A kinetic-dynamic model for regulatory RNA processing.
A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.
Singh
Sher
S
National Taiwan University Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC.
Yang
Hsiu-Yi Ou
HY
Chen
Mei-Ying
MY
Yu
Sung-Liang
SL
D007700:Kinetics; D008954:Models, Biological; D017346:Protein Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism*; D012326:RNA Splicing / Q000502:physiology*; D000072260:RNA Splicing Factors; D020871:RNA Stability / Q000502:physiology*; D017414:Ribonucleoprotein, U4-U6 Small Nuclear / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
D012322:RNA Precursors; D000072260:RNA Splicing Factors; D017414:Ribonucleoprotein, U4-U6 Small Nuclear; D029701:Saccharomyces cerevisiae Proteins; C083212:PRP4 protein, S cerevisiae; D017346:Protein Serine-Threonine Kinases