An evolutionary model for protein-coding regions with conserved RNA structure

Molecular Biology and Evolution
Jakob Skou PedersenJotun Hein

Abstract

Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume evolutionary independence between short nucleotide tuples. In our model we address this by replacing context dependencies within codons by annotation-specific heterogeneity in the substitution process. Through a general procedure, we fragment the alignment into sets of short nucleotide tuples based on both the protein coding and the structural annotation. These individual tuples are assumed to evolve independently, and the different tuple sets are assigned different annotation-specific substitution models shared between their members. This allows us to build a composite model of the substitution process from components of traditiona...Continue Reading

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Citations

Jan 19, 2008·Theory in Biosciences = Theorie in Den Biowissenschaften·Athanasius F BompfünewererChristina Witwer
Jul 15, 2009·Omics : a Journal of Integrative Biology·Petr O IlyinskiiAlexander M Shneider
Dec 8, 2005·Bioinformatics·Tanja Gesell, Arndt von Haeseler
Apr 15, 2006·Bioinformatics·Stephen McCauley, Jotun Hein
Sep 28, 2004·Nucleic Acids Research·Jakob Skou PedersenJotun Hein
Jun 15, 2007·Genome Research·Stefan WashietlPeter F Stadler
Oct 14, 2011·Algorithms for Molecular Biology : AMB·Markus E NebelFrank Weinberg
Oct 18, 2013·RNA·Daniel LaiIrmtraud M Meyer
Apr 22, 2006·PLoS Computational Biology·Jakob Skou PedersenDavid Haussler
May 9, 2014·Nucleic Acids Research·Daniel Lai, Irmtraud M Meyer
Aug 31, 2010·Virus Research·Michael P MurtaughFrederick C-C Leung
Mar 3, 2010·New Biotechnology·Ebbe Sloth Andersen
May 20, 2008·Current Opinion in Structural Biology·Irmtraud M Meyer
Dec 15, 2016·BMC Bioinformatics·Amir H BayeganPeter Clote
May 25, 2006·Molecular Biology and Evolution·Jiaye Yu, Jeffrey L Thorne
Dec 10, 2020·Viruses·Franziska HufskyVolker Thiel

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