Noncoding RNAs and LRRFIP1 regulate TNF expression

Journal of Immunology

Volumn 192, Issue 7, 2014, Pages 3057-3067

  Shi, Lihua ^a   Song, Li ^a   Fitzgerald, Michael ^a   Maurer, Kelly ^a   Bagashev, Asen ^b   Sullivan, Kathleen E ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b TEMPLE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; POLYADENYLATED RNA; TRANSCRIPTION FACTOR EZH2; TRANSCRIPTION FACTOR LRRFIP1; TUMOR NECROSIS FACTOR; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; BINDING KINETICS; CONTROLLED STUDY; GENE; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE REPRESSION; GENE SEQUENCE; GENE SILENCING; GENE STRUCTURE; GENE TARGETING; HUMAN; HUMAN CELL; LRRFIP1 GENE; NORMAL HUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; SUZ12 GENE; TRANSCRIPTION REGULATION;

BASE SEQUENCE; BLOTTING, WESTERN; CELL LINE; CELL LINE, TUMOR; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; HUMANS; K562 CELLS; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA, LONG NONCODING; RNA-BINDING PROTEINS; TUMOR NECROSIS FACTOR-ALPHA;

EID: 84897477133     PISSN: 00221767     EISSN: 15506606     Source Type: Journal    
DOI: 10.4049/jimmunol.1302063     Document Type: Article

References (94)

1. Beutler, B., and T. Brown. 1991. A CAT reporter construct allows ultrasensitive estimation of TNF synthesis, and suggests that the TNF gene has been silenced in non-macrophage cell lines. J. Clin. Invest. 87: 1336-1344.
2. Cerami, A., and B. Beutler. 1986. Cachectin: the dark side of tumor necrosis factor. Cold Spring Harb. Symp. Quant. Biol. 51: 625-629.
3. Cerami, A., and B. Beutler. 1988. The role of cachectin/TNF in endotoxic shock and cachexia. Immunol. Today 9: 28-31.
4. Gardam, M. A., E. C. Keystone, R. Menzies, S. Manners, E. Skamene, R. Long, and D. C. Vinh. 2003. Anti-tumour necrosis factor agents and tuberculosis risk: mechanisms of action and clinical management. Lancet Infect. Dis. 3: 148-155.
5. Jacobs, M., D. Togbe, C. Fremond, A. Samarina, N. Allie, T. Botha, D. Carlos, S. K. Parida, S. Grivennikov, S. Nedospasov, et al. 2007. Tumor necrosis factor is critical to control tuberculosis infection. Microbes Infect. 9: 623-628.
6. Roach, D. R., A. G. Bean, C. Demangel, M. P. France, H. Briscoe, and W. J. Britton. 2002. TNF regulates chemokine induction essential for cell recruitment, granuloma formation, and clearance of mycobacterial infection. J. Immunol. 168: 4620-4627.
7. Bean, A. G., D. R. Roach, H. Briscoe, M. P. France, H. Korner, J. D. Sedgwick, and W. J. Britton. 1999. Structural deficiencies in granuloma formation in TNF gene-targeted mice underlie the heightened susceptibility to aerosol Mycobacterium tuberculosis infection, which is not compensated for by lymphotoxin. J. Immunol. 162: 3504-3511.
8. Marino, M. W., A. Dunn, D. Grail, M. Inglese, Y. Noguchi, E. Richards, A. Jungbluth, H. Wada, M. Moore, B. Williamson, et al. 1997. Characterization of tumor necrosis factor-deficient mice. Proc. Natl. Acad. Sci. USA 94: 8093-8098.
9. Butler, D. M., A. M. Malfait, L. J. Mason, P. J. Warden, G. Kollias, R. N. Maini, M. Feldmann, and F. M. Brennan. 1997. DBA/1 mice expressing the human TNF-alpha transgene develop a severe, erosive arthritis: characterization of the cytokine cascade and cellular composition. J. Immunol. 159: 2867-2876.
10. Carballo, E., W. S. Lai, and P. J. Blackshear. 1998. Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science 281: 1001-1005.
11. Dal Canto, R. A., M. K. Shaw, G. P. Nolan, L. Steinman, and C. G. Fathman. 1999. Local delivery of TNF by retrovirus-transduced T lymphocytes exacerbates experimental autoimmune encephalomyelitis. Clin. Immunol. 90: 10-14.
12. Douni, E., K. Akassoglou, L. Alexopoulou, S. Georgopoulos, S. Haralambous, S. Hill, G. Kassiotis, D. Kontoyiannis, M. Pasparakis, D. Plows, et al. 1995-1996. Transgenic and knockout analyses of the role of TNF in immune regulation and disease pathogenesis. J. Inflamm. 47: 27-38.
13. Kontoyiannis, D., M. Pasparakis, T. T. Pizarro, F. Cominelli, and G. Kollias. 1999. Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AUrich elements: implications for joint and gut-associated immunopathologies. Immunity 10: 387-398.
14. Willuweit, A., G. Sass, A. Schöneberg, U. Eisel, G. Tiegs, and M. Clauss. 2001. Chronic inflammation and protection from acute hepatitis in transgenic mice expressing TNF in endothelial cells. J. Immunol. 167: 3944-3952.
15. Armstrong, L., S. I. Godinho, K. M. Uppington, H. A. Whittington, and A. B. Millar. 2006. Contribution of TNF-alpha converting enzyme and proteinase-3 to TNF-alpha processing in human alveolar macrophages. Am. J. Respir. Cell Mol. Biol. 34: 219-225.
16. Buxadé, M., J. L. Parra, S. Rousseau, N. Shpiro, R. Marquez, N. Morrice, J. Bain, E. Espel, and C.G. Proud. 2005. TheMnks are novel components in the control of TNF alpha biosynthesis and phosphorylate and regulate hnRNPA1. Immunity 23: 177-189.
17. Yang, Y., J. F. Chang, J. R. Parnes, and C. G. Fathman. 1998. T cell receptor (TCR) engagement leads to activation-induced splicing of tumor necrosis factor (TNF) nuclear pre-mRNA. J. Exp. Med. 188: 247-254.
18. Osman, F., N. Jarrous, Y. Ben-Asouli, and R. Kaempfer. 1999. A cis-acting element in the 39-untranslated region of human TNF-alpha mRNA renders splicing dependent on the activation of protein kinase PKR. Genes Dev. 13: 3280-3293.
19. Sullivan, K. E., A. B. Reddy, K. Dietzmann, A. R. Suriano, V. P. Kocieda, M. Stewart, and M. Bhatia. 2007. Epigenetic regulation of tumor necrosis factor alpha. Mol. Cell. Biol. 27: 5147-5160.
20. Mahlknecht, U., J. Will, A. Varin, D. Hoelzer, and G. Herbein. 2004. Histone deacetylase 3, a class I histone deacetylase, suppresses MAPK11-mediated activating transcription factor-2 activation and represses TNF gene expression. J. Immunol. 173: 3979-3990.
21. Wessels, I., E. Rosenkranz, M. Ventura Ferreira, S. Neuss, M. Zenke, L. Rink, and P. Uciechowski. 2013. Activation of IL-1b and TNFa genes is mediated by the establishment of permissive chromatin structures during monopoiesis. Immunobiology 218: 860-868.
22. Heinz, S., C. Benner, N. Spann, E. Bertolino, Y. C. Lin, P. Laslo, J. X. Cheng, C. Murre, H. Singh, and C. K. Glass. 2010. Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38: 576-589.
23. Pham, T. H., S. Langmann, L. Schwarzfischer, C. El Chartouni, M. Lichtinger, M. Klug, S. W. Krause, and M. Rehli. 2007. CCAAT enhancer-binding protein beta regulates constitutive gene expression during late stages of monocyte to macrophage differentiation. J. Biol. Chem. 282: 21924-21933.
24. Pham, T. H., C. Benner, M. Lichtinger, L. Schwarzfischer, Y. Hu, R. Andreesen, W. Chen, and M. Rehli. 2012. Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. Blood 119: e161-e171.
