Search for unusual RNAs in RNA-seq data

Thesis: Bachelor, Master (if looking at both data sets)

Field: Genomics, NGS

Advisors:  Engelmann

Courses Required: Transcriptomics with RNA-seq or Sequenzing, Practical Bioinformatics II

Objective: RNA-seq, for the first time, allows to detect the expression of all RNAs, coding and non-coding, on a genome scale independent of annotation. Many novel linear RNAs like transcript isoforms have been characterized based on high throughput sequencing data, but recently also circular RNAs and trans-spliced RNAs, where parts of RNA from different strands are merged together, have been found. Their function is largely unclear. One sequence aligner, segemehl, uses multiple split read alignment and therefore is able to detect circular RNAs and trans-splicing events. In this project, segemehl is to be applied on RNA-seq data and unusual splicing events are to be identified.

Data: very deep RNA-seq data of human skin differentiation, polyA and non-polyA transcripts (coding and non-coding), deep RNA-seq of Arabidopsis  (plant)

First-Steps: get familiar with the use of segemehl, understand alternative splicing background

Questions: can you detect unusual splicing events in the human (and plant) data set? Make models of how these RNAs look like. Derive criteria for ranking the most likely candidates.

Start Reading:

"A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection" Hoffmann et al (2014) Genome Biology; genomebiology.com/2014/15/2/R34/abstract

"Detecting and characterizing circular RNAs" Jeck et al (2014) Nature Biotechnology www.nature.com/nbt/journal/v32/n5/full/nbt.2890.html