Modeling RNA Splicing Kinetics

Kayla McCue, Massachusetts Institute of Technology

Messenger RNAs, commonly known as mRNAs, represent an intermediate step in the process of translating DNA sequences into proteins in the cell and are therefore a vital component of life as we know it. In eukaryotic organisms there are processing steps that typically occur between the initial transcription of the DNA into RNA and the formation of a functional, mature mRNA. One such step is splicing, in which regions of the RNA transcript, known as introns, are removed in order to produce the proper mature transcript. In animals, this process of intron removal may be a rate-limiting step in maturation, with intron splicing half-lives on the order of minutes. By comparison, fully matured mRNAs generally have half-lives on the order of hours, making these transient unspliced intermediates comparatively difficult to observe or study.

Using data from a metabolic-labeling and high-throughput RNA-sequencing strategy in Drosophila S2 cells, we were able to observe transcripts that have been elongated in a relatively short time window – including partially transcribed and incompletely spliced mRNA transcripts. The complexity introduced by the mixture of these transcripts necessitates the development of new analyses for the data. We developed a mathematical model to estimate the contribution of reads from: (1) incompletely transcribed transcripts, (2) incompletely spliced transcripts, and (3) spliced transcripts. Using these estimations and characterizing intron splicing as a first-order decay process, we analyzed the dataset in order to estimate the splicing kinetics for each intron in all sufficiently expressed Drosophila genes. To test the efficacy of this modeling framework, we simulated data over a range of half-lives and assessed our ability to recover the correct value.

Abstract Author(s): Kayla McCue, Athma Pai, Chris Burge