Background: Genome-wide association studies (GWAs) have identified almost one hundred genetic loci associated with variances in human blood lipid phenotypes including very low-density lipoprotein cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, total cholesterol and triglycerides. Nevertheless the revealed loci only explain a small fraction of heritability and therefore a subtile phenotype of cholesterol homoestasis was examined in our study for the very first time. Methods and Results: Using a multi-stage approach of a GWA, firstly, a genome-wide analysis (Affymetrix 500K GeneChip) for serum lanosterol and serum total cholesterol using LC-MS/MS was conducted in 1495 participants of the KORA-S3/F3 cohort with subsequent replication in two additional independent samples of the the KORA-S3/F3 cohort (n = 1157) and CARLA cohort (n = 1760). Two genetic variants, SNP rs7703051 and rs17562686, in the HMGCR locus were significantly associated with serum lanosterol and showed similar effects of elevated serum lanosterol for each minor allele (combined n = 4412: p = 1,4 x 10-10, +7,1% and p = 4,3 x 10-6, +7,8%). Furthermore, rs7703051 showed a nominal statistical significance to serum cholesterol (p = 0,04). A combined analysis of both SNPs demonstrated that observed associations of rs17562686 can be partly explained by LD with rs7703051 being the primary polymorphism in that study. Nevertheless, rs17562686 shows consistent independent effects on serum lanosterol, thus being associated to a lipid phenotype for the very first time. The following SNP-fine mapping of the HMGCR locus was carried out in the CARLA cohort with subsequent validation in the LE-Heart cohort (n = 1895). The recently published SNP rs3846662 being in tight LD with rs7703051 could be associated with variances of serum lanosterol in both cohorts and functional in vivo studies of gen expression using qRT-PCR assays demonstrated a highly significant association of higher expression of alternatively spliced HMGCR mRNA lacking exon 13 with homozygosity for the rs3846662 major allele in 51 human liver samples (p < 0,01) and 958 human PBMCs (p = 2,1 x 10-7). The overall HMGCR gen expression was not affected. Further investigation of in vivo HMG-CoA reductase enzyme activity in both human samples (n = 48 and n = 55) using anionic exchange column chromatography and scintillation counting of [3-14C]-HMG-CoA and [5-3H]-mevalonolacton did not show any significant results. In addition there was not any association in the LE-Heart cohort between these SNPs and the development of CAD. Finally, rs7703051 could be replicated for already published total cholesterol (combined n = 4412) and rs3846662 for LDL-cholesterol (LE-Heart n = 1895). Since fine mapping in CARLA showed several SNPs throughout the HMGCR locus being in LD with rs17562686 we performed a DNA sequencing of the extended 5´-HMGCR promotor region in six human liver samples. A unknown SNP was discovered in the promotor but could not be associated with any of the examined phenotypes mentioned above. The minor allele of SNP rs5909 situated next to the stop codon and being in high LD with rs17562686 was associated with elevated serum lanosterol and slightly reduced HMGCR gen expression, but further studies including the above mentioned as well as measurement of 3’-UTR transcript lengths using qRT-PCR assays did not produce significant results. Conclusion: The phenotype serum lanosterol could be associated with genetic polymorphisms (e.g. rs7703051) in the HMGCR locus. Therefore already published associations of HMGCR with total cholesterol and LDL-cholesterol can be explained by variances of cholesterol homeostasis. The SNP rs17562686 could be associated with a phenotype of human blood lipids for the very first time. Subsequent gen expression analyses demonstrated a highly significant association of rs3846662 with variant patterns of HMGCR alternative splicing. A significant effect of alternatively spliced protein on enzyme activity and a association of these SNPs with CAD could not be shown.

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on March 10, 2010). Vita. Thesis advisor: Lorson, Christian L. "December 2008" Includes bibliographical references

BPS/IC (Bladder Pain Syndrome/Interstitial Cystitis) ist ein sehr schweres und noch weitgehend unverstandenes Krankheitsbild in der Urologie. Viele Frauen sind im Alltag durch den ständigen Harndrang und die Schmerzen stark eingeschränkt und von Depressionen betroffen. Die Aufklärung der Pathogenese ist deshalb sehr wichtig, um eine adäquate Therapie für die Betroffenen zu entwickeln und die Krankheit möglichst frühzeitig diagnostizieren zu können. Das Schwangerschaftshormon hCG (humanes Choriongonadotropin) besitzt differenzierende und wachstumsfördernde Eigenschaften und eine Rolle in der Urothelregeneration und – stabilisierung scheint möglich. Daher ist das Ziel dieser Arbeit seinen Rezeptor, den LHCGR (Luteinizing-Hormone/Choriogonadotropin Rezeptor), in der Harnblase nachzuweisen und die urothelialen und muskulären Charakteristika zwischen gesunden und an BPS/IC erkrankten Harnblasen zu vergleichen. Die Darstellung des LHCGR erfolgte auf Proteinebene mittels indirekter Immunfluoreszenz und auf mRNA-Ebene durch Standard-PCR. Es zeigten sich im Urothel von Harnblase und Ureter 5 unterschiedliche Verteilungsmuster des Rezeptors hinsichtlich seiner Expression in verschiedenen Zellschichten und seiner subzellulären Lokalisation. Je nach Urothelzustand und zwischen den Entitäten Kontroll- bzw. BPS/IC-Harnblase variierten diese Muster in ihrer Häufigkeit. In anderen Epithelien, wie dem Vaginalepithel, änderte sich die zelluläre Verteilung des LHCGR in Abhängigkeit vom Differenzierungsgrad der Zellen. Es scheint möglich, dass auch die Rezeptorexpression in Urothelzellen deren verschiedene Differenzierungszustände widerspiegelt. Dies unterstützt den für hCG vermuteten Einfluss auf die Epithelregeneration. Ein Vergleich