Zusammenfassung Ziel: Eine lagerungsbedingte einseitige Abflachung des Hinterkopfes aufgrund externer Kräfte (Lagerungsplagiocephalus, LP) ist die häufigste Kopfdeformität im Säuglingsalter. Die im Rahmen der ersten Kindervorsorgeuntersuchung (U1) erhobenen Daten wurden bezüglich der bekannten Risikofaktoren für die Entstehung eines LP ausgewertet. Im Rahmen der vorliegenden klinischen Pilotstudie wurde der Lagerungsplagiozephalus mitels der non-invasiven dreidimensionalen Sterophotogrammetrie untersucht und erstmals eine Normdatenbank von Säuglingen ohne Kopfdeformitäten erstellt. Die Therapie und Effektivität mittels modellierender individuell angefertigter Kopforthese, wurde evaluiert. Patienten und Methode: Untersucht wurden 20 Säuglinge mit einem Lagerungsplagiozephalus und schwerer Asymmetrie (Alter 6,0+0,97 Monate) und 20 Säuglinge ohne Kopfdeformität (Alter 6,4+0,3 Monate). Es erfolgte eine 3D-Weichteilanalyse des gesamten Kopfes. Zur Evaluation der Kopforthesentherapie wurden prä- und posttherapeutisch angefertigte sterophotogrammtriesche Aufnahmen dreidimensional ausgewertet. Ergebnisse: Anhand der im Rahmen der Erstuntersuchung erhobenen Daten zeigten sich bezüglich der Geburtslage und Art der Entbindung nur geringe Unterschiede. In der Patientengruppe kamen eine Beckenendlage und die Geburt durch Kaiserschnitt gehäuft vor. Die Anzahl der Spontangeburten zeigte sich in der Kontrollgruppe mit 70% größer als in der Patientengruppe mit 60%. Köpergröße, Körpergewicht und Kopfumfanges fielen in der Patientengruppe kleiner aus. Im Rahmen der vorliegenden Untersuchung wurden erstmalig 3D-Oberflächendaten von gesunden Säuglingsköpfen erhoben. Hierzu wurden die 360° Aufnahmen mittels lichtoptischen Verfahrens durchgeführt. Die reliable Auswertung der Säuglingsköpfe erfolgte in einem virtuellen Raum und diente zur Erstellung einer Normdatenbank. Bestehende Asymmetrien lassen sich mit diesem Verfahren quantifizieren. Die non-invasive 3D-Bildgebung kann somit zusätzlich zur klinischen Untersuchung und Sonographie als reliables Instrument in der Diagnostik und Verlaufsbeurteilung eingesetzt werden. Mittels der durchgeführten Aufnahmen konnten folgenden Parameter bei Säuglingen mit LP charakterisiert werden: - Die maximale Kopflänge zeigt sich bei vergrößertem Breiten/Längen-Index reduziert. Kompensatorisch erfolgt eine Vergrößerung der Vertexhöhe. - Die Ohrachse zeigt sich verschoben. - Die betroffenen Säuglinge weisen eine vergrößerte 30° Diagonalendifferenz auf und zeigen asymmetrische anteriore und posteriore Volumina des Neurokraniums. Schlussfolgerung: Die im Rahmen der Erstuntersuchung (U1) ermittelten Daten zeigten nur geringe Unterschiede zwischen der Patienten- und der Kontrollgruppe bezüglich Risikofaktoren für die Entstehung eines LP. Die Anzahl an Kaiserschnitten war innerhalb der Patientengruppe erhöht. Die im Rahmen der Pilotstudie untersuchte Anzahl Kinder ist allerdings zu gering um eine definitive Aussage treffen zu können. Die Therapie mittels individuell gefertigter Kopforthese hat eine Harmonisierung des Breiten/Längen-Index zur Folge. Eine posttherapeutische Verbesserung kann bezüglich der neurokraniellen Asymmetrie mit einer Reduktion der 30° Diagonalendifferenz und einer Angleichung der posterioren Volumina beobachtet werden. Die frühzeitige Korrektur, ab dem sechsten Lebensmonat, kann eine lagerungsbedingten Kopfdeformität frühzeitig korrigieren. Bezüglich der Bewertung des Langzeiterfolges der Helmtherapie sind noch weitere Studien notwendig. Insbesondere der longitundinale Aufbau einer Normdatenbank ist erforderlich, um physiologische Referenzdaten zu schaffen. / OBJECTIVE: Unilateral positional plagiocephaly is the most common deformity of the head in infants. As part of a prospective controlled clinical study, the pathomorphology of the positional plagiocephaly in early infancy was examined. The goal was to use noninvasive three-dimensional (3D) imaging to generate, for the first time ever, a standard database of infants without head deformities, to quantify the asymmetry of the positional plagiocephaly, and to evaluate the effectiveness of functional growth control using head orthesis. PATIENTS AND METHODS: In the present study, 3D soft-tissue data of the entire head were collected from a total of 40 infants: 20 with positional plagiocephaly (6.0 ± 0.97 months) and 20 infants without a head deformity (6.4 ± 0.3 months). Functional growth was controlled using a custom-made head orthesis. To evaluate the therapy, pre- and posttherapeutic scans were evaluated in three dimensions. RESULTS: The newbornscreening confirms the known risk factors of DP as male gender, number of deliveries and abnormal presentation. Compared with the control group, infants with positional plagiocephaly demonstrated a reduced maximum length of the head, an increased head height, a shift in the ear axis as well as asymmetric anterior and posterior volumes of the neurocranium in lateral comparisons. Therapy using head orthesis led to a significant improvement of the asymmetry, with a reduction of the diagonal difference and an adjustment of the posterior volumes. CONCLUSION: Conservative growth control of extrinsically deformed infant skulls represents an interdisciplinary medical expansion of the orthodontic therapeutic spectrum. To prevent potential effects of positional plagiocephaly on the viscerocranium, head orthesis therapy is advisable in infancy

The concept of the gene has been constantly challenged by new discoveries in the life sciences. Recent challenging observations include the high frequency of alternative splicing events and the common transcription of non-protein-coding-RNAs (ncRNAs) from the genome. The latter has long been considered noise in biological systems. Multiple lines of evidence from genomic studies indicate that alternative splicing and ncRNA play important roles in expanding proteome diversity in eukaryotes. Here, the aim is to find the link between alternative splicing and ncRNAs by studying the expression profile of the spliceosomal snRNAs (U snRNA). Spliceosomal snRNAs are essential for pre-mRNA splicing in eukaryotes. They participate in splice site selection, recruitment of protein factors and catalyzing the splicing reaction. Because of this, both the abundance and diversity of U snRNAs were expected to be large. In our study we deeply analyzed the U snRNA population in primates using a combination of bioinformatical, biochemical and high throughput sequencing approaches. This transcriptome profiling has revealed that human, chimpanzee and rhesus have similar U snRNA populations, i.e. the vast majority of U snRNAs originate from few well-defined gene loci and the heterogeneity observed in U snRNA populations was largely due to the presence of SNPs at these loci. It seems that the gene loci that could potentially encode a significantly heterogeneous population of U snRNAs are mostly silent. Only few minority transcripts were detected in our study, and among them three U1-like snRNAs might play a role in the regulation of alternative splicing by recognizing non-canonical splicing sites. Mutations of U snRNA have been shown to impact the splicing process. Therefore, our study provides a reference to study the biological significance of SNPs in U snRNA genes and their association with diseases.

