Identifying the patterns of RNA-protein interaction is key in understanding the role RNA binding proteins play in the post-transcriptional regulation of gene expression. We have developed an integrative orthogonality-regularised nonnegative matrix factorisation (iONMF) method to integrate multiple data sources and discover non-overlapping and class-specific patterns of varying abundances. Our integration of the largest compendium to date, which included 31 experimental data sets on 19 RNA binding proteins, revealed that the integration of multiple data sources improves the ability to predict interaction sites. We also identified the key predictive factors of protein-RNA interaction: RNA structure, sequence motifs and co-binding of other RNA binding proteins.
COBISS.SI-ID: 1537001923
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
This is an invited scientific commentary by the elite journal Brain on their publication ‘Serum microRNAs in patients with genetic amyotrophic lateral sclerosis and pre-manifest mutation carriers’ by Freischmidt et al. Defective RNA processing has occupied centre stage in the pathogenesis of amyotrophic lateral sclerosis (ALS) since the identification of TARDBP (also known as TDP-43) inclusions in 95% of cases and pathogenic mutations in RNA processing genes such as TARDBP, FUS and MATR3 (Sreedharan et al., 2008; Vance et al., 2009; Johnson et al., 2014). FUS and TARDBP are known to regulate mRNA transcription, splicing, stability and transport (Tollervey et al., 2011; Rogelj et al., 2012) but they are also part of the large Drosha complex that regulates microRNA (miRNA) biogenesis (Gregory et al., 2004). Dysregulation of miRNA expression has been shown in many cancers and more recently in Alzheimer’s disease and is predicted to play a mechanistic role and/or be an indirect biomarker of disease. Freischmidt et al. (2014) report that levels of a specific subset of miRNAs are reduced in the serum of patients with familial and sporadic ALS, and that these reductions are even detectable in presymptomatic carriers of pathogenic ALS mutations. If these results can be replicated in larger cohorts then this will become a landmark study.
COBISS.SI-ID: 28055335
Prerazporeditev, drugače pretežno jedrnih RNA-vezavnih proteinov, TDP-43 in FUS, v citoplazmo, je posledica motnje prenosa le-teh proteinov med jedrom in citoplazmo in je možen dogodek, ki vodi v patogenezo amiotrofične lateralne skleroze (ALS) in frontotemporalne lobarne degeneracije (FTLD). Abnormalnosti v jedrnem prenosu so bile pred kratkim povezane s ponovitvami zaporedja heksanukleotidov, gre za mutacijo, ki se nahaja v genu C9orf72 in je najpogostejši genetski vzrok za ALS in FTLD in vodi do kopičenja vključkov TDP-43 v citoplazmi. Mutacije v C9orf72 lahko motijo jedrni transport na ravni proteinov C9ORF72, RNA, ki se prepiše iz heksanukleotidne ponovitve in/ali preko proteinov, ki se prevedejo iz te RNA. V preglednem članku so opisani defekti v jedrnem transport kot možni vzroki, ki vodijo do obolenja.
COBISS.SI-ID: 29663527