The chicken BG system is a highly polymorphic and polygenic multigene family encoding type I transmembrane proteins, with butryophilins as homologues in mammals, some of which are crucial in T cell regulation. There are three genomic locations where BG genes are found: one singleton BG gene (BG0) on chromosome 2, another singleton gene (BG1) in BF-BL region (the so-called minimal essential chicken MHC) on chromosome 16, and many BG genes arranged tandemly in the BG region just outside the MHC. BG genes in BG region have copy number variation between different chicken haplotypes, so it has been unclear which BG genes are alleles, as very little sequence information has been available for haplotypes other than B12, the best characterized one. Also, the functions of chicken BG genes have been a mystery for half a century, although there is evidence for cytoskeletal regulation and for viral disease resistance. Therefore, the aim of the research was to develop new procedures and reagents to understand the BG system. A novel PCR protocol was established to overcome the difficulty of amplifying full length polymorphic BG transcripts, and then was applied to systematically examine the BG cDNA sequences from T cells and B cells of four different chicken haplotypes. In total 23 BG genes were found, most with alternative splicing isoforms; most strikingly, the transcripts potentially encoding soluble BG proteins were only seen in B cells, indicating functional differences of the same gene in T and B cells. By comparing the dominantly expressed BG genes as 'functional alleles' in these cells, only the cytoplasmic tail region is clearly seen to be under selection, based on the overwhelming preponderance of non-synonymous changes. With many other unexpected findings discovered in this project, a clearer picture of chicken BG genes is presented, and more questions were raised for future study. In order to explore BG functions and further characterize BG proteins, fourteen stable cell lines were developed expressing fusion proteins of the Ig-V domains of the 14 BG genes from the B12 haplotype chicken with the human IgG1 Fc fragment. These BG-Fc fusion proteins were used in sandwich enzyme-linked immunosorbent assays (ELISAs) to screen 290 BG monoclonal antibody (mAb) tissue culture supernatants, and these BG mAbs were further characterized for specificity by western blot using BG-Fc fusion proteins. These solid tools (BG-Fc fusion proteins and BG mAbs) provide the basis to further understand chicken BG functions and answer other interesting questions.

RNA sequencing (RNA-seq) technologies facilitate the characterisation of genes and transcripts in different cell types as well as their expression analysis across various conditions. Due to its ability to provide in-depth insights into transcription and post-transcription mechanisms, RNA-seq has been extensively used in functional genetics and transcriptomics, system biology and developmental biology in animals, plants, diseases, etc. The aim of this project is to use mathematical and computational models to integrate big genomic and transcriptomic data from high-throughput technologies in plant biology and develop new methods to identify which genes or transcripts have significant expression variation across experimental conditions of interest, then to interpret the regulatory causalities of these expression changes by distinguishing the effects from the transcription and alternative splicing. We performed a high resolution ultra-deep RNA-seq time-course experiment to study Arabidopsis in response to cold treatment where plants were grown at 20^oC and then the temperature was reduced to 4^oC. We have developed a high quality <i>Arabidopsis thaliana</i> Reference Transcript Dataset (AtRTD2) transcriptome for accurate transcript and gene quantification. This high quality time-series dataset was used as the benchmark for novel method development and downstream expression analysis. The main outcomes of this project include three parts. i) A pipeline for differential expression (DE) and differential alternative splicing (DAS) analysis at both gene and transcript levels. Firstly, we implemented data pre-processing to reduce the noise/low expression, batch effects and technical biases of read counts. Then we used the limma-voom pipeline to compare the expression at corresponding time-points of 4^oC to the time-points of 20^oC. We identified 8,949 genes with altered expression of which 2,442 showed significant DAS and 1,647 were only regulated by AS. Compared with current publications, 3,039 of these genes were novel cold-responsive genes. In addition, we identified 4,008 differential transcript usage (DTU) transcripts of which the expression changes were significantly different to their cognate DAS genes. ii) A TSIS R package for time-series transcript isoform switch (IS) analysis was developed. IS refers to the time-points when a pair of transcript isoforms from the same gene reverse their relative expression abundances. By using a five metric scheme to evaluate robustly the qualities of each switch point, we identified 892 significant ISs between the high abundance transcripts in the DAS genes and about 57% of these switches occurred very rapidly between 0-6h following transfer to 4^oC. iii) A RLowPC R package for co-expression network construction was generated. The RLowPC method uses a two-step approach to select the high-confidence edges first by reducing the search space by only picking the top ranked genes from an initial partial correlation analysis, and then computes the partial correlations in the confined search space by only removing the linear dependencies from the shared neighbours, largely ignoring the genes showing lower association. In future work, we will construct dynamic transcriptional and AS regulatory networks to interpret the causalities of DE and DAS. We will study the coupling and de-coupling of expression rhythmicity to the Arabidopsis circadian clock in response to cold. We will develop new methods to improve the statistical power of expression comparative analysis, such as by taking into account the missing values of expression and by distinguishing the technical and biological variabilities.

