a type III secreted protein of Chlamydia psittaci, targets the inner nuclear membrane of infected cells and uninfected neighbors. Molecular Biology of the Cell 2015, 26, 1918-1934, 10.1091/mbc.E14-11-1530.
  50. Arunava Bandyopadhaya; Amy Tsurumi; Damien Maura; Kate L. Jeffrey; Laurence G Rahme; A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming.. Nature Microbiology 2016, 1, 1-9, 10.1038/nmicrobiol.2016.174.
  51. Yin, L.; Chung, W.O; Epigenetic regulation of human beta-defensin 2 and CC chemokine ligand 20 expression in gingival epithelial cells in response to oral bacteria. Mucosal Immunol. 2011, 4, 409–419.
  52. Kenichi Imai; Harumi Inoue; Muneaki Tamura; Marni E. Cueno; Hiroko Inoue; O. Takeichi; Kaoru Kusama; Ichiro Saito; Kuniyasu Ochiai; The periodontal pathogen Porphyromonas gingivalis induces the Epstein–Barr virus lytic switch transactivator ZEBRA by histone modification. Biochimie 2012, 94, 839-846, 10.1016/j.biochi.2011.12.001.
  53. A. Wilson Aruni; Arunima Mishra; Yuetan Dou; Ozioma Chioma; Brittany N. Hamilton; Hansel Fletcher; Filifactor alocis--a new emerging periodontal pathogen.. Microbes and Infection 2015, 17, 517-530, 10.1016/j.micinf.2015.03.011.
  54. A. Wilson Aruni; Kangling Zhang; Yuetan Dou; Hansel Fletcher; Proteome Analysis of Coinfection of Epithelial Cells with Filifactor alocis and Porphyromonas gingivalis Shows Modulation of Pathogen and Host Regulatory Pathways. Infection and Immunity 2014, 82, 3261-3274, 10.1128/iai.01727-14.
  55. Barros, S.P.; Offenbacher, S; Modifiable risk factors in periodontal disease: Epigenetic regulation of gene expression in the inflammatory response. Periodontology 2000 2014, 64, 95–110.
  56. Stephanie R. Shames; Amit Bhavsar; Matthew Croxen; Robyn J. Law; Shinghung Mak; Wanyin Deng; Yuling Li; Roza Bidshari; Carmen L. De Hoog; Leonard J. Foster; et al.B. Brett Finlay The pathogenic Escherichia coli type III secreted protease NleC degrades the host acetyltransferase p300. Cellular Microbiology 2011, 13, 1542-1557, 10.1111/j.1462-5822.2011.01640.x.
  57. Márió Gajdács; Carbapenem-Resistant but Cephalosporin-Susceptible Pseudomonas aeruginosa in Urinary Tract Infections: Opportunity for Colistin Sparing. Antibiotics 2020, 9, 153, 10.3390/antibiotics9040153.
  58. Melissa Cantley; A. A. S. S. K. Dharmapatni; Kent Algate; T. N. Crotti; P. M. Bartold; D R Haynes; Class I and II histone deacetylase expression in human chronic periodontitis gingival tissue. Journal of Periodontal Research 2015, 51, 143-151, 10.1111/jre.12290.
  59. M.D. Martins; Luciana O. Almeida; Carlos Garaicoa-Pazmiño; J.M. Le; C.H. Squarize; N. Inohara; William V. Giannobile; Y. Jiao; L. Larsson; R.M. Castilho; et al. Epigenetic Modifications of Histones in Periodontal Disease. Journal of Dental Research 2015, 95, 215-222, 10.1177/0022034515611876.
  60. Grabiec, A.M.; Potempa, J; Epigenetic regulation in bacterial infections: Targeting histone deacetylases. Crit. Rev. Microbiol. 2018, 44, 336–350.
