The unconventional splicing of Hac1 by the ribonuclease Ire1 is a key event in the activation of the unfolded protein response (UPR) in Saccharomyces cerevisiae. This splicing is independent of the spliceosome and is mediated by a secondary structure at the intron-exon boundaries of the mRNA. Similar unconventional splicing was also described for the gene Xbp1 in human, mouse, Caenorhabditis elegans and Drosophila melanogaster, and for Hac1 in five other fungi. We used reported RNA structures to build a multiple sequence alignment and the Infernal package to search for homologous structures. We identified homologous non-canonical intron structures in 128 out of 156 searched eukaryotic genomes. Our results show that the sequence of the Hac1/Xbp1 intron is highly conserved only around the splice sites recognized by Ire1. The consensus structure of the Hac1/Xbp1 mRNA is well conserved in Fungi and Metazoa and resembles structures previously described. We show that a typical Hac1/Xbp1 intron is very short, only 20-26 bases, whereas yeast species have a long intron (> 100 bases). We identified six species with unambiguous Hac1/Xbp1 homologs that have lost the non-canonical intron structure. We propose that these species use a different mechanism to regulate the UPR.
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blanchette, M
Kent, WJ
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kent, WJ
Riemer, C
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Riemer, C
Elnitski, L
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Elnitski, L
Smit, AFA
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Smit, AFA
Roskin, KM
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Roskin, KM
Baertsch, R
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Baertsch, R
Rosenbloom, K
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Rosenbloom, K
Clawson, H
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Clawson, H
Green, ED
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Green, ED
Haussler, D
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Haussler, D
Miller, W
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Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Univ Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, FranceUniv Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Darty, Kevin
Denise, Alain
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Univ Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Univ Paris 11, CNRS, IGM, UMR 8621, F-91405 Orsay, FranceUniv Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Denise, Alain
Ponty, Yann
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Univ Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Univ Paris 06, INSERM, U511, F-75013 Paris, FranceUniv Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
机构:Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
Gonzalez, TN
Sidrauski, C
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机构:Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
Sidrauski, C
Dörfler, S
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机构:Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
Dörfler, S
Walter, P
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Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USAUniv Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blanchette, M
Kent, WJ
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kent, WJ
Riemer, C
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Riemer, C
Elnitski, L
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Elnitski, L
Smit, AFA
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Smit, AFA
Roskin, KM
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Roskin, KM
Baertsch, R
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Baertsch, R
Rosenbloom, K
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Rosenbloom, K
Clawson, H
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Clawson, H
Green, ED
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Green, ED
Haussler, D
论文数: 0引用数: 0
h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Haussler, D
Miller, W
论文数: 0引用数: 0
h-index: 0
机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:
Univ Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, FranceUniv Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Darty, Kevin
Denise, Alain
论文数: 0引用数: 0
h-index: 0
机构:
Univ Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Univ Paris 11, CNRS, IGM, UMR 8621, F-91405 Orsay, FranceUniv Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Denise, Alain
Ponty, Yann
论文数: 0引用数: 0
h-index: 0
机构:
Univ Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
Univ Paris 06, INSERM, U511, F-75013 Paris, FranceUniv Paris 11, LRI, CNRS, UMR 8623, F-91405 Orsay, France
机构:Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
Gonzalez, TN
Sidrauski, C
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
Sidrauski, C
Dörfler, S
论文数: 0引用数: 0
h-index: 0
机构:Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
Dörfler, S
Walter, P
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USAUniv Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA