Statistical inference of the rate of RNA polymerase II elongation by total RNA sequencing.

ABSTRACT:

Motivation

Sequencing total RNA without poly-A selection enables us to obtain a transcriptomic profile of nascent RNAs undergoing transcription with co-transcriptional splicing. In general, the RNA-seq reads exhibit a sawtooth pattern in a gene, which is characterized by a monotonically decreasing gradient across introns in the 5'-3' direction, and by substantially higher levels of RNA-seq reads present in exonic regions. Such patterns result from the process of underlying transcription elongation by RNA polymerase II, which traverses the DNA strand in a 5'-3' direction as it performs a complex series of mRNA synthesis and processing. Therefore, data of sequenced total RNAs could be utilized to infer the rate of transcription elongation by solving the inverse problem.

Results

SUBMITTER: Kawamura Y 

PROVIDER: S-EPMC6546130 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature