Accurate de novo transcription unit annotation from run-on and sequencing data

Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, differentiation, and disease. Run-on and sequencing assays measure the production of nascent RNAs and can provide an effective data source for discovering functional elements. However, the accurate inference of functional elements from run-on sequencing data remains an open problem because the signal is noisy and challenging to model. Here we investigated computational approaches that convert run-on and sequencing data into annotations representing transcription units, including genes and non-coding RNAs. We developed a convolutional neural network, called convolutional discovery of gene anatomy using PRO-seq (CGAP), trained to identify different anatomical features of a transcription unit, which were then stitched together into transcript annotations using a hidden Markov model (HMM). Comparison with existing methods showed a significant performance improvement using our novel CGAP-HMM approach. We developed a voting system that ensembles the top three annotation strategies, resulting in large and significant improvements in transcription unit annotation accuracy over the best performing individual method. Finally, we also explore a conditional generative adversarial network (cGAN) as a possible alternative approach to transcription unit annotation. Collectively our work provides novel tools for de novo transcription unit annotation from run-on and sequencing data that are accurate enough to be useful in many applications.