To increase diversity of enzymes and proteins, cells mix and match exonic and intronic regions retained in mature mRNAs by alternative splicing. An estimated 94% of all multi-exon genes express one or more alternatively spliced transcripts generating proteins with similar or modified functions. Cyclooxygenase is a signaling enzyme that catalyzes the rate-limiting step in the synthesis of diverse bioactive lipids termed prostaglandins. Prostaglandins are involved in myriad physiological and pathopysiological processes including vasoregulation, stomach mucosal maintenance, parturition, pain, fever, inflammation, neoplasia and angiogenesis and are inhibited by aspirin-like drugs known as NSAIDs. In 2002 an alternatively spliced, intron-1 retaining variant of COX-1 was cloned from canine brain tissue. This new variant, termed COX-3 or COX-1b, is an enzymatically active prostaglandin synthase expressed at relatively high levels in a tissue and cell type dependant manner in all species examined. In humans and most rodent species intron-1 is 94 and 98 nucleotides long respectively. Retention of the intron in these species introduces a frameshift and is predicted to result in translation of a very small 8-16kD protein with little similarity to either 72kD COX-1 or COX-2, calling into question the role of this variant. In this dissertation, I present my results from cloning and ectopically expressing a complete and accurate COX-3 cDNA from both rat and human. I confirmed that COX-3 mRNA encodes multiple large molecular weight cyclooxygenase-like proteins in the same reading frame as COX-1. Translation of these proteins relies on several recoding mechanisms including cap-independent translation initiation, alternative start site selection, and ribosomal frameshifting. Using siRNA and Western blotting I have identified some of these proteins in tissues and cells. Two COX-3 encoded proteins are active prostaglandin synthase enzymes with activities similar to COX-1 and represent novel targets of NSAIDs. Other COX-3 proteins have unknown function, but their size and cellular location suggest potential roles as diverse as cytosolic enzymes and nuclear factors.

Hereditary hearing loss is the most common sensory disorder, affecting 1 in 500 newborns. There are more than 538 million individuals with genetic hearing loss worldwide and this number is expected to grow to 1 billion over the next three decades. Currently, the only option for individuals with hearing loss is mechanical intervention such as hearing aids or cochlear implants. In the past decade, many studies have highlighted the need for personalized gene therapy or molecular intervention to treat genetic deafness. However, in order to fulfill this vision a comprehensive understanding of the intricate mutation-gene-phenotype nuances and relationships is required. Toward this goal, we unraveled novel mutation-gene-phenotype associations and mechanisms in four deafness-causing genes (CIB2, COL11A1, CEACAM16 and DFNA5), by using a combination of in-depth phenotyping, human genetics, cutting edge genomic technologies, murine mutant models, and functional assays. These novel insights revealed mutations in CIB2 do not cause Usher Syndrome, mutations in COL11A1 can cause either non-syndromic or syndromic hearing loss, CEACAM16-related deafness is due to two distinct mechanisms, loss of function and gain of function, and coding variants can influence mRNA assembly and cause DFNA5-related hearing loss. Elucidating these novel mutation-gene-phenotype relationships has improved our knowledge of the pathogenic mechanisms underlying hearing loss and provided much needed answers to individuals seeking a diagnosis for their deafness. Recognizing the complexities associated with genetic hearing loss and the challenges in interpreting the clinical significance of genetic variants, we established the first deafness-specific variant database, the Deafness Variation Database (DVD), which classifies over 876,000 variants across 152 deafness-associated genes. This breadth of data provided us with a unique opportunity to explore the molecular landscape of deafness. We show that over 96% of coding variants are rare and novel and that mutational signatures are unique to each gene and are driven by minor allele frequency thresholds, variant effect, and protein domain. The mutational landscape we define shows complex gene-specific variability, making an understanding of these nuances foundational for improved accuracy in variant interpretation. Overall the work presented in this thesis improves our understanding of deafness biology, identifies novel targets for therapeutics and enhances clinical decision-making.

The polyglutamine diseases are a clinically heterogeneous group of inherited neurodegenerative disorders caused by expansion of polyglutamine-encoding (CAG)n trinucleotide repeats within the disease genes. It is increasingly clear that the amino acid sequences flanking the polyglutamine expansion in each disease protein, i.e. the specific protein context, contribute to selective neuronal toxicity by influencing the behavior of the disease protein within selectively vulnerable neuronal populations. In the studies described here, I explore the role that protein context plays in the polyglutamine disease, Spinocerebellar ataxia type 3 (SCA3). Toward this end, I utilize biochemical, cell-based, and animal models to gain a broader understanding of the SCA3 disease protein, ataxin-3, and generate tools for further exploration of the molecular properties of ataxin-3 that modulate its toxicity during disease. In Chapter 1, I provide an overview of the recognized polyglutamine diseases, emphasizing the elements of protein context that are distinct among the polyglutamine disease proteins and may contribute to the neuropathological and clinical heterogeneity within this family of diseases. Alternative splicing of the polyglutamine disease gene products adds an additional level of complexity to the tissue-specific protein context of expanded polyglutamine, yet this phenomenon has been underinvestigated. In Chapter 2, I examine the significance of ataxin-3 splice variation. Several minor 5' variants and both known 3' splice variants of ataxin-3, a deubiquitinating enzyme, are expressed at the mRNA level in brain. At the protein level, however, the C-terminal splice isoform with three ubiquitin interacting motifs (3UIM ataxin-3) is the predominant isoform in brain, independent of age or (CAG)n expansion. Although both C-terminal ataxin-3 splice isoforms display similar in vitro deubiquitinating activity, 2UIM ataxin-3 is more prone to aggregate and is more rapidly degraded by the proteasome. These observations demonstrate how alternative splicing of sequences distinct from the polyglutamine-encoding (CAG)n repeat can alter disease-related components of protein context. Knock-in models of polyglutamine diseases utilize pathogenic (CAG)n expansions within the endogenous genomic, transcript, and protein context to recreate key features of individual polyglutamine diseases. In chapter 3, I describe the creation of the first knock-in mouse model of SCA3. Hemizygous knock-in mice transmit the knock-in allele in Mendelian ratios and broadly express both the expanded Atxn3(Q3KQ82) protein and the wildtype murine Atxn3(Q6) protein. In this chapter, I also compare the gene targeting efficiencies and rates of chromosomal instability of a novel C57BL/6J ES cell line (UMB6JD7) and two well established ES cell lines (W4 and Bruce4.G9). Of these, Bruce4.G9 ES cells proved superior based on lower rates of aneuploidy and the production of germline transmitting chimeras. Finally, in Chapter 4 I discuss questions and concepts raised during the course of these studies, and suggest avenues of future research aimed at broadening our understanding of ataxin-3 physiology and of protein context-dependent elements in polyglutamine disease pathogenesis.

Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (Multivariate Analysis of Transcript Splicing), a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT-PCR validation rate of 86% for differential alternative splicing events with a MATS FDR of < 10%. Additionally, over the full list of RT-PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.