der urothelialen Fluoreszenzintensitäten zwischen weiblichen Kontroll – und BPS/IC-Harnblasen zeigte eine signifikant stärkere Expression des Rezeptors bei erkrankten Patienten. Dem gegenüber war kein Unterschied im Detrusor, weder zwischen Kontroll – und BPS/IC-Harnblasen noch im geschlechtsspezifischen Vergleich, festzustellen. Damit scheint der Rezeptor seine Hauptaufgabe vorrangig im Urothel zu entfalten. Die Korrelationsanalysen ergaben keinen signifikanten Zusammenhang zwischen dem Erkrankungsalter (Zeitpunkt der Diagnosestellung und Biopsieentnahme) und der LHCGR-Immunfluoreszenz. Ein endokrinologischer Einfluss auf die Rezeptorexpression wurde dadurch unwahrscheinlich und unterstützt die immer akzeptiertere Auffassung, dass BPS/IC nicht mehr mit der Menopause assoziiert ist. Neben dem Urothel und Detrusor zeigten auch Lamina propria und Gefäße von Harnblase und Ureter die Expression des LHCGR in der Immunhistochemie. Unterschiedliche Clustermuster des Rezeptors im Detrusor ließen auf die Oligomerisierung des Rezeptors schließen. Die Bedeutung dieser Zusammenschlüsse ist jedoch noch unklar, wobei unterschiedliche funktionelle Zustände des Rezeptors vermutet werden. Orientierung bieten andere Rezeptoren, die durch Dimerisierung verschiedener Rezeptorvarianten ihre Funktionalität verbessern oder verschlechtern konnten. Obwohl für keine bisher entdeckte Variante des LHCGR eine definitive Aufgabe ermittelt werden konnte, scheinen doch viele Varianten auch unterschiedliche Funktionen wahrnehmen zu können. Besonders auf der Regulierbarkeit des Rezeptors mittels interagierender Splicevarianten sollte das Augenmerk zukünftiger Studien liegen. Ob durch Komplexbildung verschiedener Varianten oder Bildung nichtfunktioneller trunkierter Rezeptoren, die Kontrollmöglichkeiten sind vielfältig und können auch auf Liganden wirken. Letztlich ließ der Nachweis des LHCGR in allen Schichten von Harnblase und Ureter eher eine globale Rolle des Rezeptors im Harntrakt des Menschen vermuten. Dazu passten auch die bereits nachgewiesenen Einflüsse seiner Liganden auf die Blasenfunktion von Hunden. Die hier vorgelegte Arbeit untersuchte zum ersten Mal die Expression des LHCGR mittels PCR und Immunhistochemie in humanen Harnblasen und Ureteren. Dabei löste sie sich von den sonst üblichen Vorstellungen einer Beziehung des Rezeptors zu Blasentumoren, Schwangerschaft oder Inkontinenz. Diagnose und Therapie von BPS/IC sind zur Zeit noch ständigen Wandlungen unterworfen und dabei entgehen viele Patienten der (frühen) Diagnosestellung und einer adäquaten Behandlung. Diese Studie sollte dazu beitragen neue Einblicke in die Pathophysiologie der Erkrankung zu erlangen, um eine kausale Therapie entwickeln zu können. Zukünftig könnten diese Ergebnisse dabei helfen die Anwendung einer sensitiven und vor allem spezifischen Diagnostik auf molekularer Ebene (mRNA - oder Proteinnachweis) zu ermöglichen.

The extracellular matrix (ECM) is a complex network of molecules secreted by cells, which is essential for providing structural support and facilitating cell processes including adhesion, migration and survival. Tenascin-C is an immunomodulatory ECM protein that exhibits limited expression in healthy tissues, but is transiently elevated at sites of tissue injury, and is persistently expressed in chronic inflammatory diseases and tumours. Alternative splicing of 9 of tenascin-C's fibronectin type III-like domains (FnIII- A1, A2, A3, A4, B, AD2, AD1, C and D) generates enormous diversity in form; yielding 511 possible isoforms. Post-transcriptional modification of tenascin-C has been studied in cancer and during development where disease and tissue specific isoforms exhibit distinct adhesive, migratory and proliferative effects. However, little is known of how tenascin-C is expressed or alternatively spliced during inflammation. This study characterises inflammation and disease specific tenascin-C isoforms made by immune cells and fibroblasts, and investigates their functional relevance. Biosynthesis and alternative splicing of tenascin-C was examined using standard curve qPCR, ELISA, Western blot and confocal immunocytochemistry in resting and activated primary human immune cells, dermal fibroblasts, and in synovial fibroblasts isolated from healthy controls and from osteoarthritis (OA) and rheumatoid arthritis (RA) patients. Based on these data, three recombinant proteins comprising FnIII domains AD2-AD1, B-C-D and B-AD2-AD1-C-D were cloned, expressed and purified, and their impact on cell behaviour including adhesion, morphology and migration was assessed. Basal tenascin-C expression was lower in myeloid and lymphoid cells than fibroblasts, and was induced in all following inflammatory stimulation. Tenascin-C expression was elevated in disease with RA and OA synovial fibroblasts containing higher levels than healthy controls. Alternative splicing following cell activation was cell-type specific: all FnIII except AD2 and AD1 were upregulated in dendritic cells and macrophages, in T-cells all FnIII remained unchanged with FnIII A1 absent; and no change in splicing was observed in activated dermal fibroblasts. Normal and OA synovial fibroblasts exhibited similar tenascin-C splicing patterns, but FnIII B and D were specifically elevated in RA. Functional analysis revealed differences in the adhesion, morphology and migration of myeloid cells and dermal fibroblasts cultured on FnIII AD2-AD1, B-C-D, B-AD2-AD1-C-D and full length tenascin-C substrates; FnIII B-C-D promoted MDDC migration while B-AD2-AD1-C-D promoted fibroblast adhesion, compared to full length tenascin-C. For the first time, this study reveals differences in tenascin-C biosynthesis and alternative splicing by immune cells and fibroblasts following activation with inflammatory stimuli; and starts to reveal how alternative splicing of tenascin-C may influence the behaviours of both stromal and immune cells types during inflammation and in inflammatory diseases.

