The role of transposable elements in the regulation of IFN-λ1 gene expression

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 28, 2009, Pages 11564-11569

  Thomson, Scott J P ^a   Goh, Fui G ^a   Banks, Helen ^a,c   Krausgruber, Thomas ^a   Kotenko, Sergei V ^b   Foxwell, Brian M J ^a   Udalova, Irina A ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Alu repeats; Gene regulation; Interferon; NF B; Transcription enhancer

Indexed keywords

BACTERIUM LIPOPOLYSACCHARIDE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERFERON REGULATORY FACTOR 3; INTERFERON REGULATORY FACTOR 7; INTERLEUKIN 29; TRANSCRIPTION FACTOR RELA;

ALU SEQUENCE; ARTICLE; BINDING SITE; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE INDUCTION; GENE LOCUS; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; TRANSPOSON;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HUMANS; INTERLEUKINS; LUCIFERASES; MYELOID CELLS; NF-KAPPA B; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

BACTERIA (MICROORGANISMS);

EID: 67650869803     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0904477106     Document Type: Article

References (39)

1. Lutfalla G, et al. (2003) Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: The class II cytokine receptors and their ligands in mammals and fish. BMC Genomics 4:29-44.
2. Zou J, Tafalla C, Truckle J, Secombes CJ (2007) Identification of a second group of type I IFNs in fish sheds light on IFN evolution in vertebrates. J Immunol 179:3859-3871.
3. Sheppard P, et al. (2003) IL-28, IL-29, and their class II cytokine receptor IL-28R. Nat Immunol 4:63-68.
4. Commins S, Steinke JW, Borish L (2008) The extended IL-10 superfamily: IL-10, IL-19, IL-20, IL-22, IL-24, IL-26, IL-28, and IL-29. J Allergy Clin Immunol 121:1108-1111.
5. Renauld JC (2003) Class II cytokine receptors and their ligands: Key antiviral and inflammatory modulators. Nat Rev Immunol 3:667-676.
6. Kotenko SV, et al. (2003) IFN-λs mediate antiviral protection through a distinct class II cytokine receptor complex. Nat Immunol 4:69-77.
7. Platanias LC, Fish EN (1999) Signaling pathways activated by interferons. Exp Hematol 27:1583-1592.
8. Onoguchi K, et al. (2007) Viral infections activate types I and III interferon genes through a common mechanism. J Biol Chem 282:7576-7581.
9. Osterlund PI, Pietila TE, Veckman V, Kotenko SV, Julkunen I (2007) IFN regulatory factor family members differentially regulate the expression of type III IFN (IFN-λ) genes. J Immunol 179:3434-3442.
10. Thanos D, Maniatis T (1995) Virus induction of human IFN-β gene expression requires the assembly of an enhanceosome. Cell 83:1091-1100.
11. Fitzgerald KA, et al. (2003) IKKε and TBK1 are essential components of the IRF3 signaling pathway. Nat Immunol 4:491-496.
12. Sharma S, et al. (2003) Triggering the interferon antiviral response through an IKK-related pathway. Science 300:1148-1151.
13. Sommereyns C, Paul S, Staeheli P, Michiels T (2008) IFN-λ is expressed in a tissue-dependent fashion and primarily acts on epithelial cells in vivo. PLoS Pathog 4:e1000017.
14. Coccia EM, et al. (2004) Viral infection and Toll-like receptor agonists induce a differential expression of type I and λ interferons in human plasmacytoid and monocyte-derived dendritic cells. Eur J Immunol 34:796-805.
15. Mennechet FJ, Uze G (2006) Interferon-λ-treated dendritic cells specifically induce proliferation of FOXP3-expressing suppressor T cells. Blood 107:4417-4423.
16. Wolk K, et al. (2008) Maturing dendritic cells are an important source of IL-29 and IL-20 that may cooperatively increase the innate immunity of keratinocytes. J Leukocyte Biol 83:1181-1193.
17. Verreck FA, de Boer T, Langenberg DM, van der Zanden L, Ottenhoff TH (2006) Phenotypic and functional profiling of human proinflammatory type 1 and antiinflammatory type 2 macrophages in response to microbial antigens and IFN-γ- and CD40L-mediated costimulation. J Leukocyte Biol 79:285-293.
18. Foxwell B, et al. (1998) Efficient adenoviral infection with IκBα reveals that macrophage tumor necrosis factor α production in rheumatoid arthritis is NF-κB dependent. Proc Natl Acad Sci USA 95:8211-8215.
19. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451:535-540.
20. Arnosti DN, Kulkarni MM (2005) Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J Cell Biochem 94:890-898.
21. Papatsenko D, Levine M (2007) A rationale for the enhanceosome and other evolutionarily constrained enhancers. Curr Biol 17:R955-957.
22. Apostolou E, Thanos D (2008) Virus infection induces NF-κB- dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell 134:85-96.
23. Bosisio D, et al. (2006) A hyper-dynamic equilibrium between promoter-bound and nucleoplasmic dimers controls NF-κB-dependent gene activity. EMBO J 25:798-810.
24. Lowe CB, Bejerano G, Haussler D (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA 104:8005-8010.
25. Mikkelsen TS, et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in noncoding sequences. Nature 447:167-177.
26. Pestka S, Krause CD, Walter MR (2004) Interferons, interferon-like cytokines, and their receptors. Immunol Rev 202:8-32.
27. Medstrand P, et al. (2005) Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 110:342-352.
28. van de Lagemaat LN, Medstrand P, Mager DL (2006) Multiple effects govern endogenous retrovirus survival patterns in human gene introns. Genome Biol 7:R86.
29. Wang T, et al. (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci USA 104:18613-18618.
30. Benit L, Lallemand JB, Casella JF, Philippe H, Heidmann T (1999) ERV-L elements: A family of endogenous retrovirus-like elements active throughout the evolution of mammals. J Virol 73:3301-3308.
31. Chen C, Gentles AJ, Jurka J, Karlin S (2002) Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc Natl Acad Sci USA 99:2930-2935.
32. Grover D, Majumder PP, Rao CB, Brahmachari SK, Mukerji M (2003) Nonrandom distribution of alu elements in genes of various functional categories: Insight from analysis of human chromosomes 21 and 22. Mol Biol Evol 20:1420-1424.
33. Brosius J (1999) Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107:209-238.
34. Shankar R, Grover D, Brahmachari SK, Mukerji M (2004) Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III-dependent mobile Alu elements. BMC Evol Biol 4:37-46.
35. Ackerman H, Udalova I, Hull J, Kwiatkowski D (2002) Evolution of a polymorphic regulatory element in interferon-γ through transposition and mutation. Mol Biol Evol 19:884-890.
36. Liu G, et al. (2003) Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res 13:358-368.
37. Udalova IA, Knight JC, Vidal V, Nedospasov SA, Kwiatkowski D (1998) Complex NF-κB interactions at the distal tumor necrosis factor promoter region in human monocytes. J Biol Chem 273:21178-21186.
38. Saccani S, Pantano S, Natoli G (2001) Two waves of nuclear factor κB recruitment to target promoters. J Exp Med 193:1351-1359.
39. Vlieghe D, et al. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res 34:D95-D97.