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Article

Effects of Combined Tristetraprolin/Tumor Necrosis Factor Receptor Deficiency on the Splenic Transcriptome

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Pages 1395-1411 | Received 09 Dec 2015, Accepted 23 Feb 2016, Published online: 17 Mar 2023

REFERENCES

  • Brewer BY, Malicka J, Blackshear PJ, Wilson GM. 2004. RNA sequence elements required for high affinity binding by the zinc finger domain of tristetraprolin: conformational changes coupled to the bipartite nature of Au-rich MRNA-destabilizing motifs. J Biol Chem 279:27870–27877. http://dx.doi.org/10.1074/jbc.M402551200.
  • Worthington MT, Pelo JW, Sachedina MA, Applegate JL, Arseneau KO, Pizarro TT. 2002. RNA binding properties of the AU-rich element-binding recombinant Nup475/TIS11/tristetraprolin protein. J Biol Chem 277:48558–48564. http://dx.doi.org/10.1074/jbc.M206505200.
  • Blackshear PJ, Lai WS, Kennington EA, Brewer G, Wilson GM, Guan X, Zhou P. 2003. Characteristics of the interaction of a synthetic human tristetraprolin tandem zinc finger peptide with AU-rich element-containing RNA substrates. J Biol Chem 278:19947–19955. http://dx.doi.org/10.1074/jbc.M301290200.
  • Lai WS, Carrick DM, Blackshear PJ. 2005. Influence of nonameric AU-rich tristetraprolin-binding sites on mRNA deadenylation and turnover. J Biol Chem 280:34365–34377. http://dx.doi.org/10.1074/jbc.M506757200.
  • Lai WS, Perera L, Hicks SN, Blackshear PJ. 2014. Mutational and structural analysis of the tandem zinc finger domain of tristetraprolin. J Biol Chem 289:565–580. http://dx.doi.org/10.1074/jbc.M113.466326.
  • Lai WS, Kennington EA, Blackshear PJ. 2003. Tristetraprolin and its family members can promote the cell-free deadenylation of AU-rich element-containing mRNAs by poly(A) ribonuclease. Mol Cell Biol 23:3798–3812. http://dx.doi.org/10.1128/MCB.23.11.3798-3812.2003.
  • Taylor GA, Carballo E, Lee DM, Lai WS, Thompson MJ, Patel DD, Schenkman DI, Gilkeson GS, Broxmeyer HE, Haynes BF, Blackshear PJ. 1996. A pathogenetic role for TNF alpha in the syndrome of cachexia, arthritis, and autoimmunity resulting from tristetraprolin (TTP) deficiency. Immunity 4:445–454. http://dx.doi.org/10.1016/S1074-7613(00)80411-2.
  • Carballo E, Blackshear PJ. 2001. Roles of tumor necrosis factor-alpha receptor subtypes in the pathogenesis of the tristetraprolin-deficiency syndrome. Blood 98:2389–2395. http://dx.doi.org/10.1182/blood.V98.8.2389.
  • Lai WS, Carballo E, Strum JR, Kennington EA, Phillips RS, Blackshear PJ. 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. http://dx.doi.org/10.1128/MCB.19.6.4311.
  • Carballo E, Lai WS, Blackshear PJ. 1998. Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science 281:1001–1005. http://dx.doi.org/10.1126/science.281.5379.1001.
  • Brooks SA, Blackshear PJ. 2013. Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. Biochim Biophys Acta 1829:666–679. http://dx.doi.org/10.1016/j.bbagrm.2013.02.003.
  • Ross CR, Brennan-Laun SE, Wilson GM. 2012. Tristetraprolin: roles in cancer and senescence. Ageing Res Rev 11:473–484. http://dx.doi.org/10.1016/j.arr.2012.02.005.
  • Sanduja S, Blanco FF, Young LE, Kaza V, Dixon DA. 2012. The role of tristetraprolin in cancer and inflammation. Front Biosci (Landmark Ed) 17:174–188. http://dx.doi.org/10.2741/3920.