Gene deletions are a powerful method to uncover the cellular functions of a given gene in living systems. A limitation to this methodology is that it is not applicable to essential genes. Even for non-essential genes, gene knockouts cause complete absence of gene product thereby limiting genetic analysis of the biological pathway. Alternatives to gene deletions are mutants that are conditional, for e.g, temperature sensitive (ts) mutants are robust tools to understand temporal and spatial functions of genes. By definition, products of such mutants have near normal activity at a lower temperature or near-optimal growth temperature which is called as the permissive temperature and reduced activity at a higher, non-optimal temperature called as the non-permissive temperature. Generation of ts alleles in genes of interest is often time consuming as it requires screening a large population of mutants to identify those that are conditional. Often many essential proteins do not yield ts such alleles even after saturation mutagenesis and extensive screening (Harris et al., 1992; Varadarajan et al., 1996). The limited availability of such mutants in many essential genes prompted us to adopt a biophysical approach to design temperature-sensitive missense mutants in an essential gene of fission yeast. Several studies report that mutations in buried or solvent-inaccessible amino acids cause extensive changes in the thermal stability of proteins and specific substitutions create temperature-sensitive mutants (Rennell et al., 1991; Sandberg et al., 1995). We used the above approach to generate conditional mutants in the fission yeast gene spprp18+encoding an essential predicted second splicing factor based on its homology with human and S. cerevisiae proteins. We have used a missense mutant coupled with a conditional expression system to elucidate the cellular functions of spprp18+. Further, we have employed the same biophysical principle to generate a missense mutant in spago1+ RNA silencing factor that is non-essential for viability but has critical functions in the RNAi pathway of fission yeast. Fission yeast pre-mRNA splicing: cellular functions for the protein factor SpPrp18 Pre-mRNA splicing is an evolutionarily conserved process that excises introns from nascent transcripts. Splicing reactions are catalyzed by the large ribonuclear protein machinery called the spliceosome and occur by two invariant trans-esterification reactions (reviewed in Ruby and Abelson, 1991; Moore et al., 1993). The RNA-RNA, RNA–protein and protein-protein interactions in an assembly of such a large protein complex are numerous and highly dynamic in nature. These interactions in in vitro splicing reactions show ordered recruitment of essential small nuclear ribonucleic particles snRNPs and non–snRNP components on pre-mRNA cis-elements. Further these trans acting factors recognize and poise the catalytic sites in proximity to identify and excise introns. The precision of the process is remarkable given the diversity in architecture for exons and introns in eukaryotic genes (reviewed in Burge et al., 1999; Will and Luhrmann, 2006). Many spliceosomal protein components are conserved across various organisms, yet introns have diverse features with large variations in primary sequence. We hypothesize that co-evolution of splicing factor functions occurs with changes in gene and intron architectures and argue for alternative spliceosomal interactions for spliceosomal proteins that thus enabling splicing of the divergent introns. In vitro biochemical and genetic studies in S. cerevisiae and biochemical studies with human cell lines have indicated that ScPRP18 and its human homolog hPRP18 function during the second catalytic reaction. In S. cerevisiae, ScPrp18 is non-essential for viability at growth temperatures <30°C (Vijayraghavan et al., 1989; Vijayraghavan and Abelson, 1990; Horowitz and Abelson, 1993b). The concerted action of ScSlu7 - ScPrp18 heteromeric complex is essential for proper 3’ss definition during the second catalytic reaction (Zhang and Schwer, 1997; James et al., 2002). These in vitro studies also hinted at a possible intron -specific requirement for ScPrp18 and ScSlu7 factors as they were dispensable for splicing of intron variants made in modified ACT1 intron containing transcripts (Brys and Schwer, 1996; Zhang and Schwer, 1997). A short spacing distance between branch point adenosine to 3’splice site rendered the substrate independent of Prp18 and Slu7 for the second step (Brys and Schwer, 1996; Zhang and Schwer, 1997). Extensive mutational analyses of budding yeast ScPrp18 identified two functional domains and suggested separate roles during splicing (Bacikova and Horowitz, 2002; James et al., 2002). Fission yeast with its genome harboring multiple introns and degenerate splice signals has recently emerged as a unique model to study relationships between splicing factors and their role in genomes with short introns. Previously, studies in our lab had initiated genetic and mutational analysis of S. pombe Prp18, the predicted homolog of budding yeast Prp18. Genetic analysis showed its essentiality, but a set of missense mutants based on studies of budding yeast ScPrp18 (Bacikova and Horowitz, 2002) gave either inactive null or entirely wild type phenotype for the fission yeast protein. In this study, we have extended our previous mutational analysis of fission yeast Prp18 by