Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.

ABSTRACT: Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles because of differences in transcription time, degradation rate, and RNA-processing kinetics. Recent studies have shown that a splicing-associated RNA production delay can be significant. To investigate this issue more generally, it is useful to develop methods applicable to genome-wide datasets. We introduce a joint model of transcriptional activation and mRNA accumulation that can be used for inference of transcription rate, RNA production delay, and degradation rate given data from high-throughput sequencing time course experiments. We combine a mechanistic differential equation model with a nonparametric statistical modeling approach allowing us to capture a broad range of activation

SUBMITTER: Honkela A 

PROVIDER: S-EPMC4620908 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature