The phenotypic variability in human populations is partly the result of gene polymorphisms and differential gene expression. Studying the variability of gene expression across human populations is essential to understanding the molecular basis for diversity. However, key issues remain unanswered with respect to human expression variability. For example, the role of gene methylation in expression variability is uncertain, nor is it clear what role tissue-specific factors may have. Moreover, the contribution that expression variability has in aging and development is unknown. Here we classified human genes based on their expression variability in normal human breast and brain samples and identified functional aspects associated with high and low expression variability. Interestingly, both high variability and low variability gene sets are enriched for developmentally essential genes. There is limited overlap between the variably expressed genes of different tissues, indicating that tissue-specific rather than individual-specific factors are at work. We also find that methylation likely has a key role in controlling expression variability insofar as genes with low expression variability are likely to be non-methylated. Importantly, we find that genes with high population expression variability are likely to have age-, but not sex-dependent expression. Taken together, our work indicates that gene expression variability is tissue-specific, methylation-dependent, and is an important component of the natural aging process.

In this study, we assessed pirAB toxin transcription in Photorhabdus luminescens laumondii (strain TT01) (Enterobacteriaceae) by comparing mRNA abundance under in vivo and in vitro conditions. In vivo assays considered both natural and forced infections with two lepidopteran hosts: Galleria mellonella and Manduca sexta. Three portals of entry were utilized for the forced infection assays: (a) integument; (b) the digestive route (via mouth and anus); and (c) the tracheal route (via spiracles). We also assessed plu4093-2 transcription during the course of a natural infection; this is when the bacteria are delivered by Heterorhabditis bacteriophora nematodes. Transcript abundance in G. mellonella was higher than in M. sexta at two of the observed time points: 15 and 18 h. Expression of pirAB plu4093-2 reached above endogenous control levels at 22 h in G. mellonella but not in M. sexta. Overall, pirAB plu4093-2 transcripts were not as highly expressed in M. sexta as in G. mellonella, from 15 to 22 h. This is the first study to directly compare pirAB plu4093-2 toxin transcript production considering different portals of entry.

The majority of genetic differences between species and individuals have been hypothesised to impact on the regulation, rather than the structure, of genes. As the details of genetic variation are uncovered by the various genome sequencing projects, understanding the functional effects on gene regulation will be key to uncovering the molecular mechanisms underying the genesis and inheritance of common phenotypes, such as complex human disease and commercially important traits in plants and animals. Unlike coding sequence polymorphisms, genetic variants affecting gene expression will reside in the transcriptional machinery and its regulatory inputs. As these are largely specific to cell- or tissue-types, we would expect that regulatory variants will also affect final mRNA levels in a tissue specific manner. Genetic variation between individuals may therefore be more complex than the sum total of sequence differences between them. Demonstrating this hypothesis is the main focus of this thesis. We use microarrays to measure mRNA levels of approximately 22,000 transcripts in inbred and recombinant inbred strains of mice, and present compelling evidence that the genetic influences on these levels are tissue-specific in at least 85% of cases. We uncover two loci which apparently influence transcript levels of multiple genes in a tissue-specific manner. We also present evidence that failure of microarray data normalisation may cause spurious linkage of expression phenotypes leading to erroneous biological conclusions, and detail a novel, extensible mathematical framework for performing tailored normalisation which can remove such systematic bias. The wider context of these results is then discussed.

