Workshop on Non-coding RNA, targets, and high-throughput sequence data

University of Copenhagen, at Feb 02 09:30 am, LIFE, Room A1-01.15, Bülowsvej 17, 1st Floor, Frederiksberg

Registration is not necessary. Refreshments will be served.


09:30-10:15 State-of-the-art in RNA secondary structure analysis and prediction of RNA-RNA interactions
Rolf Backofen, Dept. of Bioinformatics, University of Freiburg, Germany

Abstract: During the last few years, a multitude of regulatory non-coding RNAs (ncRNAs) have been discovered. Many of these act as post-transcriptional regulators by base pairing to a target mRNA, causing mRNA cleavage or translational repression or activation. We will discuss two problem related to ncRNA.
The first task is related to the problem of detecting and classifying ncRNAs. The main basis for this task are comparison methods that are based on both sequence and structure to determine conserved RNA-motifs, and we will discuss problems and approaches related to this problem.
The second task is the computational detection of possible targets since experimental verification of targets is difficult. Many existing target prediction programs neglect intra-molecular binding, while other approaches are either specialized to certain types of ncRNAs or too slow for genome-wide searches. We introduce a new fast and general approach to the prediction of RNA-RNA interactions incorporating accessibility of target sites as well as the existence of a user-definable seed. We further discuss approaches that can handle more complex RNA-RNA interaction structures.

10:15-10:30 Break

10:30-11:15 Beyond microRNAs: Treasures in short-read sequencing data
Peter F. Stadler, Dept of Bioinformatics, University of Leipzig

Abstract: Current methods for high throughput sequencing offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. Primarily focussed at quantifying microRNA expression, extensive datasets of small RNAs with a length of less than 30nt are being produced. These data sets turn out to be a rich treasure trove of information on novel RNA classes as well as details of RNA processing.
The well-known classes of structured ncRNAs, including snoRNAs, snRNAs, and tRNAs, undergo maturation processes that lead to the production of shorter RNAs that are similar to mature microRNAs. The corresponding read patterns are largely determined by the parental structure. They can be employed, therefore, for the detection of new housekeeping ncRNAs from short-read libraries. In addition these data sets also contain novel classes of short RNAs such as microRNA-offset RNAs (moRNAs). Surprisingly, microRNA precursors that also produce moRNAs are typically evolutionarily old.
Many aspects of the RNA maturation, furthermore, leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. In particular, chemical modifications leave their signatures in forms of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures focusing on particular types of deviations can help to unravel post-transcriptional modification, maturation and degradation processes.  Starting from the recovery of many well-known modified sites in tRNAs we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which, surprisingly, can be found in a diverse collection of transcripts, including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.