关于真核生物mRNA降解及代谢过程的计算机模拟资料.ppt

关于真核生物mRNA降解及代谢过程的计算机模拟;Dan Cao and Roy Parker Howard Hughes Medical Institute Department of Molecular Cellular Biology University of Arizona;DNA;Why want to model this process?;Why want to model this process(Cont’d)? ;Major assumptions;;rates for all steps;A sample screenshot;Determine the fitness of the model with the in vivo decay network: MFA2pG PGK1pG;Comparison of modeling results with experimental observations;Modeling of MFA2pG in transcriptional pulse chase;Modeling of PGK1pG in transcriptional pulse chase;The fact that we can reproduce the experimental results by modeling suggests that our model is quite accurate, and we have a relatively robust understanding of the in vivo process. The obtaining of a good model for both MFA2pG and PGK1pG allows us to further analyze the whole network. We have used our model to examine how transcripts respond to a variety of perturbations by performing a series of in silico experiments. E.g.: increase or decrease the rate of transport, deadenylation, decapping, 5’ to 3’ exonucleolytic decay, 3’ to 5’ exonucleolytic decay…, see how the transcript level, half-life, steady state distribution are affected. ;What have we learned?;Comparison of in silico mutants;3’ to 5’ decay rate for full length. Obtained by matching the calculated t ? with the observed t ? in dcp1? mutant.;Half-life. Measured by transcriptional shut-off experiment. At the point where transcript reaches half of its initial level. t ? is thought to represent how long the mRNA is persist in the cell. Average life span. Calculated from the simulation for transcriptional pulse chase experiment. More accurate representation of the average time the mRNA is present in the cell.;The difference is due to the distribution of mRNA at steady state. Certain % of mRNAs has already passed several decay steps.;The measurement of measure a half-life can predominantly different steps in the decay network;Different mRNAs will be affected differentially by certain change on