By analyzing high-throughput sequencing data, we have shown that genes active in human brain have a tendency to be longer than in other tissues. We have shown that longest introns in some of these genes are removed in two splicing steps by employing recursive splicing, a mechanism previously only seen in Drosophila. By performing sequence analysis, we found that for recursive splicing to work, a recursive splice site (RS) signal is required. We found that such site also requires a cryptic exon, and is normally removed without a trace. However, when two cryptic exons are present, recursive splicing is inefficient, which leads to their inclusion and results in an aberrant transcript that becomes recognized by a machinery that degrades this transcript. We postulate that this may serve as a binary switch for the quality control of new, cryptic isoforms, and as a checkpoint for the evolution of new transcripts. Many of the identified genes are linked to autism and other neurological disorders.
COBISS.SI-ID: 1536358339
The iCLIP method uses ultraviolet light to crosslink RNA-binding proteins to RNA. Before sequencing, crosslinked fragments are reverse transcribed. The reverse transcription terminates at the crosslinked site, which allows the detection of crosslinked sites at a nucleotide resolution. Detected crosslinked sites are thus expected to cluster within a narrow region, which should be close to the site of direct protein-RNA interaction site. In the publication, we show that for several RNA-binding proteins, the positions of detected sites depend on the length of the sequenced fragments, and are usually shifted upstream of the known RNA-binding sites. We have developed a software tool (http://biolab.si/iCLIPro) that identifies such shifts and can be used to improve the positioning of RBP binding sites.
COBISS.SI-ID: 1536523459
Here we present a proteomic study to analyze the effect of loss of TDP-43 on the proteome. MS data are available via ProteomeXchange with identifier PXD001668. Our results indicate that TDP-43 is an important regulator of RNA metabolism and intracellular transport. We show that Ran-binding protein 1 (RanBP1), DNA methyltransferase 3 alpha (Dnmt3a) and chromogranin B (CgB) are downregulated upon TDP-43 knockdown. Subsequently, transportin 1 level is increased as a result of RanBP1 depletion. Improper regulation of these proteins and the subsequent disruption of cellular processes may play a role in the pathogenesis of the TDP-43 proteinopathies ALS and FTLD.
COBISS.SI-ID: 28427047