Linked Life Data

15585129

Source:http://linkedlifedata.com/resource/pubmed/id/15585129

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
10
pubmed:dateCreated
2004-12-9
pubmed:abstractText
During mitochondrial replication, spontaneous mutations occur and accumulate asymmetrically during the time spent single stranded by the heavy strand (DssH). The predominant mutations appear to be deaminations from adenine to hypoxanthine (A --> H, which leads to an A --> G substitution) and cytosine to thymine (C --> T). Previous findings indicated that C --> T substitutions accumulate rapidly and then saturate at high DssH, suggesting protection or repair, whereas A --> G accumulates linearly with DssH. We describe here the implementation of a simple hidden Markov model (HMM) of among-site rate correlations to provide an almost continuous profile of the asymmetry in substitution response for any particular substitution type. We implement this model using a phylogeny-based Bayesian Markov chain Monte Carlo (MCMC) approach. We compare and contrast the relative asymmetries in all 12 possible substitution types, and find that the observed transition substitution responses determined using our new method agree quite well with previous predictions of a saturating curve for C --> T transition substitutions and a linear accumulation of A --> G transitions. The patterns seen in transversion substitutions show much lower among-site variation, and are nonlinear and more complex than those seen in transitions. We also find that, after accounting for the principal linear effect, some of the residual variation in A --> G/G --> A response ratios is explained by the average predicted nucleic acid secondary structure propensity at a site, possibly due to protection from mutation when secondary structure forms.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Oct
pubmed:issn
1044-5498
pubmed:author
pubmed:issnType
Print
pubmed:volume
23
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
707-14
pubmed:dateRevised
2011-9-26
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes.
pubmed:affiliation
Biological Computation and Visualization Center, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't