  • Ciais D, Cherradi N, Feige JJ. 2013. Multiple functions of tristetraprolin/TIS11 RNA-binding proteins in the regulation of mRNA biogenesis and degradation. Cell Mol Life Sci 70:2031–2044. http://dx.doi.org/10.1007/s00018-012-1150-y.
  • Lai WS, Stumpo DJ, Kennington EA, Burkholder AB, Ward JM, Fargo DL, Blackshear PJ. 2013. Life without TTP: apparent absence of an important anti-inflammatory protein in birds. Am J Physiol Regul Integr Comp Physiol 305:R689–R700. http://dx.doi.org/10.1152/ajpregu.00310.2013.
  • Cao H, Tuttle JS, Blackshear PJ. 2004. Immunological characterization of tristetraprolin as a low abundance, inducible, stable cytosolic protein. J Biol Chem 279:21489–21499. http://dx.doi.org/10.1074/jbc.M400900200.
  • Chen G, Goeddel DV. 2002. TNF-R1 signaling: a beautiful pathway. Science 296:1634–1635. http://dx.doi.org/10.1126/science.1071924.
  • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. http://dx.doi.org/10.1186/gb-2009-10-3-r25.
  • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36. http://dx.doi.org/10.1186/gb-2013-14-4-r36.
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
  • Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. http://dx.doi.org/10.1093/bioinformatics/btq033.
  • Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. 2010. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26:2204–2207. http://dx.doi.org/10.1093/bioinformatics/btq351.
  • Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. 2013. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31:46–53. http://dx.doi.org/10.1038/nbt.2450.
  • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc B Met 57:289–300.
  • Lai WS, Stumpo DJ, Blackshear PJ. 1990. Rapid insulin-stimulated accumulation of an mRNA encoding a proline-rich protein. J Biol Chem 265:16556–16563.
  • Blackshear PJ, Manzella JM, Stumpo DJ, Wen L, Huang JK, Oyen O, Young WS, III. 1989. High level, cell-specific expression of ornithine decarboxylase transcripts in rat genitourinary tissues. Mol Endocrinol 3:68–78. http://dx.doi.org/10.1210/mend-3-1-68.
  • Young WS, III, Mezey E, Siegel RE. 1986. Quantitative in situ hybridization histochemistry reveals increased levels of corticotropin-releasing factor mRNA after adrenalectomy in rats. Neurosci Lett 70:198–203. http://dx.doi.org/10.1016/0304-3940(86)90463-5.
  • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80. http://dx.doi.org/10.1186/gb-2004-5-10-r80.
  • Smyth G. 2005. Limma: linear models for microarray data, p 397–420. In Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S (ed), Bioinformatics and computational biology solutions using R and Bioconductor. Springer, New York, NY.
  • Law CW, Chen Y, Shi W, Smyth GK. 2014. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15:R29. http://dx.doi.org/10.1186/gb-2014-15-2-r29.
  • Altboum Z, Steuerman Y, David E, Barnett-Itzhaki Z, Valadarsky L, Keren-Shaul H, Meningher T, Mendelson E, Mandelboim M, Gat-Viks I, Amit I. 2014. Digital cell quantification identifies global immune cell dynamics during influenza infection. Mol Syst Biol 10:720. http://dx.doi.org/10.1002/msb.134947.
  • Lai WS, Parker JS, Grissom SF, Stumpo DJ, Blackshear PJ. 2006. Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts. Mol Cell Biol 26:9196–9208. http://dx.doi.org/10.1128/MCB.00945-06.