Le gène nucleoredoxin-like 1 (NXNL1), composé de deux exons et d'un intron, code pour RdCVF lorsque l'intron est retenu et RdCVF-long (RdCVFL), une thiorédoxine active, lorsque qu'il est excisé. RdCVFL est une enzyme protégeant les photorécepteurs du stress oxydatif. RdCVF exprimé et sécrété que par les bâtonnets interagit avec son récepteur basigin 1 (BSG1) à la surface des cônes, stimule l'entrée du glucose. Dans la rétinopathie pigmentaire, les bâtonnets dégénèrent progressivement, RdCVF n'est plus exprimé et les cônes meurent. RdCVF tronqué dans le motif thiorédoxine ne possède pas d'activité thiol-oxydoréductase. Les cônes sont les ancêtres des bâtonnets. NXNL1 codait à l'origine pour RdCVFL, et les cônes des mammifères n'expriment donc plus que cette protéine. Chez l'hydre, apparue il y a 600 millions d'années, NXNL ancestral est exprimé. RdCVFL la protège contre les radicaux libres, RdCVF est exprimé, mais n'interagit pas avec basigin, il manque chez l'hydre un des acteurs de la signalisation métabolique de RdCVF. Il y a 400 millions d'années, chez la lamproie, seuls les bâtonnets expriment RdCVF. Son récepteur BSG1 se lie à RdCVF; les acteurs de la signalisation étaient donc présents chez les vertébrés anciens avec des bâtonnets fonctionnels. Le bénéfice pour la vision par l'addition d'une nouvelle fonction de NXNL1 a joué un rôle durant l'évolution de ce système. Une séquence en 3' du premier exon du gène NXNL1 lie la protéine nucléoline impliquée dans l'épissage et exprimée par les bâtonnets mais pas par les cônes. Cette protéine doit réguler l'épissage alternatif du gène NXNL1. / The nucleoredoxin-like 1 gene (NXNL1), which is composed by two exons and one intron, encodes for RdCVF made from an unspliced mRNA and RdCVF-long (RdCVFL), an active thioredoxin, when the intron is excised. RdCVFL is an enzyme that protects photoreceptors against oxidative stress. RdCVF is only expressed and secreted by the rods and interacts with its receptor basigin 1 (BSG1), expressed by cones and stimulates glucose entry. So in retinitis pigmentosa, characterized by progressive rods degeneration, RdCVF is no longer expressed and cones die. RdCVF corresponds to a truncated thioredoxin-like protein with no thiol-oxidoreductase activity. According to the knowledge of retina evolution, the cones are rods ancestors and NXNL1 originally encode for the RdCVFL, and today, mammalian cones only expresses this protein. In hydra that appeared 600 million years ago, ancestral NXNL gene was found, RdCVFL protects it against free radicals attack and RdCVF already existed. But hydra basigin doesn’t interact with RdCVF, so it lacks one of the metabolic signaling actors of RdCVF in hydra. 400 million years ago, In lamprey only rods produce RdCVF. Lamprey BSG1 binds RdCVF; actors signaling were present in oldest vertebrate that present functional rods. This original alternative splicing system has played a role during evolution by adding a new function of NXNL1 gene leading to a benefit in vision. I identified a sequence in 3’ RNA of exon n°1 of NXNL1 gene that binds the nucleolin protein involved in splicing and expressed by the rods but not by the cones. This protein must regulate the NXNL1 alternative splicing.

<p>Our genome operates by sending instructions, conveyed by mRNA, for the manufacture of proteins from chromosomal DNA in the nucleus of the cell to the protein synthesizing machinery in the cytoplasm. Alternative splicing is a natural process in which a single gene can encode multiple related proteins. During RNA splicing, introns are selectively removed resulting in alternatively spliced gene products. Alternatively spliced protein products can have very different biological effects, such that one protein isoform is disease-related while another isoform is desirable. Splice switching opens the door to new drug targets, and antisense oligonucleotides (asONs), designed to switch splicing, are effective drug candidates. Cellular uptake of oligonucleotides(ONs) is poor, therefore utilization of cell-penetrating peptides (CPPs), well recognized for intracellular cargo delivery, is a promising approach to overcome this essential issue. Most CPPs are internalized by endocytosis, although the mechanisms involved remain controversial.</p><p>Here, evaluation of CPP-mediated ON delivery over cellular membranes has been performed. A protocol that allows for convenient assessment of CPP-mediated cellular uptake and characterization of corresponding internalization routes is established. The protocol is based on both fluorometric uptake measurements and a functional splice-switching assay, which in itself is based on biological activity of conveyed ONs. Additionally, splice switching ONs (SSOs) have been optimized for high efficiency and specificity. Data suggest that SSO activity is improved for chimeric phosphorothioate SSOs containing locked nucleic acid (LNA) monomers. It is striking that the LNA monomers in such chimeric constructs give rise to low mismatch discrimination of target pre-mRNA, which highlight the necessity to optimize sequences to minimize risk for off-target effects.</p><p>The results are important for up-coming work aimed at developing compounds consisting of peptides and novel synthetic nucleic acids, making these entities winning allies in the competition to develop therapeutics regulating protein expression patterns.</p>