25. Pham, T. H., J. Minderjahn, C. Schmidl, H. Hoffmeister, S. Schmidhofer, W. Chen, G. Längst, C. Benner, and M. Rehli. 2013. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. 41: 6391-6402.
26. Barthel, R., A. V. Tsytsykova, A. K. Barczak, E. Y. Tsai, C. C. Dascher, M. B. Brenner, and A. E. Goldfeld. 2003. Regulation of tumor necrosis factor alpha gene expression by mycobacteria involves the assembly of a unique enhanceosome dependent on the coactivator proteins CBP/p300. Mol. Cell. Biol. 23: 526-533.
27. Tsai, E. Y., J. V. Falvo, A. V. Tsytsykova, A. K. Barczak, A. M. Reimold, L. H. Glimcher, M. J. Fenton, D. C. Gordon, I. F. Dunn, and A. E. Goldfeld. 2000. A lipopolysaccharide-specific enhancer complex involving Ets, Elk-1, Sp1, and CREB binding protein and p300 is recruited to the tumor necrosis factor alpha promoter in vivo. Mol. Cell. Biol. 20: 6084-6094.
28. Kuprash, D. V., I. A. Udalova, R. L. Turetskaya, D. Kwiatkowski, N. R. Rice, and S. A. Nedospasov. 1999. Similarities and differences between human and murine TNF promoters in their response to lipopolysaccharide. J. Immunol. 162: 4045-4052.
29. Lai, W. S., E. Carballo, J. R. Strum, E. A. Kennington, R. S. Phillips, and P. J. Blackshear. 1999. Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor alpha mRNA. Mol. Cell. Biol. 19: 4311-4323.
30. López de Silanes, I., S. Galbán, J. L. Martindale, X. Yang, K. Mazan-Mamczarz, F. E. Indig, G. Falco, M. Zhan, and M. Gorospe. 2005. Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1. Mol. Cell. Biol. 25: 9520-9531.
31. Ronkina, N., M. B. Menon, J. Schwermann, C. Tiedje, E. Hitti, A. Kotlyarov, and M. Gaestel. 2010. MAPKAP kinases MK2 and MK3 in inflammation: complex regulation of TNF biosynthesis via expression and phosphorylation of tristetraprolin. Biochem. Pharmacol. 80: 1915-1920.
32. Loflin, P., C. Y. Chen, and A. B. Shyu. 1999. Unraveling a cytoplasmic role for hnRNP D in the in vivo mRNA destabilization directed by the AU-rich element. Genes Dev. 13: 1884-1897.
33. Min, H., C. W. Turck, J. M. Nikolic, and D. L. Black. 1997. A new regulatory protein, KSRP, mediates exon inclusion through an intronic splicing enhancer. Genes Dev. 11: 1023-1036.
34. Zhang, W., B. J. Wagner, K. Ehrenman, A. W. Schaefer, C. T. DeMaria, D. Crater, K. DeHaven, L. Long, and G. Brewer. 1993. Purification, characterization, and cDNA cloning of an AU-rich element RNA-binding protein, AUF1. Mol. Cell. Biol. 13: 7652-7665.
35. Suriano, A. R., A. N. Sanford, N. Kim, M. Oh, S. Kennedy, M. J. Henderson, K. Dietzmann, and K. E. Sullivan. 2005. GCF2/LRRFIP1 represses tumor necrosis factor alpha expression. Mol. Cell. Biol. 25: 9073-9081.
36. Sullivan, K. E., A. Suriano, K. Dietzmann, J. Lin, D. Goldman, and M. A. Petri. 2007. The TNFalpha locus is altered in monocytes from patients with systemic lupus erythematosus. Clin. Immunol. 123: 74-81.
37. Cabili, M. N., C. Trapnell, L. Goff, M. Koziol, B. Tazon-Vega, A. Regev, and J. L. Rinn. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25: 1915-1927.