adopting biophysical and computational approaches to generate temperature-sensitive mutants. A missense mutant was used to understand the splicing functions and interactions of SpPrp18 and the findings are summarized below. Fission yeast SpPrp18 is an essential splicing factor with transcript-specific functions and links efficient splicing with cell cycle progression We initiated our analysis of SpPrp18 by adopting a biophysical approach to generate ts mutants. We used the PREDBUR algorithm to predict a set of buried residues, which when mutated could result in a temperature-sensitive phenotype that complements the null allele at permissive temperature. These predictions are based upon two biophysical properties of amino acids: 1) Hydrophobicity, which is calculated in a window of seven amino acids 2) Hydrophobic moment, which is calculated in a sliding window of nine amino acids in a given protein sequence. Several studies correlate these properties to protein stability and function (Varadarajan et al., 1996). One of the buried residue mutants V194R, in helix 1 of SpPrp18 conferred weak temperature- sensitivity and strong cold-sensitivity even when the protein was over expressed from a plasmid. Through semi-quantitative RT-PCR we showed splicing-defects for tfIId+ intron1 in these cells even when grown at permissive temperature. The primary phenotype was the accumulation of pre-mRNA. Further, we showed this splicing arrest is co-related with reduced levels of SpPrp18 protein, linking protein stability and splicing function. Next we examined the effects of this mutation on function by further reduction of protein levels. This was done by integrating the expression cassette nmt81:spprp18+/spprp18V194R at the leu1 chromosomal locus and by metabolic depletion of the integrated allele. Through RT-PCRs we demonstrated that depletion of wild type or missense protein has intron specific splicing defects. These findings showed its non-global and possibly substrate-specific splicing function. In the affected introns, precursor accumulation is the major phenotype, confirming prior data from our lab that hinted at its likely early splicing role. This contrasts with the second step splicing role of the human or budding yeast Prp18 proteins. Previous data from our lab showed loss of physical interaction between SpPrp18 and SpSlu7 by co-immunoprecipitation studies. This again differs from the strong and functionally important ScPrp18 and ScSlu7 interaction seen in budding yeast. We show the absence of charged residues in SpSlu7 interaction region formed by SpPrp18 helix1 and helix2 which can explain the altered associations for SpPrp18 in fission yeast. Importantly, as the V194R mutation in helix 1 shows splicing defects even at permissive temperature, the data indicate a critical role for helix 1 for splicing interactions, possibly one that bridges or stabilizes the proposed weak association of SpPrp18-SpSlu7 with a yet unknown splicing factor. We also investigated the effects of mutations in other helices; surprisingly we recovered only mutations with very subtle growth phenotypes and very mild splicing defects. Not surprisingly, stop codon at L239 residue predicted to form a truncated protein lacking helices 3, 4 and 5 conferred recessive but null phenotype implicating essential functions for other helices. Other amino acid substitutions at L239 position had near wild type phenotype at 30°C and 37°C. Helix 3 buried residue mutant I259A conferred strong cold-sensitivity when over expressed from plasmid, but semi quantitative analysis indicated no splicing defects for intron1 in the constitutively expressed transcript tfIId+. These findings indicate cold sensitivity either arises due to compromised splicing of yet unknown transcripts or that over-expressed protein has near wild type activity. We find mutations in the helix 5 buried residues L324 also conferred near WT phenotype. Earlier studies in the lab found that substitution of surface residues KR that are in helix 5 with alanine lead to null phenotypes (Piyush Khandelia and Usha Vijayraghavan unpublished data). We report stable expression of all of these mutant proteins; L239A, L239P, L239G, I259A, I259V, L324F, L324A as determined by our immunoblot analysis at 30°C and 37°C. The mild phenotypes of many buried residues can be attributed to orientation of their functional groups into a protein cavity between the helices. Lastly, our microscopic cellular and biochemical analysis of cellular phenotypes of spprp18 mutant provided a novel and direct role of this factor in G1-S transition of cell cycle. Our RT-PCR data suggest spprp18+ is required for efficient splicing of several intron containing transcripts involved in G1-S transition and subsequent activation of MBF complex (MluI cell cycle box-binding factor complex) during S-phase and shows a mechanistic link between cell cycle progression and splicing. A tool to study links between RNA interference, centromeric non-coding RNA transcription and heterochromatin formation S.pombe possesses fully functional RNA interference machinery with a single copy for essential RNAi genes ago1+, dcr1+ and rdp1+. Deletion of any of these genes causes loss of heterochromatinzation with abnormal cytokinesis, cell-cycle deregulation and mating defects (Volpe et al., 2002). In S.pombe, exogenous or endogenously generated dsRNA’s from transcription of centromeric repeats are processed by the