Non-coding RNAs (ncRNAs) have emerged as highly diverse and powerful key players in the cell, the range of capabilities spanning from catalyzing essential processes in all living organisms, e.g. protein synthesis, to being highly specific regulators of gene expression. To fully understand the functional significance of ncRNAs, it is of critical importance to identify and characterize the repertoire of ncRNAs in the cell. Practically every genome-wide screen to identify ncRNAs has revealed large numbers of expressed ncRNAs and often identified species-specific ncRNA families of unknown function. Recent years' advancement in high-throughput sequencing techniques necessitates efficient and reliable methods for computational identification and annotation of genes. A major aim in the work underlying this thesis has been to develop and use computational tools for the identification and characterization of ncRNA genes. We used computational approaches in combination with experimental methods to study the ncRNA repertoire of the model organism Dictyostelium discoideum. We report ncRNA genes belonging to well-characterized gene families as well as previously unknown and potentially species-specific ncRNA families. The complicated task of de novo ncRNA gene prediction was successfully addressed by developing a method for nucleotide composition-based gene prediction using maximal-scoring partial sums and considering overlapping dinucleotides. We also report a substantial heterogeneity among human spliceosomal snRNAs. Northern blot analysis and cDNA cloning, as well as bioinformatical analysis of publicly available microarray data, revealed a large number of expressed snRNAs. In particular, U1 snRNA variants with several nucleotide substitutions that could potentially have dramatic effects on splice site recognition were identified. In conclusion, we have by using computational approaches combined with experimental analysis identified a rich and diverse ncRNA repertoire in the eukaryotes D. discoideum and Homo sapiens. The surprising diversity among the snRNAs in H. sapiens suggests a functional involvement in recognition of non-canonical introns and regulation of messenger RNA splicing.

Les ARNs non codants sont des régulateurs de l'expression génétique à plusieurs niveaux. Chez la bactérie et chez la souris, des ARNs non codants (6S et B2) ont la propriété de se lier à l'ARN polymérase et d'inhiber son activité. Afin de déterminer si l'ARN polymérase II (RNAPII) humaine était associée à des ARNs non codants, une immunoprécipitation anti-RNAPII a été réalisée sur des cellules HeLa mitotiques. Les ARNs co-immunoprécipités ont été purifiés et marqués et l'ARN U1 s'est trouvé particulièrement enrichi par rapport au contrôle. Cette co-immunoprécipitation reflète l'association de la snRNP U1 avec la RNAPII. Pour vérifier cette association sur un site de transcription actif, des lignées ont été établies avec l'insertion en multiples copies d'un gène à un site unique, créant ainsi un unique super site de transcription visualisable par FISH (Fluorescence In Situ Hybridization). Deux lignées distinctes ont été créées, l'une avec un gène comportant un intron, l'autre avec le même gène où l'intron comporte trois mutations ponctuelles abolissant l'épissage. Alors que les snARNs U2, U4, U5 et U6 sont absents du site non épissé, l'ARN U1 est enrichi de la même façon indépendamment de l'épissage. La présence des protéines spécifiques de la snRNP U1 indique que la snRNP U1 est recrutée au complet au site de transcription. Ces résultats laissent supposer un rôle pour l'association RNAPII - U1snRNP dans l'épissage cotranscriptionnel.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23049号 / 理博第4726号 / 新制||理||1677(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 大野 睦人, 教授 青山 卓史, 教授 川口 真也 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

No description available.

Selecionamos consecutivamente 63 pacientes com doença mista do tecido conectivo (DMTC) (Kasukawa, 87) para determinar a relevância do padrão SD. Ter uma capilaroscopia periungueal (CPU) até cinco anos antes do início do estudo foi o principal critério de inclusão. Na entrada, avaliamos o envolvimento de órgãos e os auto-anticorpos. A idade média e o tempo de doença foram 45,3 + 10 e 8,45 + 5,42 anos, respectivamente. O padrão SD foi observado em 41 pacientes na entrada (65%) e em 45 na CPU prévia (71,5%), p = 0,20. Dez pacientes (16%) alteraram a CPU, 7 normalizaram e 3 desenvolveram padrão SD. O tempo de doença, número e freqüência de órgãos envolvidos foram semelhantes em pacientes com e sem padrão SD. Em contraste, a análise de cada parâmetro do padrão SD mostrou uma freqüência significativamente menor de áreas avasculares (AA) moderadas/graves na entrada, comparada com a CPU anterior (26,5 e 53%, p = 0,013). Além disto, 76% dos pacientes com doença intersticial pulmonar (TCAR) tiveram AA na entrada, enquanto apenas 24% dos pacientes com esta alteração não apresentavam este achado à CPU (p = 0,017). Adicionalmente, reduzida densidade capilar foi freqüentemente observada em pacientes submetidos à terapia imunossupressora, quando comparados com o grupo sem este tratamento (66,7 e 33,3%, p = 0,001). A CPU na DMTC é um processo dinâmico e a análise de cada parâmetro do padrão SD parece ser um bom indicador de doença intersticial pulmonar e gravidade de doença. / For determining the clinical relevance of SD-pattern in MCTD, sixty-three MCTD patients (Kasukawa´s criteria) were consecutively selected. The main inclusion criterion was availability of previous nailfold capillaroscopy (NC) 5 years before inclusion. At entry, organ involvement and autoantibody evaluation were performed. The mean age and disease duration were 45.3 + 10 and 8.45 + 5.42 years, respectively. SD-pattern was observed in 41 patients at entry (65%) and in 45 at previous NC (71.5%), p = 0.20. Ten patients (16%) changed NC, 7 normalized, and 3 developed SD-pattern. Disease duration, number and frequency of organ involvement were similar in patients with and without SD-pattern. In contrast, analysis of each SD-pattern parameter revealed a significant lower frequency of moderate/severe avascular areas (AA) at entry compared to previous examination (26.5 vs. 53%, p = 0.013). Moreover, 76% of patients with interstitial lung disease (HRCT) had AA at entry, whereas only 24% of patients with this alteration did not have this NC finding (p = 0.017). Furthermore, reduced capillary density was frequently observed in patients taking immunosuppressive therapy than those without (66.7 vs. 33.3%, p = 0.001). NC in MCTD is a dynamic process and analysis of each SD-pattern parameter seems to be a good indicator of lung involvement and disease severity

Selecionamos consecutivamente 63 pacientes com doença mista do tecido conectivo (DMTC) (Kasukawa, 87) para determinar a relevância do padrão SD. Ter uma capilaroscopia periungueal (CPU) até cinco anos antes do início do estudo foi o principal critério de inclusão. Na entrada, avaliamos o envolvimento de órgãos e os auto-anticorpos. A idade média e o tempo de doença foram 45,3 + 10 e 8,45 + 5,42 anos, respectivamente. O padrão SD foi observado em 41 pacientes na entrada (65%) e em 45 na CPU prévia (71,5%), p = 0,20. Dez pacientes (16%) alteraram a CPU, 7 normalizaram e 3 desenvolveram padrão SD. O tempo de doença, número e freqüência de órgãos envolvidos foram semelhantes em pacientes com e sem padrão SD. Em contraste, a análise de cada parâmetro do padrão SD mostrou uma freqüência significativamente menor de áreas avasculares (AA) moderadas/graves na entrada, comparada com a CPU anterior (26,5 e 53%, p = 0,013). Além disto, 76% dos pacientes com doença intersticial pulmonar (TCAR) tiveram AA na entrada, enquanto apenas 24% dos pacientes com esta alteração não apresentavam este achado à CPU (p = 0,017). Adicionalmente, reduzida densidade capilar foi freqüentemente observada em pacientes submetidos à terapia imunossupressora, quando comparados com o grupo sem este tratamento (66,7 e 33,3%, p = 0,001). A CPU na DMTC é um processo dinâmico e a análise de cada parâmetro do padrão SD parece ser um bom indicador de doença intersticial pulmonar e gravidade de doença. / For determining the clinical relevance of SD-pattern in MCTD, sixty-three MCTD patients (Kasukawa´s criteria) were consecutively selected. The main inclusion criterion was availability of previous nailfold capillaroscopy (NC) 5 years before inclusion. At entry, organ involvement and autoantibody evaluation were performed. The mean age and disease duration were 45.3 + 10 and 8.45 + 5.42 years, respectively. SD-pattern was observed in 41 patients at entry (65%) and in 45 at previous