Advancement: Analyzing Macrophages polyadenylated RNAs with Oxford Nanopore Sequencing and Illumina platforms

Speaker Name: 
Rojin Safavi
Speaker Title: 
PhD Student (Advisor: Mark Akeson)
Speaker Organization: 
Biomolecular Engineering & Bioinformatics
Start Time: 
Thursday, August 30, 2018 - 10:00am
End Time: 
Thursday, August 30, 2018 - 12:00pm
Location: 
Physical Sciences, Room 305
Organizer: 
Mark Akeson

Abstract:  Macrophages are the key component of the innate immune system. They are best known for their roles in phagocytosis, a process which involves ingestion of parasites and microbes. Macrophages activation upon bacterial endotoxin detection leads to expression of highly coordinated genes. Through differential gene expression analysis, scientists have identified mRNAs and long noncoding RNAs (lncRNAs) that play critical regulatory roles in macrophages inflammatory pathways. To aid this growing field, the proposed research uses Nanopore direct RNA sequencing technology to analyze mouse macrophages poly-adenylated RNAs in three areas; detecting novel intergenic lncRNAs (lincRNAs), identifying A-to-I conversion through the raw signal, and differential gene expression analysis. Nanopore direct RNA sequencing technology is the only sequencing platform that is capable of sequencing polyadenylated RNA molecules directly, without cDNA synthesis and PCR! amplification. This novel technology brings in the advantage of sequencing native RNA molecules in real-time, without suffering from PCR amplification bias. Using macrophages direct RNA sequencing data, first I propose a computational method to classify lincRNAs into potential novel lincRNAs, annotated lincRNAs, and novel lincRNA isoforms. Second, I propose a contextual detection of A-to-I editing in mouse macrophage poly-A RNA by generating a training set that will be used to train the signalAlign [1] HMM-HDP model and an ensemble learner. Third, I will assess the Nanopore direct RNA sequencing performance in detecting differentially expressed genes compared to Illumina.