<p>Alternativ splicing är en process som ger upphov till att olika mRNA-sekvenser bildas från en enda gen, vilket bidrar till en ökad proteindiversitet hos organismen. Olika mRNA-sekvenser kan uppstå eftersom att det förekommer olika varianter av alternativ splicing som även kan kombineras på flera olika sätt: cassette exon (inkludering/exkludering av exon), intron retention (intronet behålls), alternative 5´splice-site choice (olika 5´ splice sites kan väljas) och slutligen alternative 3´ splice-site choice (andra 3´ splice sites kan väljas). För att alternativ splicing ska äga rum i olika pre-mRNA måste den regleras av cis-reglerande element. De cis-reglerande elementen utgörs av fyra grupper: exonic splicing enhancers (ESE), exonic splicing silencers (ESS), intronic splicing enhancers (ISE) samt intronic splicing silencers (ISS). Som namnen förtäljer finns de antingen i exoner eller introner, där de interagerar med transagerande faktorer, SR-proteiner (aktiverare) eller hnRNPs (hämmare). Alternativ splicing förekommer både i djur och i växter. Hos <em>Homo sapiens </em>genomgår över 74 % av de 25,000 gener som finns hos organismen, alternativ splicing. Däremot i växten <em>Arabidopsis thaliana</em>, genomgår endast 22 %, av den totala mängden på cirka 26,000 gener, alternativ splicing. Eftersom att processen bidrar till en ökad proteindiversitet, kommer det medföra att olika processer i organismerna påverkas, exempelvis celltillväxt, celldöd samt utvecklingen av olika sjukdomar, såsom Parkinson och cystisk fibros. Många studier har gjorts som bekräftar dess betydelse för organismerna men på grund av processens komplexitet är det fortfarande ett ämne som ständigt måste utforskas.</p><p> </p>

<p>Poly(A) polymerase (PAP) is the enzyme catalyzing the synthesis of the adenine tail to the 3’-end of mRNA. This A-tail is present on the majority of the primary RNA transcripts of protein-coding genes, and is important for mRNA stability, export to the cytoplasm and translation. Therefore, PAP is a key regulator of eukaryotic gene expression. This thesis describes the heterogeneity of PAP and the functional significance of multiple isoforms of PAP. </p><p>PAP exists in many different isoforms generated by three different mechanisms, gene duplication, alternative mRNA processing and post-translational modification. In HeLa cell extracts three different forms of PAP being 90, 100 and 106 kDa in size have been detected, where the 106 kDa isoform is a phosphorylated version of the 100 kDa species. It is shown that the N-terminal region of PAP contains a region required for catalysis, while the C-terminal end is important for the interaction with the cleavage and polyadenylation specificity factor (CPSF). Interestingly, it was found that also the extreme N-terminal end is important for the interaction with CPSF. This region is post-translationally modified by phosphorylation. Five alternatively spliced forms of PAP mRNAs are encoded by the PAPOLA gene while one unique species is encoded by the PAPOLG gene. The analysis showed that the exact structure of the alternatively spliced C-terminal end of PAP played an important role for catalytic efficiency. Thus, the C-terminal end contains a region important for modulating the catalytic efficiency of PAP.</p><p>Aminoglycoside antibiotics inhibit PAP activity, most likely by displacement of catalytically important divalent metal ions. Data shows that different aminoglycosides inhibit PAP activity by different mechanisms suggesting that the binding sites for the different aminoglycosides do not completely overlap. It is concluded that aminoglycosides interfere with enzymes important for housekeeping functions in mammalian cell, which may explain some of the toxic side effects caused by aminoglycoside antibiotics in clinical practice.</p>