NC (71.5%), p = 0.20. Ten patients (16%) changed NC, 7 normalized, and 3 developed SD-pattern. Disease duration, number and frequency of organ involvement were similar in patients with and without SD-pattern. In contrast, analysis of each SD-pattern parameter revealed a significant lower frequency of moderate/severe avascular areas (AA) at entry compared to previous examination (26.5 vs. 53%, p = 0.013). Moreover, 76% of patients with interstitial lung disease (HRCT) had AA at entry, whereas only 24% of patients with this alteration did not have this NC finding (p = 0.017). Furthermore, reduced capillary density was frequently observed in patients taking immunosuppressive therapy than those without (66.7 vs. 33.3%, p = 0.001). NC in MCTD is a dynamic process and analysis of each SD-pattern parameter seems to be a good indicator of lung involvement and disease severity

It is currently believed that the splicing of most pre-mRNAs occurs, at least in part, co-transcriptionally. In order to validate this principle in yeast and establish an experimental system for monitoring spliceosome assembly in vivo, I have employed the chromatin immunoprecipitation (ChIP) assay to study co-transcriptional splicing events. Here, I use ChIP to examine key questions with respect to the recent proposal that RNA polymerase II (Pol II) recruits pre-mRNA splicing factors to active genes. In my thesis, I address: 1) whether the U1 snRNP, which binds to the 5¡¦ splice site of each intron, is recruited co-transcriptionally in vivo and 2) if so, where along the length of active genes the U1 snRNP is concentrated. U1 snRNP accumulates on downstream positions of genes containing introns but not within promoter regions or along intronless genes. More specifically, accumulation correlated with the presence and position of the intron, indicating that the intron is necessary for co-transcriptional U1 snRNP recruitment and/or retention (Kotovic et al., 2003). In contrast to capping enzymes, which bind directly to Pol II (Komarnitsky et al., 2000; Schroeder et al., 2000), the U1 snRNP is poorly detected in promoter regions, except in genes harboring promoter-proximal introns. Detection of the U1 snRNP is dependent on RNA synthesis and is abolished by intron removal. Microarray data reveals that intron-containing genes are preferentially selected by ChIP with the U1 snRNP furthermore indicating recruitment specificity to introns. Because U1 snRNP levels decrease on downstream regions of intron-containing genes with long second exons, our lab is expanding the study to 3¡¦ splice site factors in hopes to address co-transcriptional splicing. In my thesis, I also focus on questions pertaining to the requirements for recruitment of the U1 snRNP to sites of transcription. To test the proposal that the cap-binding complex (CBC) promotes U1 snRNP recognition of the 5¡¦ splice site (Colot et al., 1996), I use a ?´CBC mutant strain and determine U1 snRNP accumulation by ChIP. Surprisingly, lack of the CBC has no effect on U1 snRNP recruitment. The U1 snRNP component Prp40p has been identified as playing a pivotal role in not only cross-intron bridging (Abovich and Rosbash, 1997), but also as a link between Pol II transcription and splicing factor recruitment (Morris and Greenleaf, 2000). My data shows that Prp40p recruitment mirrors that of other U1 snRNP proteins, in that it is not detected on promoter regions, suggesting that Prp40p does not constitutively bind the phosphorylated C-terminal domain (CTD) of Pol II as previously proposed. This physical link between Pol II transcription and splicing factor recruitment is further tested in Prp40p mutant strains, in which U1 snRNP is detected at normal levels. Therefore, U1 snRNP recruitment to transcription units is not dependent on Prp40p activity. My data indicates that co-transcriptional U1 snRNP recruitment is not dependent on the CBC or Prp40p and that any effects of these players on spliceosome assembly must be reflected in later spliceosome events. My data contrasts the proposed transcription factory model in which Pol II plays a central role in the recruitment of mRNA processing factors to TUs. According to my data, splicing factor recruitment acts differently than capping enzyme and 3¡¦ end processing factor recruitment; U1 snRNP does not accumulate at promoter regions of intron-containing genes or on intronless genes rather, accumulation is based on the synthesis of the intron. These experiments have lead me to propose a kinetic model with respect to the recruitment of splicing factors to active genes. In this model, U1 snRNP accumulation at the 5¡¦ splice site requires a highly dynamic web of protein-protein and protein-RNA interactions to occur, ultimately leading to the recruitment and/or stabilization of the U1 snRNP.

