Conserved RNA structures in the non-canonical Hac1/Xbp1 intron

RNA Biology

Volumn 8, Issue 4, 2011, Pages 552-556

  Hooks, Katarzyna B ^a   Griffiths Jones, Sam ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

HAC1; Intron; RNA structure; Splicing; Unfolded protein response; XBP1

Indexed keywords

RNA; X BOX BINDING PROTEIN 1;

ARTICLE; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; FUNGAL GENE; HAC1 GENE; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA SPLICING; RNA STRUCTURE; SEQUENCE HOMOLOGY;

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; FUNGI; METAZOA; SACCHAROMYCES CEREVISIAE;

EID: 79960079763     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.8.4.15396     Document Type: Article

References (27)

1. Hotamisligil GS. Endoplasmic reticulum stress and the inflammatory basis of metabolic disease. Cell 2010; 140:900-17.
2. Uemura A, Oku M, Mori K, Yoshida H. Unconventional splicing of XBP1 mRNA occurs in the cytoplasm during the mammalian unfolded protein response. J Cell Sci 2009; 122:2877-86.
3. Sidrauski C, Walter P. The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell 1997; 90:1031-9. (Pubitemid 27408517)
4. Kawahara T, Yanagi H, Yura T, Mori K. Endoplasmic reticulum stress-induced mRNA splicing permits synthesis of transcription factor Hac1p/Ern4p that activates the unfolded protein response. Mol Biol Cell 1997; 8:1845-62. (Pubitemid 27451106)
5. Cox JS, Walter P. A novel mechanism for regulating activity of a transcription factor that controls the unfolded protein response. Cell 1996; 87:391-404. (Pubitemid 26374314)
6. Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Cell 2001; 107:881-91. (Pubitemid 34084979)
7. Tirasophon W, Welihinda AA, Kaufman RJ. A stress response pathway from the endoplasmic reticulum to the nucleus requires a novel bifunctional protein kinase/endoribonuclease (Ire1p) in mammalian cells. Genes Dev 1998; 12:1812-24. (Pubitemid 28304334)
8. Calfon M, Zeng H, Urano F, Till JH, Hubbard SR, Harding HP, et al. IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA. Nature 2002; 415:92-6. (Pubitemid 34062456)
9. Saloheimo M, Valkonen M, Penttila M. Activation mechanisms of the HAC1-mediated unfolded protein response in filamentous fungi. Mol Microbiol 2003; 47:1149-61. (Pubitemid 36232808)
10. Wimalasena TT, Enjalbert B, Guillemette T, Plumridge A, Budge S, Yin Z, et al. Impact of the unfolded protein response upon genome-wide expression patterns and the role of Hac1 in the polarized growth, of Candida albicans. Fungal Genet Biol 2008; 45:1235-47.
11. Oh MH, Cheon SA, Kang HA, Kim JY. Functional characterization of the unconventional splicing of Yarrowia lipolytica HAC1 mRNA induced by unfolded protein response. Yeast 2010; 27:443-52.
12. Guerfal M, Ryckaert S, Jacobs PP, Ameloot P, Van Craenenbroeck K, Derycke R, Callewaert N. The HAC1 gene from Pichia pastoris: characterization and effect of its overexpression on the production of secreted, surface displayed and membrane proteins. Microb Cell Fact 2010; 9:49.
13. Shen X, Ellis RE, Lee K, Liu CY, Yang K, Solomon A, et al. Complementary signaling pathways regulate the unfolded protein response and are required for C. elegans development. Cell 2001; 107:893-903. (Pubitemid 34084980)
14. Ryoo HD, Domingos PM, Kang MJ, Steller H. Unfolded protein response in a Drosophila model for retinal degeneration. EMBO J 2007; 26:242-52. (Pubitemid 46094715)
15. Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proc Natl Acad Sci USA 2006; 103:9566-71. (Pubitemid 43955865)
16. Gonzalez TN, Sidrauski C, Dorfler S, Walter P. Mechanism of non-spliceosomal mRNA splicing in the unfolded protein response pathway. EMBO J 1999; 18:3119-32. (Pubitemid 29255620)
17. Ruegsegger U, Leber JH, Walter P. Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell 2001; 107:103-14. (Pubitemid 32972041)
18. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, et al. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 2009; 37:555-9.
19. Griffiths-Jones S. RALEE - RNA ALignment editor in Emacs. Bioinformatics 2005; 21:257-9. (Pubitemid 40202027)
20. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999; 288:911-40. (Pubitemid 29248642)
21. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004; 14:708-15. (Pubitemid 38500244)
22. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 2010; 38:613-9.
23. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335-7.
24. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009; 37:136-40.
25. Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25:1974-5.
26. Fitzpatrick DA, Logue ME, Stajich JE, Butler G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 2006; 6:99.
27. Gerlach D, Wolf M, Dandekar T, Muller T, Pokorny A, Rahmann S. Deep metazoan phylogeny. In Silico Biol 2007; 7:151-4. (Pubitemid 47335230)