Inference of RNA binding proteins (RBP) occupancy transcriptome-wide

Supervisor: Heejung Shim

Available for: MSc and undergraduate research projects.

Location: Melbourne Integrative Genomics, University of Melbourne

Project title: Inference of RNA binding proteins (RBP) occupancy transcriptome-wide

Background: RNA binding proteins (RBP) play a key role in regulating protein translation. However, our understanding of their modes of action, transcriptome-wide binding patterns, and target motif sequence preferences remains limited. Current technologies available for studying RBP often requires laborious optimization and experimentation for each individual RBP. As a consequence, the progress in studying RBP regulation of protein translation has been slow and contradicting results are not uncommon. To address this issue, we are developing methods to increase the throughput, accuracy and precision in annotating and surveying RBP target sites genome-wide. To survey transcriptome-wide RBP binding, we are adapting Bayesian mixture models, which incorporates the binding motif sequence information and the fine structure patterns in the sequencing data (Pique-Regi et al. 2011, Raj et al. 2015), to analyze RNase footprint sequencing data (Silverman et al. 2014).

Proposed project: The on-going project includes initial data exploration and further adaptation of the existing methods for analyzing transcription factor binding based on observations made during exploratory analysis. Since transcription factors bind double-stranded DNA, the method development will incorporate features unique to RNA transcripts, such as potential secondary
structure and directionality of the motif.