It is currently believed that the splicing of most pre-mRNAs occurs, at least in part, co-transcriptionally. In order to validate this principle in yeast and establish an experimental system for monitoring spliceosome assembly in vivo, I have employed the chromatin immunoprecipitation (ChIP) assay to study co-transcriptional splicing events. Here, I use ChIP to examine key questions with respect to the recent proposal that RNA polymerase II (Pol II) recruits pre-mRNA splicing factors to active genes. In my thesis, I address: 1) whether the U1 snRNP, which binds to the 5¡¦ splice site of each intron, is recruited co-transcriptionally in vivo and 2) if so, where along the length of active genes the U1 snRNP is concentrated. U1 snRNP accumulates on downstream positions of genes containing introns but not within promoter regions or along intronless genes. More specifically, accumulation correlated with the presence and position of the intron, indicating that the intron is necessary for co-transcriptional U1 snRNP recruitment and/or retention (Kotovic et al., 2003). In contrast to capping enzymes, which bind directly to Pol II (Komarnitsky et al., 2000; Schroeder et al., 2000), the U1 snRNP is poorly detected in promoter regions, except in genes harboring promoter-proximal introns. Detection of the U1 snRNP is dependent on RNA synthesis and is abolished by intron removal. Microarray data reveals that intron-containing genes are preferentially selected by ChIP with the U1 snRNP furthermore indicating recruitment specificity to introns. Because U1 snRNP levels decrease on downstream regions of intron-containing genes with long second exons, our lab is expanding the study to 3¡¦ splice site factors in hopes to address co-transcriptional splicing. In my thesis, I also focus on questions pertaining to the requirements for recruitment of the U1 snRNP to sites of transcription. To test the proposal that the cap-binding complex (CBC) promotes U1 snRNP recognition of the 5¡¦ splice site (Colot et al., 1996), I use a ?´CBC mutant strain and determine U1 snRNP accumulation by ChIP. Surprisingly, lack of the CBC has no effect on U1 snRNP recruitment. The U1 snRNP component Prp40p has been identified as playing a pivotal role in not only cross-intron bridging (Abovich and Rosbash, 1997), but also as a link between Pol II transcription and splicing factor recruitment (Morris and Greenleaf, 2000). My data shows that Prp40p recruitment mirrors that of other U1 snRNP proteins, in that it is not detected on promoter regions, suggesting that Prp40p does not constitutively bind the phosphorylated C-terminal domain (CTD) of Pol II as previously proposed. This physical link between Pol II transcription and splicing factor recruitment is further tested in Prp40p mutant strains, in which U1 snRNP is detected at normal levels. Therefore, U1 snRNP recruitment to transcription units is not dependent on Prp40p activity. My data indicates that co-transcriptional U1 snRNP recruitment is not dependent on the CBC or Prp40p and that any effects of these players on spliceosome assembly must be reflected in later spliceosome events. My data contrasts the proposed transcription factory model in which Pol II plays a central role in the recruitment of mRNA processing factors to TUs. According to my data, splicing factor recruitment acts differently than capping enzyme and 3¡¦ end processing factor recruitment; U1 snRNP does not accumulate at promoter regions of intron-containing genes or on intronless genes rather, accumulation is based on the synthesis of the intron. These experiments have lead me to propose a kinetic model with respect to the recruitment of splicing factors to active genes. In this model, U1 snRNP accumulation at the 5¡¦ splice site requires a highly dynamic web of protein-protein and protein-RNA interactions to occur, ultimately leading to the recruitment and/or stabilization of the U1 snRNP.