Alternative splicing is the process of producing a variety of transcripts from one and the same gene. This adds further possible variability to gene expression and can in theory mean that one protein coding gene can produce multiple proteins with potentially different functions. Therefore, to understand the function of a gene, alternative splicing must be accounted for. However, this is made more complex by the fact that the existence of different messenger RNA isoforms does not necessarily entail different protein isoforms, which in turn means that an analysis of both the transcripts and final protein is necessary. Far Upstream Element Binding Protein 1 Like 1 (FUBL-1, or C12D8.1) is an RNA binding protein in Caenorhabditis elegans which is believed to take part in gene regulation, and which seemingly interacts within an argonaut effector pathway called ERGO-1. The gene has five proposed isoforms for which there are varying amounts of RNA data but only the first isoform, FUBL-1a has proteomics data available. In other words, different messenger RNA isoforms exist but it is unclear which are translated into protein. In this study, I have looked at fubl-1 and its isoforms to gain further understanding of this protein. This entailed both analysing long read RNA sequencing data to identify messenger RNA isoforms as well as a laboratory analysis of the protein to look for protein isoforms. I found evidence for all isoforms existing as messenger RNAs, and fubl-1a was by far the most highly expressed. In my protein analysis, I found indications of different isoforms, but not conclusive evidence.

<p>3’ end cleavage and polyadenylation are important steps in the maturation of eukaryotic mRNAs. Poly(A) polymerase (PAP), the enzyme catalysing the addition of adenosine residues, exists in multiple isoforms. In this study the functional significance of multiple poly(A) polymerases have been investigated. It is concluded (i) that at least three mechanisms generate the multiple isoforms i.e. gene duplication, post-translational modification and alternative mRNA processing and (ii) that the different isoforms of poly(A) polymerases have different catalytic properties. The study highlights regulation of poly(A) polymerase activity through modulation of its affinity for the substrate as visualised by the K_M parameter. We suggest that trans-acting factors modulating the K_M of poly(A) polymerase will play important roles in regulating its activity.</p><p>A new human poly(A) polymerase (PAPγ) encoded by the PAPOLG gene was identified. PAPγ is 65% homologous to the previously identified PAP. In human cells three isoforms of poly(A) polymerases being 90, 100 and 106 kDa in sizes are present. These native isoforms were purified. The PAPOLA gene encoded the 100 and 106 kDa isoforms while the 90 kDa isoform was encoded by the PAPOLG gene. Native PAPγ was found to be more active than 100 kDa PAP while the hyperphosphorylated 106 kDa PAP isoform was comparably inactive due to a 500-fold decrease in affinity for the RNA substrate. </p><p>The PAPOLG gene was shown to encode one unique mRNA while the PAPOLA gene generated five different PAP mRNAs by alternative splicing of the last three exons. The PAPOLA encoded mRNAs were divided into two classes based on the composition of the last three exons. Poly(A) polymerases from the two classes were shown to differ in polyadenylation activities. These differences revealed two novel regulatory motifs in the extreme C-terminal end of PAP, one being inactivating and the other activating for polyadenylation activity.</p>

3’ end cleavage and polyadenylation are important steps in the maturation of eukaryotic mRNAs. Poly(A) polymerase (PAP), the enzyme catalysing the addition of adenosine residues, exists in multiple isoforms. In this study the functional significance of multiple poly(A) polymerases have been investigated. It is concluded (i) that at least three mechanisms generate the multiple isoforms i.e. gene duplication, post-translational modification and alternative mRNA processing and (ii) that the different isoforms of poly(A) polymerases have different catalytic properties. The study highlights regulation of poly(A) polymerase activity through modulation of its affinity for the substrate as visualised by the KM parameter. We suggest that trans-acting factors modulating the KM of poly(A) polymerase will play important roles in regulating its activity. A new human poly(A) polymerase (PAPγ) encoded by the PAPOLG gene was identified. PAPγ is 65% homologous to the previously identified PAP. In human cells three isoforms of poly(A) polymerases being 90, 100 and 106 kDa in sizes are present. These native isoforms were purified. The PAPOLA gene encoded the 100 and 106 kDa isoforms while the 90 kDa isoform was encoded by the PAPOLG gene. Native PAPγ was found to be more active than 100 kDa PAP while the hyperphosphorylated 106 kDa PAP isoform was comparably inactive due to a 500-fold decrease in affinity for the RNA substrate. The PAPOLG gene was shown to encode one unique mRNA while the PAPOLA gene generated five different PAP mRNAs by alternative splicing of the last three exons. The PAPOLA encoded mRNAs were divided into two classes based on the composition of the last three exons. Poly(A) polymerases from the two classes were shown to differ in polyadenylation activities. These differences revealed two novel regulatory motifs in the extreme C-terminal end of PAP, one being inactivating and the other activating for polyadenylation activity.