  • Blackshear PJ, Phillips RS, Ghosh S, Ramos SB, Richfield EK, Lai WS. 2005. Zfp36l3, a rodent X chromosome gene encoding a placenta-specific member of the Tristetraprolin family of CCCH tandem zinc finger proteins. Biol Reprod 73:297–307. http://dx.doi.org/10.1095/biolreprod.105.040527.
  • Carballo E, Gilkeson GS, Blackshear PJ. 1997. Bone marrow transplantation reproduces the tristetraprolin-deficiency syndrome in recombination activating gene-2 (−/−) mice. Evidence that monocyte/macrophage progenitors may be responsible for TNFalpha overproduction. J Clin Invest 100:986–995.
  • Qiu LQ, Stumpo DJ, Blackshear PJ. 2012. Myeloid-specific tristetraprolin deficiency in mice results in extreme lipopolysaccharide sensitivity in an otherwise minimal phenotype. J Immunol 188:5150–5159. http://dx.doi.org/10.4049/jimmunol.1103700.
  • Kratochvill F, Machacek C, Vogl C, Ebner F, Sedlyarov V, Gruber AR, Hartweger H, Vielnascher R, Karaghiosoff M, Rulicke T, Muller M, Hofacker I, Lang R, Kovarik P. 2011. Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation. Mol Syst Biol 7:560. http://dx.doi.org/10.1038/msb.2011.93.
  • Molle C, Zhang T, Ysebrant de Lendonck L, Gueydan C, Andrianne M, Sherer F, Van Simaeys G, Blackshear PJ, Leo O, Goriely S. 2013. Tristetraprolin regulation of interleukin 23 mRNA stability prevents a spontaneous inflammatory disease. J Exp Med 210:1675–1684. http://dx.doi.org/10.1084/jem.20120707.
  • Qiu LQ, Lai WS, Bradbury A, Zeldin DC, Blackshear PJ. 2015. Tristetraprolin (TTP) coordinately regulates primary and secondary cellular responses to proinflammatory stimuli. J Leukoc Biol 97:723–736. http://dx.doi.org/10.1189/jlb.3A0214-106R.
  • Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. 2014. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci U S A 111:16219–16224. http://dx.doi.org/10.1073/pnas.1408886111.
  • Darshan D, Frazer DM, Anderson GJ. 2010. Molecular basis of iron-loading disorders. Expert Rev Mol Med 12:e36. http://dx.doi.org/10.1017/S1462399410001687.
  • Bayeva M, Khechaduri A, Puig S, Chang HC, Patial S, Blackshear PJ, Ardehali H. 2012. mTOR regulates cellular iron homeostasis through tristetraprolin. Cell Metab 16:645–657. http://dx.doi.org/10.1016/j.cmet.2012.10.001.
  • Puig S, Askeland E, Thiele DJ. 2005. Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. Cell 120:99–110. http://dx.doi.org/10.1016/j.cell.2004.11.032.
  • Puig S, Vergara SV, Thiele DJ. 2008. Cooperation of two mRNA-binding proteins drives metabolic adaptation to iron deficiency. Cell Metab 7:555–564. http://dx.doi.org/10.1016/j.cmet.2008.04.010.
  • Meguro K, Igarashi K, Yamamoto M, Fujita H, Sassa S. 1995. The role of the erythroid-specific delta-aminolevulinate synthase gene expression in erythroid heme synthesis. Blood 86:940–948.
  • Theurl I, Aigner E, Theurl M, Nairz M, Seifert M, Schroll A, Sonnweber T, Eberwein L, Witcher DR, Murphy AT, Wroblewski VJ, Wurz E, Datz C, Weiss G. 2009. Regulation of iron homeostasis in anemia of chronic disease and iron deficiency anemia: diagnostic and therapeutic implications. Blood 113:5277–5286. http://dx.doi.org/10.1182/blood-2008-12-195651.
  • Weiss G, Goodnough LT. 2005. Anemia of chronic disease. N Engl J Med 352:1011–1023. http://dx.doi.org/10.1056/NEJMra041809.
  • Gay L, Karfilis KV, Miller MR, Doe CQ, Stankunas K. 2014. Applying thiouracil tagging to mouse transcriptome analysis. Nat Protoc 9:410–420. http://dx.doi.org/10.1038/nprot.2014.023.

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