For more than a decade, studies focused on RNA interference (RNAi) pathway as a pivotal gene regulatory mechanism. RNAi components are attracting considerable interest due to the recent evidence demonstrating that they play a role not only in post-transcriptional regulation but also in transcriptional level. The involvement of RNAi components in heterochromatin formation and RNA Pol II processivity and alternative splicing in different organisms has been shown. Dicer protein, a highly conserved protein among kingdoms, is one of the main effectors in this pathway. There is a considerable amount of literature on Dicer’s role in the cytoplasm; however, there is still vast ambiguity concerning nuclear Dicer. More recent evidence reveals the existence of Dicer1 variants that are differentially expressed in some cancer cells. Our experiments set out to investigate one of these variants that we hypothesise is responsible for the nuclear function. We undertook genomic and biochemical approaches applied to HAP 1 cells as a model system to characterise Dicer1-s, taking advantage of a custom-made antibody in our research group. Here, as anticipated, our experiments proved that Dicer1-s is enriched in the nuclear compartment compared to full-length Dicer1, indicating that it might be a putative contributor to nuclear gene regulation activity. Unfortunately, it was not possible to establish a mutant cell line to investigate the significant nuclear function of Dicer1-s, due to the need for further optimisation of the methods used. Exploitation of previously optimised gene knock-out tools might accelerate shedding light on protein, DNA, and RNA partners, disclosing the exact nuclear mechanisms that might exhibit similar activity.

Polyadenylation signals in yeast are not very well defined and are believed to be largely degenerate. Here, we present a computational and experimental genome-wide analysis of polyadenylation signals in Schizosaccharomyces pombe (S. pombe), identifying the canonical AATAAA motif as the most frequent and functional signal. RNA-Seq data from cells grown under various physiological conditions were used to map 3’UTRs, which classify as commonly heterogenic. We have shown that many genes have alternative 3’UTRs. Our results are summarised and can be accessed in a user-friendly online database Pomb(A). It has been shown that convergent genes require trans elements, like Cohesin, for efficient transcription termination. We demonstrate that convergent genes lacking Cohesin are generally associated with longer overlapping transcripts. Furthermore, we analysed ChIP-chip data of Rad21 and Mis4 as well as other Cohesin and loading complex subunits and show that regions of Rad21/Mis4 co-localisation are generally associated with highly transcribed genes. They are also cohesive, while sites with Rad21 only are less cohesive. Rad21/Mis4 co-localisation sites are in close proximity to annotated origins of replication, suggesting that cohesive sites may facilitate replication. microRNAs (miRNAs) are well studies in higher eukaryotes and participate on post-transcriptional gene silencing by degrading target mRNA or blocking translation. It is believed that miRNAs do not exist in yeast. We reanalyzed miRNA presence in yeast using recently available small RNA data sets. Potential miRNA genes and targets in S. pombe were computationally predicted based on the described alternative 3’UTR data and further experimentally tested. Dicer is an enzyme, which recognizes long dsRNA substrates and cleaves them into siRNA e↵ector molecules, essential for gene silencing. Dicer has been thought to be a purely cytoplasmic protein. However, we employed ChIP-Seq and dsRNA RNA-Seq data to show that Dicer localises in the nucleus of mammalian cells and associates with the chromatin on numerous loci. Furthermore, we present evidence that Dicer processes long dsRNA into siRNA in the nucleus and the lack of Dicer causes the accumulation of long dsRNA. This consequently induces the interferon response pathway, which ultimately leads to apoptosis and cell death.