DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins

TL;DR

DeeperBind is a deep learning model that accurately predicts DNA binding specificities of transcription factors by modeling positional dynamics and sequence contributions, outperforming existing methods on high-throughput datasets.

Contribution

The paper introduces DeeperBind, a novel deep recurrent convolutional network that improves prediction accuracy of protein-DNA binding specificities using high-throughput data.

Findings

DeeperBind achieves the most accurate predictions on PBM datasets.

The model effectively captures positional effects in DNA sequences.

It handles varying-length sequences efficiently.

Abstract

Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety of domains such as drug design and development. To address this need, several \textit{in vivo} and \textit{in vitro} techniques have been developed so far that try to characterize and predict the binding specificity of a protein to different DNA loci. The major problem with these techniques is that they are not accurate enough in prediction of the binding affinity and characterization of the corresponding motifs. As a result, downstream analysis is required to uncover the locations where proteins of interest bind. Here, we propose DeeperBind, a long short term recurrent convolutional network for prediction of protein binding specificities with respect to DNA probes. DeeperBind can model the positional dynamics of probe sequences and hence reckons with the contributions made by individual sub-regions in DNA sequences, in an effective way. Moreover, it can be trained and tested on datasets containing varying-length sequences. We apply our pipeline to the datasets derived from protein binding microarrays (PBMs), an in-vitro high-throughput technology for quantification of protein-DNA binding preferences, and present promising results. To the best of our knowledge, this is the most accurate pipeline that can predict binding specificities of DNA sequences from the data produced by high-throughput technologies through utilization of the power of deep learning for feature generation and positional dynamics modeling.