  61. Hans Helmut Niller; Roland Masa; Annamária Venkei; Sándor Mészáros; Janos Minarovits; Pathogenic mechanisms of intracellular bacteria. Current Opinion in Infectious Diseases 2017, 30, 309-315, 10.1097/qco.0000000000000363.
  62. Susan C. Wu; Yi Zhang; Active DNA demethylation: many roads lead to Rome. Nature Reviews Molecular Cell Biology 2010, 11, 607-620, 10.1038/nrm2950.
  63. Gerardo Nardone; Debora Compare; Patrizia De Colibus; Germana De Nucci; Alba Rocco; Helicobacter pylori and Epigenetic Mechanisms Underlying Gastric Carcinogenesis. Digestive Diseases 2007, 25, 225-229, 10.1159/000103890.
  64. Juliana Santos; Marcelo Ribeiro; Epigenetic regulation of DNA repair machinery inHelicobacter pylori-induced gastric carcinogenesis. World Journal of Gastroenterology 2015, 21, 9021-9037, 10.3748/wjg.v21.i30.9021.
  65. Ramakrishnan Sitaraman; Helicobacter pylori DNA methyltransferases and the epigenetic field effect in cancerization. Frontiers in Microbiology 2014, 5, 115, 10.3389/fmicb.2014.00115.
  66. Y.A. Bobetsis; S.P. Barros; D.M. Lin; J.R. Weidman; D.C. Dolinoy; R.L. Jirtle; K.A. Boggess; J.D. Beck; S. Offenbacher; Bacterial infection promotes DNA hypermethylation. Journal of Dental Research 2007, 86, 169-174, 10.1177/154405910708600212.
  67. Toshihiro Masaki; Jinrong Qu; Justyna Cholewa-Waclaw; Karen Burr; Ryan Raaum; Anura Rambukkana; Reprogramming adult Schwann cells to stem cell-like cells by leprosy bacilli promotes dissemination of infection. Cell 2013, 152, 51-67, 10.1016/j.cell.2012.12.014.
  68. Cornelia Tolg; Nesrin Sabha; Rene Cortese; Trupti Panchal; Alya Ahsan; Ashraf T Soliman; Karen J Aitken; Arturas Petronis; Darius J. Bägli; Uropathogenic E. coli infection provokes epigenetic downregulation of CDKN2A (p16INK4A) in uroepithelial cells. Laboratory Investigation 2011, 91, 825-836, 10.1038/labinvest.2010.197.
  69. J. Minarovits; Microbe-induced epigenetic alterations in host cells: The coming era of patho-epigenetics of microbial infections. Acta Microbiologica et Immunologica Hungarica 2009, 56, 1-19, 10.1556/amicr.56.2009.1.1.
  70. Andrei V. Chernov; Leticia Reyes; Scott Peterson; Alex Y. Strongin; Depletion of CG-Specific Methylation in Mycoplasma hyorhinis Genomic DNA after Host Cell Invasion. PLOS ONE 2015, 10, e0142529, 10.1371/journal.pone.0142529.
  71. Wenyi Luo; Anh-Hue T. Tu; Zuhua Cao; Huilan Yu; Kevin Dybvig; Identification of an isoschizomer of the HhaI DNA methyltransferase in Mycoplasma arthritidis. FEMS Microbiology Letters 2009, 290, 195-198, 10.1111/j.1574-6968.2008.01428.x.
  72. Marek Wojciechowski; Honorata Czapinska; Matthias Bochtler; CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Proceedings of the National Academy of Sciences 2013, 110, 105-110, 10.1073/pnas.1207986110.
  73. Andrei V. Chernov; Leticia Reyes; Zhenkang Xu; Beatriz Gonzalez; Georgiy Golovko; Scott Peterson; Manuel Perucho; Yuriy Fofanov; Alex Y. Strongin; Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells. Epigenetics 2015, 10, 303-318, 10.1080/15592294.2015.1020000.
  74. Sara E. Pinney; Mammalian Non-CpG Methylation: Stem Cells and Beyond. Biology 2014, 3, 739-751, 10.3390/biology3040739.
  75. Garima Sharma; Sandeep Upadhyay; M. Srilalitha; Vinay Kumar Nandicoori; Sanjeev Khosla; The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding. Nucleic Acids Research 2015, 43, 3922-3937, 10.1093/nar/gkv261.
  76. Garima Sharma; Divya Tej Sowpati; Prakruti Singh; Mehak Zahoor Khan; Rakesh Ganji; Sandeep Upadhyay; Sharmistha Banerjee; Vinay Kumar Nandicoori; Sanjeev Khosla; Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. Scientific Reports 2016, 6, 25006, 10.1038/srep25006.
  77. Samuel Hess; Anura Rambukkana; Bacterial-induced cell reprogramming to stem cell-like cells: new premise in host-pathogen interactions. Current Opinion in Microbiology 2015, 23, 179-188, 10.1016/j.mib.2014.11.021.
  78. M. Benakanakere; M. Abdolhosseini; K. Hosur; Livia Finoti; Denis F. Kinane; TLR2 promoter hypermethylation creates innate immune dysbiosis. Journal of Dental Research 2015, 94, 183-191, 10.1177/0022034514557545.
  79. Djebali, S.; Davis, C.A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; Lagarde, J.; Lin, W.; Schlesinger, F.; et al.et al Landscape of transcription in human cells. Nature 2012, 489, 101–108.
  80. Doolittle, W.F; Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. USA 2013, 110, 5294–5300.
  81. Ines Ambite; Daniel S. C. Butler; Christoph Stork; Jenny Grönberg-Hernández; Bela Köves; Jaroslaw Zdziarski; Jerome Pinkner; Scott J. Hultgren; Ulrich Dobrindt; Björn Wullt; et al.Catharina Svanborg Fimbriae reprogram host gene expression – Divergent effects of P and type 1 fimbriae. PLOS Pathogens 2019, 15, e1007671, 10.1371/journal.ppat.1007671.
  82. Alessandro Fatica; Irene Bozzoni; Long non-coding RNAs: new players in cell differentiation and development. Nature Reviews Microbiology 2014, 15, 7-21, 10.1038/nrg3606.
  83. Wenqian Hu; Juan R Alvarez-Dominguez; H F Lodish; Regulation of mammalian cell differentiation by long non‐coding RNAs. EMBO reports 2012, 13, 971-983, 10.1038/embor.2012.145.
  84. Orly Wapinski; Howard Y Chang; Long noncoding RNAs and human disease. Trends in Cell Biology 2011, 21, 354-361, 10.1016/j.tcb.2011.04.001.
  85. Paulina A. Latos; Florian M. Pauler; Martha V. Koerner; H. Başak Şenergin; Quanah J. Hudson; Roman R. Stocsits; Wolfgang Allhoff; Stefan H. Stricker; Ruth M. Klement; Katarzyna E. Warczok; et al.Karin AumayrPawel PasierbekDenise P. Barlow Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing. Science 2012, 338, 1469-1472, 10.1126/science.1228110.
  86. Qian Liu; Jianguo Huang; Nanjiang Zhou; Ziqiang Zhang; Ali Zhang; Zhaohui Lu; Fangting Wu; Yin-Yuan Mo; LncRNA loc285194 is a p53-regulated tumor suppressor. Nucleic Acids Research 2013, 41, 4976-4987, 10.1093/nar/gkt182.
  87. Vivek Sharma; Simran Khurana; Nard Kubben; Kotb Abdelmohsen; Philipp Oberdoerffer; Myriam Gorospe; Tom Misteli; A BRCA 1‐interacting lnc RNA regulates homologous recombination. EMBO reports 2015, 16, 1520-1534, 10.15252/embr.201540437.
  88. Yul W Yang; Ryan A. Flynn; Yong Chen; Kun Qu; Bingbing Wan; Kevin C Wang; Ming Lei; Howard Y Chang; Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. eLife 2014, 3, e02046, 10.7554/eLife.02046.