38. Ponting, C. P. 2008. The functional repertoires of metazoan genomes. Nat. Rev. Genet. 9: 689-698.
39. Guttman, M., I. Amit, M. Garber, C. French, M. F. Lin, D. Feldser, M. Huarte, O. Zuk, B. W. Carey, J. P. Cassady, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
40. Carninci, P., T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, et al; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
41. Xu, Z., W. Wei, J. Gagneur, S. Clauder-Münster, M. Smolik, W. Huber, and L. M. Steinmetz. 2011. Antisense expression increases gene expression variability and locus interdependency. Mol. Syst. Biol. 7: 468.
42. Ogawa, Y., B. K. Sun, and J. T. Lee. 2008. Intersection of the RNA interference and X-inactivation pathways. Science 320: 1336-1341.
43. Splinter, E., E. de Wit, E. P. Nora, P. Klous, H. J. van de Werken, Y. Zhu, L. J. Kaaij, W. van Ijcken, J. Gribnau, E. Heard, and W. de Laat. 2011. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev. 25: 1371-1383.
44. Carpenter, S., D. Aiello, M. K. Atianand, E. P. Ricci, P. Gandhi, L. L. Hall, M. Byron, B. Monks, M. Henry-Bezy, J. B. Lawrence, et al. 2013. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341: 789-792.
45. Guttman, M., J. Donaghey, B. W. Carey, M. Garber, J. K. Grenier, G. Munson, G. Young, A. B. Lucas, R. Ach, L. Bruhn, et al. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477: 295-300.
46. Peng, X., L. Gralinski, M. T. Ferris, M. B. Frieman, M. J. Thomas, S. Proll, M. J. Korth, J. R. Tisoncik, M. Heise, S. Luo, et al. 2011. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. MBio 2: pii: e00198-11.
47. Kretz, M., Z. Siprashvili, C. Chu, D. E. Webster, A. Zehnder, K. Qu, C. S. Lee, R. J. Flockhart, A. F. Groff, J. Chow, et al. 2013. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493: 231-235.
48. Chu, C., K. Qu, F. L. Zhong, S. E. Artandi, and H. Y. Chang. 2011. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44: 667-678.
49. Khalil, A. M., M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B. E. Bernstein, A. van Oudenaarden, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106: 11667-11672.
50. Redrup, L., M. R. Branco, E. R. Perdeaux, C. Krueger, A. Lewis, F. Santos, T. Nagano, B. S. Cobb, P. Fraser, and W. Reik. 2009. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 136: 525-530.
51. Kanduri, C. 2008. Functional insights into long antisense noncoding RNA Kcnq1ot1 mediated bidirectional silencing. RNA Biol. 5: 208-211.
52. Martianov, I., A. Ramadass, A. Serra Barros, N. Chow, and A. Akoulitchev. 2007. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670.
53. Suzuki, K., T. Juelich, H. Lim, T. Ishida, T. Watanebe, D. A. Cooper, S. Rao, and A. D. Kelleher. 2008. Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J. Biol. Chem. 283: 23353-23363.
54. Ting, A. H., K. E. Schuebel, J. G. Herman, and S. B. Baylin. 2005. Short doublestranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat. Genet. 37: 906-910.
55. Weinberg, M. S., L. M. Villeneuve, A. Ehsani, M. Amarzguioui, L. Aagaard, Z. X. Chen, A. D. Riggs, J. J. Rossi, and K. V. Morris. 2006. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12: 256-262.
56. Janowski, B. A., K. E. Huffman, J. C. Schwartz, R. Ram, R. Nordsell, D. S. Shames, J. D. Minna, and D. R. Corey. 2006. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat. Struct. Mol. Biol. 13: 787-792.
57. Han, J., D. Kim, and K. V. Morris. 2007. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl. Acad. Sci. USA 104: 12422-12427.
58. Kim, D. H., L. M. Villeneuve, K. V. Morris, and J. J. Rossi. 2006. Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol. 13: 793-797.
59. Lee, J. Y., and K. E. Sullivan. 2001. Gamma interferon and lipopolysaccharide interact at the level of transcription to induce tumor necrosis factor alpha expression. Infect. Immun. 69: 2847-2852.
60. Wang, X., S. Arai, X. Song, D. Reichart, K. Du, G. Pascual, P. Tempst, M. G. Rosenfeld, C. K. Glass, and R. Kurokawa. 2008. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454: 126-130.
