Discovery of genome-wide RNA-switches


In the post-transcriptional gene regulatory network controlled by cis-regulatory elements, RNA binding motifs and miRNA target sites are most researched. However, the study of their interactions is still in its infancy. The aim of this project is to develop novel probabilistic models and methods for genome-wide discovery of cis-regulatory element interactions and deciphering their functional mechanisms. We will analyze a large amount of CLIP-seq data for the various RNA-binding proteins available at present to determine RNA binding motifs as well as miRNA target sites and to demonstrate the widespread occurrence of RNA switches controlling miRNA targeting, in cooperation and competition with RNA-binding proteins.

Recent papers related to this project:

Wen J., Parker BJ., Jacobsen A., and Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA, (2011) 17(5):820-34. IF 4.94

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Jacobson A., Wen J., Marks DS., and Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Research (2010) 20(8):1010-9. IF 15.57

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Wen J., Leucci, E., Lund, A, Krogh A. and Parker BJ. Transcriptome dynamics of the microRNA inhibition response. Nucleic Acids Research, (2015). 43(13):6207-21. IF 9.1.

Parker BJ.*, and Wen J. * Predicting microRNA targets in time-series microarray experiments via functional data analysis. BMC Bioinformatics, (2009) 10:S32. (*equal first authors.) IF 3.45

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