Ancient nature of alternative splicing and functions of introns

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Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron length of the gene. Introns with tendency to be retained had either stop codons or length of 3n+1 or 3n+2 presumably triggering nonsense-mediated mRNA decay (NMD), but introns ... continued below

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Zhou, Kemin; Salamov, Asaf; Kuo, Alan; Aerts, Andrea & Grigoriev, Igor March 21, 2011.

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Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron length of the gene. Introns with tendency to be retained had either stop codons or length of 3n+1 or 3n+2 presumably triggering nonsense-mediated mRNA decay (NMD), but introns retained in major isoforms (0.2-6percent of all introns) were biased toward 3n length and stop codon free. Stopless introns were biased toward phase 0, but 3n introns favored phase 1 that introduced more flexible and hydrophilic amino acids on both ends of introns which would be less disruptive to protein structure. We proposed a model in which minor RI intron could evolve into major RI that could facilitate intron loss through exonization.

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  • DOE JGI User Meeting, Walnut Creek, CA, March 21-24, 2011

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  • Report No.: LBNL-4520E-Poster
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 1015997
  • Archival Resource Key: ark:/67531/metadc839650

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  • March 21, 2011

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  • May 19, 2016, 3:16 p.m.

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  • June 15, 2016, 6:44 p.m.

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Zhou, Kemin; Salamov, Asaf; Kuo, Alan; Aerts, Andrea & Grigoriev, Igor. Ancient nature of alternative splicing and functions of introns, article, March 21, 2011; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc839650/: accessed April 23, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.