61. Mapendano, C. K., S. Lykke-Andersen, J. Kjems, E. Bertrand, and T. H. Jensen. 2010. Crosstalk between mRNA 39 end processing and transcription initiation. Mol. Cell 40: 410-422.
62. Seidl, C. I., S. H. Stricker, and D. P. Barlow. 2006. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J. 25: 3565-3575.
63. Bochnig, P., R. Reuter, P. Bringmann, and R. Luhrmann. 1987. A monoclonal antibody against 2, 2, 7-trimethylguanosine that reacts with intact, class U, small nuclear ribonucleoproteins as well as with 7-methylguanosine-capped RNAs. Eur. J. Biochem. 168: 461-467.
64. Patrone, G., F. Puppo, R. Cusano, M. Scaranari, I. Ceccherini, A. Puliti, and R. Ravazzolo. 2000. Nuclear run-on assay using biotin labeling, magnetic bead capture and analysis by fluorescence-based RT-PCR. Biotechniques 29: 1012-1014, 1016-1017.
65. Bendak, K., F. E. Loughlin, V. Cheung, M. R. O'Connell, M. Crossley, and J. P. Mackay. 2012. A rapid method for assessing the RNA-binding potential of a protein. Nucleic Acids Res. 40: e105.
66. Lee, J. Y., N. A. Kim, A. Sanford, and K. E. Sullivan. 2003. Histone acetylation and chromatin conformation are regulated separately at the TNF-alpha promoter in monocytes and macrophages. J. Leukoc. Biol. 73: 862-871.
67. Garrett, S., K. Dietzmann-Maurer, L. Song, and K. E. Sullivan. 2008. Polarization of primary human monocytes by IFN-gamma induces chromatin changes and recruits RNA Pol II to the TNF-alpha promoter. J. Immunol. 180: 5257-5266.
68. Rinn, J. L., M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, J. A. Helms, P. J. Farnham, E. Segal, and H. Y. Chang. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129: 1311-1323.
69. Wilson, S. A., E. C. Brown, A. J. Kingsman, and S. M. Kingsman. 1998. TRIP: a novel double stranded RNA binding protein which interacts with the leucine rich repeat of flightless I. Nucleic Acids Res. 26: 3460-3467.
70. Cao, R., and Y. Zhang. 2004. The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr. Opin. Genet. Dev. 14: 155-164.
71. Cao, R., and Y. Zhang. 2004. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol. Cell 15: 57-67.
72. Viré, E., C. Brenner, R. Deplus, L. Blanchon, M. Fraga, C. Didelot, L. Morey, A. Van Eynde, D. Bernard, J. M. Vanderwinden, et al. 2006. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439: 871-874.
73. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.
74. Santiago, F. S., and L. M. Khachigian. 2004. Ets-1 stimulates platelet-derived growth factor A-chain gene transcription and vascular smooth muscle cell growth via cooperative interactions with Sp1. Circ. Res. 95: 479-487.
75. Khachigian, L. M., F. S. Santiago, L. A. Rafty, O. L. Chan, G. J. Delbridge, A. Bobik, T. Collins, and A. C. Johnson. 1999. GC factor 2 represses plateletderived growth factor A-chain gene transcription and is itself induced by arterial injury. Circ. Res. 84: 1258-1267.
76. Reed, A. L., H. Yamazaki, J. D. Kaufman, Y. Rubinstein, B. Murphy, and A. C. Johnson. 1998. Molecular cloning and characterization of a transcription regulator with homology to GC-binding factor. J. Biol. Chem. 273: 21594-21602.
77. Soler, G., S. Nusbaum, B. Varet, E. A. Macintyre, M. Vekemans, S. P. Romana, and I. Radford-Weiss. 2009. LRRFIP1, a new FGFR1 partner gene associated with 8p11 myeloproliferative syndrome. Leukemia 23: 1359-1361.
78. Lee, Y. H., and M. R. Stallcup. 2006. Interplay of Fli-I and FLAP1 for regulation of beta-catenin dependent transcription. Nucleic Acids Res. 34: 5052-5059.
79. Ohtsuka, H., M. Oikawa, K. Ariake, T. Rikiyama, F. Motoi, Y. Katayose, M. Unno, and A. C. Johnson. 2011. GC-binding factor 2 interacts with dishevelled and regulates Wnt signaling pathways in human carcinoma cell lines. Int. J. Cancer 129: 1599-1610.
80. Goodall, A. H., P. Burns, I. Salles, I. C. Macaulay, C. I. Jones, D. Ardissino, B. de Bono, S. L. Bray, H. Deckmyn, F. Dudbridge, et al; Bloodomics Consortium. 2010. Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function. Blood 116: 4646-4656.
81. Yang, P., H. An, X. Liu, M. Wen, Y. Zheng, Y. Rui, and X. Cao. 2010. The cytosolic nucleic acid sensor LRRFIP1 mediates the production of type I interferon via a beta-catenin-dependent pathway. Nat. Immunol. 11: 487-494.
82. Li, Y., W. Li, Y. Yang, Y. Lu, C. He, G. Hu, H. Liu, J. Chen, J. He, and H. Yu. 2009. MicroRNA-21 targets LRRFIP1 and contributes to VM-26 resistance in glioblastoma multiforme. Brain Res. 1286: 13-18.
83. Dai, P., S. Y. Jeong, Y. Yu, T. Leng, W. Wu, L. Xie, and X. Chen. 2009. Modulation of TLR signaling by multiple MyD88-interacting partners including leucine-rich repeat Fli-I-interacting proteins. J. Immunol. 182: 3450-3460.
84. Rikiyama, T., J. Curtis, M. Oikawa, D. B. Zimonjic, N. Popescu, B. A. Murphy, M. A. Wilson, and A. C. Johnson. 2003. GCF2: expression and molecular analysis of repression. Biochim. Biophys. Acta 1629: 15-25.
85. Sjöblom, T., S. Jones, L. D. Wood, D. W. Parsons, J. Lin, T. D. Barber, D. Mandelker, R. J. Leary, J. Ptak, N. Silliman, et al. 2006. The consensus coding sequences of human breast and colorectal cancers. Science 314: 268-274.
86. Arakawa, R., A. Bagashev, L. Song, K. Maurer, and K. E. Sullivan. 2010. Characterization of LRRFIP1. Biochem. Cell Biol. 88: 899-906.
87. Paul, J., and J. D. Duerksen. 1975. Chromatin-associated RNA content of heterochromatin and euchromatin. Mol. Cell. Biochem. 9: 9-16.
88. Kino, T., D. E. Hurt, T. Ichijo, N. Nader, and G. P. Chrousos. 2010. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 3: ra8.
89. Hung, T., Y. Wang, M. F. Lin, A. K. Koegel, Y. Kotake, G. D. Grant, H. M. Horlings, N. Shah, C. Umbricht, P. Wang, et al. 2011. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 43: 621-629.
90. Tsai, M. C., O. Manor, Y. Wan, N. Mosammaparast, J. K. Wang, F. Lan, Y. Shi, E. Segal, and H. Y. Chang. 2010. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329: 689-693.
91. Pandey, R. R., T. Mondal, F. Mohammad, S. Enroth, L. Redrup, J. Komorowski, T. Nagano, D. Mancini-Dinardo, and C. Kanduri. 2008. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32: 232-246.
92. Kotake, Y., T. Nakagawa, K. Kitagawa, S. Suzuki, N. Liu, M. Kitagawa, and Y. Xiong. 2011. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30: 1956-1962.
93. Huarte, M., M. Guttman, D. Feldser, M. Garber, M. J. Koziol, D. Kenzelmann- Broz, A. M. Khalil, O. Zuk, I. Amit, M. Rabani, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419.
94. Simon, M. D., C. I. Wang, P. V. Kharchenko, J. A. West, B. A. Chapman, A. A. Alekseyenko, M. L. Borowsky, M. I. Kuroda, and R. E. Kingston. 2011. The genomic binding sites of a noncoding RNA. Proc. Natl. Acad. Sci. USA 108: 20497-20502.