RNaseIII enzyme dicer to form siRNA. These siRNA’s are loaded in Ago1 to form minimal RNA induced silencing complex (RISC) complex or specialized transcription machinery complex RNA induced transcriptional silencing (RITS) complex and target chromatin or complementary mRNAs for silencing. Thus as in other eukaryotes, fission yeast cells deploy RNAi mediated silencing machinery to regulate gene-expression and influence chromatin status. Several recent studies point to emerging new roles of RNAi and its association with other RNA processes (Woolcock et al., 2011; Bayane et al., 2008; Kallgren et al., 2014). Many recent reports suggest physical interactions of RISC or RITS and RNA dependent RNA polymerase complex (RDRC) with either some factors of the spliceosomal machinery, heterochromatin machinery (CLRC complex) and the exosome mediated RNA degradation machinery (Bayne et al., 2008 and Chinen et al., 2010 ; Hiriart et al., 2012; Buhler et al., 2008; Bayne et al., 2010 ). Thus we presume conditional alleles in spago1+ will facilitate future studies to probe the genetic network between these complexes as most analyses thus far rely on ago1∆ allele or have been based on proteomic pull down analyses of RISC or RITS complexes. In this study, we employed biophysical and modeling approaches described earlier to generate temperature sensitive mutants in spago1+ and spdcr1+. We tested several mutants for their ability to repress two reporter genes in a conditional manner. Our modeling studies on SpAgo1 PAZ domain indicated structural similarities with human Ago1 PAZ domain. We created site-directed missense mutants at predicted buried residues or in catalytic residues. We also analyzed the effects of random amino acid replacements in specific predicted buried or catalytic residues of SpAgoI. These ago1 mutants were screened as pools for their effects on silencing of GFP or of ura4+ reporter genes. These assays assessed post transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) activity of these mutants. We obtained three temperature sensitive SpAgo1 mutants V324G, V324S and L215V while the V324E replacement was a null allele. Based upon our modeling, a likely explanation for the phenotype of these mutants is structural distortion or mis-orientation of the functional groups caused due to these mutations, which affect activity in a temperature dependent manner. This distortion in the PAZ domain may affect binding of siRNA and thereby lead to heterochromatin formation defects that we observed. Our data on the SpAgo1 V324 mutant shows conditional centromeric heterochromatin formation confirmed by semi quantitative RT-PCR for dh transcripts levels that shows temperature dependent increase in these transcripts. We find reduced H3K9Me2 levels at dh locus by chromatin immunoprecipitation (ChIP) assay, linking the association of siRNAs for establishment of heterochromatin at this loci. The data on PTGS of GFP transcripts show SpAgo1 V324G mutation has decreased slicing activity as semi-quantitative RT-PCR for GFP transcripts show increased levels at non permissive temperature. These studies point out the importance of siRNA binding to the PAZ domain and its effect on slicing activity of SpAgo1. The mutations in Y292 showed residue loss of centromeric heterochromatin formation phenotype. Thus, we ascribe critical siRNA binding and 3’ end recognition functions to this residue of SpAgo1. These studies point out functional and structural conservation across hAgo1 and SpAgo1. Adopting the aforementioned biophysical mutational approach, we generated mutants in spdcr1+ and screened for those with conditional activity. Our modeling studies on SpDcr1 helicase domain shows it adopts the conserved helicase domain structure seen for other DEAD Box helicases. Our data on mutational analysis of a conserved buried residue I143 in the walker motif B created inactive protein. The data confirm critical functions for dicer in generation of siRNAs and also in recognition of dsRNA ends. Mutants in buried residues L1130 and I1228 of RNase IIIb domain were inactive and the proximity of these residues to the catalytic core suggest that the critical structural alignment of catalytic residues is indispensable for carrying out dsRNA cleavage to generate siRNAs. We also attribute critical catalytic functions to SpDcr1 D1185 residue for generation of siRNA and heterochromatin formation as measured by our transcriptional gene silencing assay. Our studies employing biophysical and computational approaches to design temperature-sensitive mutants have been successfully applied to an essential splicing factor SpPrp18, which was refractory for ts mutants by other methods. Using a missense mutant, we showed its intron-specific splicing function for subsets of transcripts and deduced that its ubiquitous splicing role is arguable. We have uncovered a link between the splicing substrates of SpPrp18 and direct evidence of splicing based cell cycle regulation, thus providing a mechanistic link to the cell cycle arrest seen in some splicing factor mutants. The same methodology was applied to another important biological pathway, the RNAi machinery, where central factors SpAgoI and SpDcrI were examined We report the first instance of conditional gene silencing tool by designing Ago1 ts mutants which will be useful for future studies of the global interaction network between RNAi and other RNA processing events.