  89. Bonasio, R.; Shiekhattar, R; Regulation of Spermatogenesis by Noncoding RNAs. Annu. Rev. Genet. 2014, 48, 433–455.
  90. Kevin C. Wang; Howard Y. Chang; Molecular Mechanisms of Long Noncoding RNAs. Molecular Cell 2011, 43, 904-914, 10.1016/j.molcel.2011.08.018.
  91. Nicole A Rapicavoli; Kun Qu; Jiajing Zhang; Megan E. Mikhail; Remi-Martin Laberge; Howard Y Chang; A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. eLife 2013, 2, e00762, 10.7554/elife.00762.
  92. Yao-Zhong Ding; Zhong-Wang Zhang; Ya-Li Liu; Chong-Xu Shi; Jie Zhang; Yongguang Zhang; Relationship of long noncoding RNA and viruses. Genomics 2016, 107, 150-154, 10.1016/j.ygeno.2016.01.007.
  93. Nicholas E. Iiott; James A. Heward; Benoît Roux; Eleni Tsitsiou; Peter S. Fenwick; Luca Lenzi; Ian Goodhead; Christiane Hertz-Fowler; Andreas Heger; Neil Hall; et al.Louise DonnellyDavid SimsMark A. Lindsay Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nature Communications 2014, 5, 1-14, 10.1038/ncomms4979.
  94. Ai-Ping Mao; Jun Shen; Zhixiang Zuo; Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages.. BMC Genomics 2015, 16, 45, 10.1186/s12864-015-1270-5.
  95. Alexander J. Westermann; Konrad U. Förstner; Fabian Amman; Lars Barquist; Yanjie Chao; Leon N. Schulte; Lydia Müller; Richard Reinhardt; Peter F Stadler; Jörg Vogel; et al. Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions. Nature 2016, 529, 496-501, 10.1038/nature16547.
  96. John L Rinn; Michael Kertesz; Jordon Wang; Sharon L. Squazzo; Xiao Xu; Samantha A. Brugmann; L Henry Goodnough; Jill A. Helms; P J Farnham; Eran Segal; et al.Howard Y ChangHenry Goodnough Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs. Cell 2007, 129, 1311-1323, 10.1016/j.cell.2007.05.022.
  97. Wu, H.; Liu, J.; Li, W.; Liu, G.; Li, Z; LncRNA-HOTAIR promotes TNF-alpha production in cardiomyocytes of LPS-induced sepsis mice by activating NF-kappaB pathway. Biochem. Biophys. Res. Commun. 2016, 471, 240–246.
  98. Susan Carpenter; Daniel Aiello; Maninjay K. Atianand; Emiliano Ricci; Pallavi Gandhi; Lisa L. Hall; Meg Byron; Brian Monks; Meabh Henry-Bezy; Jeanne B. Lawrence; et al.Luke A.J. O’NeillMelissa J. MooreDaniel R. CaffreyKatherine A. Fitzgerald A Long Noncoding RNA Mediates Both Activation and Repression of Immune Response Genes. Science 2013, 341, 789-792, 10.1126/science.1240925.
  99. Mitchell Guttman; Ido Amit; Manuel Garber; Courtney French; Michael F. Lin; David M. Feldser; Maite Huarte; Or Zuk; Bryce W. Carey; John P. Cassady; et al.Moran N. CabiliRudolf JaenischTarjei S. MikkelsenTyler JacksNir HacohenBradley E. BernsteinManolis KellisAviv RegevJohn L RinnEric S. Lander Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458, 223-227, 10.1038/nature07672.
  100. Kamlesh Ganesh Pawar; Carlos Hanisch; Sergio Eliseo Palma Vera; Ralf Einspanier; Soroush Sharbati; Down regulated lncRNA MEG3 eliminates mycobacteria in macrophages via autophagy. Scientific Reports 2016, 6, 1-13, 10.1038/srep19416.
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