Jernej Ule

The paper introduces an improved CLIP protocol (iiCLIP) that produces more specific RNA binding site datasets compared to existing methods.

The paper shows that m6A modification affects alternative intron/exon inclusion in nascent RNA by disrupting splicing when METTL3 is depleted.

The paper introduces a Cas9-based method and software tool to efficiently deplete rRNA/ncRNA contaminants from Ribo-seq libraries, significantly increasing useful reads while minimizing off-target effects.

The paper identifies that most intergenic RNA originates from fuzzy transcription of known genes, with a smaller portion from long non-coding RNA loci, and characterizes their transcriptional features and degradation patterns.

The paper shows that ALS/FTD risk variants in UNC13A increase sensitivity to TDP-43 depletion by promoting cryptic exon inclusion and protein loss.

The paper identifies LIN28A as a key factor in mRNA decay during epiblast morphogenesis, linking cell identity changes to embryonic growth through nucleo-cytoplasmic translocation.

psiCLIP identifies dynamic RNA binding patterns of spliceosomal helicases before and after exon ligation, revealing their interactions with auxiliary factors.

The paper uses spliceosome iCLIP to map human spliceosome engagement with snRNAs and pre-mRNAs, identifying over 50,000 branchpoints and their associated splicing factor binding patterns.

The paper investigates FUS mislocalization in ALS, finding it occurs in both VCP-mutation related and sporadic ALS, and links it to aberrant intron retention in SFPQ transcripts.

The paper identifies DENR-dependent translation reinitiation events and links uORF usage to circadian clock regulation by analyzing ribosome profiling data in DENR-deficient cells.

The paper shows that LINE repeat sequences recruit RNA-binding proteins to repress splicing and 3' end processing in introns, contributing to lineage-specific RNA processing in mammals.

The paper identifies post-transcriptional changes during motor neurogenesis in ALS models, showing premature intron retention in VCP-mutant cells and similar effects in SOD1 and FUS mutations.

The paper evaluates computational methods for analyzing CLIP data to understand protein-RNA interactions and assesses their impact on regulatory insights.