Le cœur humain est un organe composé de différents types cellulaires tels que les cardiomyocytes, les fibroblastes, les muscles lisses et les cellules endothéliales. Ces cellules se diversifient grâce à des mécanismes moléculaires spécifiques en acquérant leurs propriétés fonctionnelles spécifiques. L’embryon de Drosophile est un modèle simple et adapté pour étudier la diversification des cellules cardiaques et leurs propriétés spécifiques. Le but du projet est d’améliorer notre connaissance sur les acteurs moléculaires qui contrôlent la diversification des cellules cardiaques. Pour atteindre cet objectif nous avons appliqué la méthode TRAP-rc ("rare cell Translation Ribosome Affinity Purification") suivie du séquençage ARN pour identifier les ARN messagers en cours de traduction spécifiques des cellules cardiaques Tin et Lb (Tin CBs et Lb CBs) à deux stades de développement corrélés avec la morphogenèse du cœur embryonnaire. Dans une première analyse focalisée sur l'analyse des données issues des TRAP-Seq sur cellules Tin nous avons mis en évidence que CAP et MSP-300 sont impliqués dans la migration des cardioblasts pendant la fermeture du cœur. En parallèle, nous avons également identifié deux autres gènes impliqués dans la morphogenèse, kon-tiki et dGrip qui semblent contrôler la cohésion des CBs au cours de la migration. En outre, nous avons trouvé qu'au stade 16, environ 60% des gènes enrichis sont communs entre les populations Tin et Lb. Parmi ces gènes, Src42, sqa et flr participent à la régulation du cytosquelette d'actine et nos analyses ont permis de démontrer qu'ils avaient également des fonctions dans la morphogenèse cardiaque. Nous avons également identifié des groupes de gènes plus spécifiques à chacune des populations ciblées. Une catégorie fonctionnelle fortement associée à la population Lb, comprend les gènes qui régulent l'épissage des ARN messagers et certains de ces gènes semblent être requis au cours de la morphogenèse cardiaque. Enfin, nous avons comparé nos données de TRAP-seq cardiaque avec des données de TRAP-Seq issues du muscle somatique (de l'équipe), et ainsi identifié près de 90 gènes qui présentent des isoformes protéiques spécifiques à chaque tissu notamment impliquées dans la formation de l'unité contractile sarcomérique. Ceci suggère que des mécanismes d'épissage spécifiques sont mis en place dans différents types cellulaires pour moduler les fonctions de certaines protéines musculaires. A travers ce projet, nous avons identifié de nouveaux acteurs généraux de la migration collective des cardioblastes au cours de la fermeture du cœur mais également de nouveaux gènes potentiellement impliqués dans l’acquisition des propriétés spécifiques dessous populations cardiaques Tin et Lb et de tissus musculaires distincts. Nous espérons que les données générées permettront dans le futur de mieux comprendre les mécanismes de la cardiogenèse des vertébrés ainsi que l’étiologie de maladies cardiaques. / Cardiac cells diversification is required for the formation of a functional heart. Human heart is a multi-lineage organ that develops through progressive diversification of progenitors derived from different heart fields. This process is underlined by numerous changes in the expression of a repertory of genes that allow cells to acquire their own identity and functions. The Drosophila embryo is a relatively simple model to study the diversification of cardiac cells and their properties. The goal of this project is to identify the repertories of genes that control the formation of different types of cardiac cells. To reach this objective we applied Translation Ribosome Affinity Purification (TRAP) method followed by RNA sequencing in order to identify mRNA engaged in translation specific to two cardiac cell types (Tinman (Tin) and Labybird (Lb) expressing cells), at two different time windows. We obtained a list of enriched genes for the different types of cardiac cells and time points. In a first part, we focused our attention on the Tindatasets and found that two genes, CAP and Msp300, are involved in cardioblasts migration during the heart closure. Then we identified two other candidate genes kontiki and dGrip that seem to contribute to maintain cohesion between CBs during heartmorphogenesis. Moreover by comparing our spatial datasets, we found that for the same time point, around 60% of Tin CBs enriched genes are common with Lb CBs enriched population and within this group we identified evolutionary conserved genes such as Src42, flr and sqa known to be involved in the cytoskeleton organization and in the actinpolymerization and depolymerisation. Our premiminary analyses show that they seem to be required for correct cardiac morphogenesis. We also identified sets of genes more specific for each cardiac cell population. Indeed, Lb CBs datasets show that in early stage there is the enrichment of genes mostly involved in transcriptional regulation and RNA splicing and some of these genes (prp8 and prp38) are involved in cardiac development. In parallel, we compared our TRAP-Seq dataset in the cardiac system with the TRAP-seqon muscle cells, and identified close to 90 genes that present cardiac or muscular specific isoforms. It is known that the alternative splicing, by increasing proteins diversity, contributes to the acquisition of specific cell properties. Furthermore, some cardiomyopathies are associated to defects in the alternative splicing of genes encoding sarcomeric proteins that we found in our dataset such as Tropomyosin and Zasp52. With this project, we have identified new actors of collective cardioblast migration and a set of genes with potential role in the acquisition of individual properties of Tin and Lbcardiac cells or of specific type of muscle tissue. We hope that our data could provide new insights into the genetic control of vertebrate cardiogenesis and into etiology of cardiac diseases.

Vysoce výkonné sekvenční technologie produkují obrovské množství dat, která mohou odhalit nové geny, identifikovat splice varianty a kvantifikovat genovou expresi v celém genomu. Objem a složitost dat z RNA-seq experimentů vyžadují škálovatelné metody matematické analýzy založené na robustníchstatistických modelech. Je náročné navrhnout integrované pracovní postupy, které zahrnují různé postupy analýzy. Konkrétně jsou to srovnávací testy transkriptů, které jsou komplikovány několika zdroji variability měření a představují řadu statistických problémů. V tomto výzkumu byla sestavena integrovaná transkripční profilová pipeline k produkci nových reprodukovatelných kódů pro získání biologicky interpretovovatelných výsledků. Počínaje anotací údajů RNA-seq a hodnocení kvality je navržen soubor kódů, který slouží pro vizualizaci hodnocení kvality, potřebné pro zajištění RNA-Seq experimentu s analýzou dat. Dále je provedena komplexní diferenciální analýza genových expresí, která poskytuje popisné metody pro testované RNA-Seq data. Pro implementaci analýzy alternativního sestřihu a diferenciálních exonů jsme zlepšili výkon DEXSeq definováním otevřeného čtecího rámce exonového regionu, který se používá alternativně. Dále je popsána nová metodologie pro analýzu diferenciálně exprimované dlouhé nekódující RNA nalezením funkční korelace této RNA se sousedícími diferenciálně exprimovanými geny kódujícími proteiny. Takto je získán jasnější pohled na regulační mechanismus a poskytnuta hypotéza o úloze dlouhé nekódující RNA v regulaci genové exprese.

BPS/IC (Bladder Pain Syndrome/Interstitial Cystitis) ist ein sehr schweres und noch weitgehend unverstandenes Krankheitsbild in der Urologie. Viele Frauen sind im Alltag durch den ständigen Harndrang und die Schmerzen stark eingeschränkt und von Depressionen betroffen. Die Aufklärung der Pathogenese ist deshalb sehr wichtig, um eine adäquate Therapie für die Betroffenen zu entwickeln und die Krankheit möglichst frühzeitig diagnostizieren zu können. Das Schwangerschaftshormon hCG (humanes Choriongonadotropin) besitzt differenzierende und wachstumsfördernde Eigenschaften und eine Rolle in der Urothelregeneration und – stabilisierung scheint möglich. Daher ist das Ziel dieser Arbeit seinen Rezeptor, den LHCGR (Luteinizing-Hormone/Choriogonadotropin Rezeptor), in der Harnblase nachzuweisen und die urothelialen und muskulären Charakteristika zwischen gesunden und an BPS/IC erkrankten Harnblasen zu vergleichen. Die Darstellung des LHCGR erfolgte auf Proteinebene mittels indirekter Immunfluoreszenz und auf mRNA-Ebene durch Standard-PCR. Es zeigten sich im Urothel von Harnblase und Ureter 5 unterschiedliche Verteilungsmuster des Rezeptors hinsichtlich seiner Expression in verschiedenen Zellschichten und seiner subzellulären Lokalisation. Je nach Urothelzustand und zwischen den Entitäten Kontroll- bzw. BPS/IC-Harnblase variierten diese Muster in ihrer Häufigkeit. In anderen Epithelien, wie dem Vaginalepithel, änderte sich die zelluläre Verteilung des LHCGR in Abhängigkeit vom Differenzierungsgrad der Zellen. Es scheint möglich, dass auch die Rezeptorexpression in Urothelzellen deren verschiedene Differenzierungszustände widerspiegelt. Dies unterstützt den für hCG vermuteten Einfluss auf die Epithelregeneration. Ein Vergleich der urothelialen Fluoreszenzintensitäten zwischen weiblichen Kontroll – und BPS/IC-Harnblasen zeigte eine signifikant stärkere Expression des Rezeptors bei erkrankten Patienten. Dem gegenüber war kein Unterschied im Detrusor, weder zwischen Kontroll – und BPS/IC-Harnblasen noch im geschlechtsspezifischen Vergleich, festzustellen. Damit scheint der Rezeptor seine Hauptaufgabe vorrangig im Urothel zu entfalten. Die Korrelationsanalysen ergaben keinen signifikanten Zusammenhang zwischen dem Erkrankungsalter (Zeitpunkt der Diagnosestellung und Biopsieentnahme) und der LHCGR-Immunfluoreszenz. Ein endokrinologischer Einfluss auf die Rezeptorexpression wurde dadurch unwahrscheinlich und unterstützt die immer akzeptiertere Auffassung, dass BPS/IC nicht mehr mit der Menopause assoziiert ist. Neben dem Urothel und Detrusor zeigten auch Lamina propria und Gefäße von Harnblase und Ureter die Expression des LHCGR in der Immunhistochemie. Unterschiedliche Clustermuster des Rezeptors im Detrusor ließen auf die Oligomerisierung des Rezeptors schließen. Die Bedeutung dieser Zusammenschlüsse ist jedoch noch unklar, wobei unterschiedliche funktionelle Zustände des Rezeptors vermutet werden. Orientierung bieten andere Rezeptoren, die durch Dimerisierung verschiedener Rezeptorvarianten ihre Funktionalität verbessern oder verschlechtern konnten. Obwohl für keine bisher entdeckte Variante des LHCGR eine definitive Aufgabe ermittelt werden konnte, scheinen doch viele Varianten auch unterschiedliche Funktionen wahrnehmen zu können. Besonders auf der Regulierbarkeit des Rezeptors mittels interagierender Splicevarianten sollte das Augenmerk zukünftiger Studien liegen. Ob durch Komplexbildung verschiedener Varianten oder Bildung nichtfunktioneller trunkierter Rezeptoren, die Kontrollmöglichkeiten sind vielfältig und können auch auf Liganden wirken. Letztlich ließ der Nachweis des LHCGR in allen Schichten von Harnblase und Ureter eher eine globale Rolle des Rezeptors im Harntrakt des Menschen vermuten. Dazu passten auch die bereits nachgewiesenen Einflüsse seiner Liganden auf die Blasenfunktion von Hunden. Die hier vorgelegte Arbeit untersuchte zum ersten Mal die Expression des LHCGR mittels PCR und Immunhistochemie in humanen Harnblasen und Ureteren. Dabei löste sie sich von den sonst üblichen Vorstellungen einer Beziehung des Rezeptors zu Blasentumoren, Schwangerschaft oder Inkontinenz. Diagnose und Therapie von BPS/IC sind zur Zeit noch ständigen Wandlungen unterworfen und dabei entgehen viele Patienten der (frühen) Diagnosestellung und einer adäquaten Behandlung. Diese Studie sollte dazu beitragen neue Einblicke in die Pathophysiologie der Erkrankung zu erlangen, um eine kausale Therapie entwickeln zu können. Zukünftig könnten diese Ergebnisse dabei helfen die Anwendung einer sensitiven und vor allem spezifischen Diagnostik auf molekularer Ebene (mRNA - oder Proteinnachweis) zu ermöglichen.

Cellular function and physiology are largely established through regulated gene expression. The first step in gene expression, transcription of the genomic DNA into RNA, is a process that is highly aligned at the levels of initiation, elongation and termination. In eukaryotes, protein-coding genes are exclusively transcribed by RNA polymerase II (Pol II). Upon transcription of the first 15-20 nucleotides (nt), the emerging nascent RNA 5’ end is modified with a 7-methylguanosyl cap. This is one of several RNA modifications and processing steps that take place during transcription, i.e. co-transcriptionally. For example, protein-coding sequences (exons) are often disrupted by non-coding sequences (introns) that are removed by RNA splicing. The two transesterification reactions required for RNA splicing are catalyzed through the action of a large macromolecular machine, the spliceosome. Several non-coding small nuclear RNAs (snRNAs) and proteins form functional spliceosomal subcomplexes, termed snRNPs. Sequentially with intron synthesis different snRNPs recognize sequence elements within introns, first the 5’ splice site (5‘ SS) at the intron start, then the branchpoint and at the end the 3’ splice site (3‘ SS). Multiple conformational changes and concerted assembly steps lead to formation of the active spliceosome, cleavage of the exon-intron junction, intron lariat formation and finally exon-exon ligation with cleavage of the 3’ intron-exon junction. Estimates on pre-mRNA splicing duration range from 15 sec to several minutes or, in terms of distance relative to the 3‘ SS, the earliest detected splicing events were 500 nt downstream of the 3‘ SS. However, the use of indirect assays, model genes and transcription induction/blocking leave the question of when pre-mRNA splicing of endogenous transcripts occurs unanswered. In recent years, global studies concluded that the majority of introns are removed during the course of transcription. In principal, co-transcriptional splicing reduces the need for post-transcriptional processing of the pre-mRNA. This could allow for quicker transcriptional responses to stimuli and optimal coordination between the different steps. In order to gain insight into how pre-mRNA splicing might be functionally linked to transcription, I wanted to determine when co-transcriptional splicing occurs, how transcripts with multiple introns are spliced and if and how the transcription termination process is influenced by pre-mRNA splicing. I chose two yeast species, S. cerevisiae and S. pombe, to study co-transcriptional splicing. Small genomes, short genes and introns, but very different number of intron-containing genes and multi-intron genes in S. pombe, made the combination of both model organisms a promising system to study by next-generation sequencing and to learn about co-transcriptional splicing in a broad context with applicability to other species. I used nascent RNA-Seq to characterize co-transcriptional splicing in S. pombe and developed two strategies to obtain single-molecule information on co-transcriptional splicing of endogenous genes: (1) with paired-end short read sequencing, I obtained the 3’ nascent transcript ends, which reflect the position of Pol II molecules during transcription, and the splicing status of the nascent RNAs. This is detected by sequencing the exon-intron or exon-exon junctions of the transcripts. Thus, this strategy links Pol II position with intron splicing of nascent RNA. The increase in the fraction of spliced transcripts with further distance from the intron end provides valuable information on when co-transcriptional splicing occurs. (2) with Pacific Biosciences sequencing (PacBio) of full-length nascent RNA, it is possible to determine the splicing pattern of transcripts with multiple introns, e.g. sequentially with transcription or also non-sequentially. Part of transcription termination is cleavage of the nascent transcript at the polyA site. The splicing status of cleaved and non-cleaved transcripts can provide insights into links between splicing and transcription termination and can be obtained from PacBio data. I found that co-transcriptional splicing in S. pombe is similarly prevalent to other species and that most introns are removed co-transcriptionally. Co-transcriptional splicing levels are dependent on intron position, adjacent exon length, and GC-content, but not splice site sequence. A high level of co-transcriptional splicing is correlated with high gene expression. In addition, I identified low abundance circular RNAs in intron-containing, as well as intronless genes, which could be side-products of RNA transcription and splicing. The analysis of co-transcriptional splicing patterns of 88 endogenous S. cerevisiae genes showed that the majority of intron splicing occurs within 100 nt downstream of the 3‘ SS. Saturation levels vary, and confirm results of a previous study. The onset of splicing is very close to the transcribing polymerase (within 27 nt) and implies that spliceosome assembly and conformational rearrangements must be completed immediately upon synthesis of the 3‘ SS. For S. pombe genes with multiple introns, most detected transcripts were completely spliced or completely unspliced. A smaller fraction showed partial splicing with the first intron being most often not spliced. Close to the polyA site, most transcripts were spliced, however uncleaved transcripts were often completely unspliced. This suggests a beneficial influence of pre-mRNA splicing for efficient transcript termination. Overall, sequencing of nascent RNA with the two strategies developed in this work offers significant potential for the analysis of co-transcriptional splicing, transcription termination and also RNA polymerase pausing by profiling nascent 3’ ends. I could define the position of pre-mRNA splicing during the process of transcription and provide evidence for fast and efficient co-transcriptional splicing in S. cerevisiae and S. pombe, which is associated with highly expressed genes in both organisms. Differences in S. pombe co-transcriptional splicing could be linked to gene architecture features, like intron position, GC-content and exon length.

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