Abstract The collagens are a family of extracellular matrix proteins with a widespread tissue distribution. Collagen biosynthesis requires the hydroxylation of a number of proline residues by prolyl 4-hydroxylase. This posttranslational modification is essential for the synthesis of all collagens, as 4-hydroxyproline deficient collagens cannot form stable triple helices at body temperature. The genes for the human and mouse prolyl 4-hydroxylase α(II) subunits were cloned and characterized in this study. The human and mouse genes are 34.6 and 30.3 kb in size, respectively, consisting of 16 exons and 15 introns. The intron sizes vary from 48-49 bp to over 8 kb in both genes. The 5' flanking regions contain no TATA box, but there are several motifs that may act as transcription factor binding sites. A novel mutually exclusively spliced exon 12a was identified in both genes. Both variants of the α(II) subunit were found to be expressed in a variety of tissues and both formed a fully active recombinant tetramer with the β subunit when expressed in insect cells. Tissue distribution of the type I and type II prolyl 4-hydroxylase isoenzymes was studied in developing, mature, and malignant cells and tissues by immunofluorescence and Western blotting. The results indicate that the type I isoenzyme is the main form in many cell types. Skeletal myocytes and smooth muscle cells appeared to have the type I isoenzyme as their only prolyl 4-hydroxylase form, whereas the type II isoenzyme was clearly the main form in chondrocytes. A strong signal for the type II enzyme was detected in cultured umbilical and capillary endothelial cells, whereas the type I isoenzyme could not be detected in these cells by immunostaining or Western blotting. Similar studies on primary chondro- and osteosarcomas and benign bone tumours indicated that the type I isoenzyme is the predominant form in both types of bone sarcoma, whereas the type II isoenzyme was more abundantly expressed in benign tumours. In chondrosarcomas, the type II isoenzyme was expressed in the nonmalignant chondrocytes, whereas their malignant counterparts switched their expression pattern to that of the type I isoenzyme. Two isoforms of the catalytic prolyl 4-hydroxylase α subunit, PHY-1 and PHY-2, have previously been characterized from Caenorhabditis elegans. This study reports the cloning and characterization of a third C. elegans α subunit isoform, PHY-3, which is much shorter than the previously characterized vertebrate and C. elegans α subunits. Nematodes homozygous for a phy-3 deletion were phenotypically wild type and fertile, but the 4-hydroxyproline content of their early embryos was reduced by about 90%. The expression of PHY-3 was found to be restricted to spermatheca of late larvae and adult nematode, indicating that PHY-3 is likely to be involved in the synthesis of collagens of the early embryo egg shells.

No description available.

Dans l’histoire évolutive, deux gènes paralogues sont issus d’un évènement de duplication de leur ancêtre commun. Les gènes paralogues sont caractérisés par des duplications globales de génome (WGD) ou à petite échelle (SSD) et par leur datation. Les WGDs ont lieu à deux reprises à la base de la lignée des vertébrés. Les évènements de SSD ont lieu à plusieurs moments pouvant être plus récents, plus anciens ou contemporain de la période des évènements de WGD. La rétention des paralogues dans le génome, associée à une divergence de l’expression spatiale est une contribution importante pour l’augmentation de la complexité de l’organisme au cours de l’évolution. Certaines études ont montré que les duplications anciennes seraient plus associées aux maladies. L’objectif de la première partie de la thèse est de créer une ressource sur les paralogues en collectant et en analysant différentes annotations. Nous avons construit une ressource robuste de paralogues humains à partir de listes publiées mais aussi à partir d’annotations externes. L’exploration de différentes annotations nous a permis d’identifier une identité de séquence élevée entre gènes paralogues pouvant biaiser la mesure d’expression des gènes et diminuer leur expression. L’objectif de la seconde partie, est d’explorer l’expression spatiale et la co- expression des paralogues au sein du cerveau humain, à partir des données RNA-seq du consortium GTEx. Les données d’expression GTEx de 13 tissus cérébraux, nous ont permis de montrer que la datation récente mais aussi que le type SSD contribuaient à une expression plus tissu-spécifique. Nous avons utilisé l’analyse de la co-expression (WGCNA) afin de regrouper les paralogues possédant une expression similaire au travers des tissus et nous avons pu suggérer une co-expression des SSD récents. Nos études sur les maladies ont montré que les SSD récents accumulaient des mutations associées à des maladies cérébrales. Finalement, nous avons trouvé que la co-expression des paralogues et leur tissu-spécificité au travers des régions cérébrales pouvaient enrichir nos connaissances sur les gènes associés à des maladies cérébrales. / In evolution history, two paralogous genes originate from the duplication event of a common ancestor gene. Paralogous genes are characterized by whole genome (WGD) or small-scale (SSD) duplications and their duplication date. The WGDs happened twice in the early vertebrate lineage. SSD events take place at any moment in evolutionary history and can be younger, older or dating to the same period than WGD events. Retention of paralogs in the genome associated with divergence of spatial expression is an important contributor to the increase of organism complexity through evolution. Different studies found that old duplications are more associated with diseases. The objective of the first part of the thesis is to create a resource on paralogs by collecting and analyzing annotations. We built a robust resource of human paralogs from published lists of paralogous genes and also from external annotations. Annotation exploration allowed us to identify a high sequence identity between paralogous genes impacting the gene expression measurement from RNA-seq data and decreasing the gene expression. The objective of the second part is to explore spatial expression and co-expression of paralogs in the human brain, from the GTEx consortium RNA-seq data. The GTEx expression data of 13 brain tissues allowed us to show that duplication youth and SSD type contributed to a more tissue-specific expression. We used co-expression analyses (WGCNA) to group paralogs with similar expression across tissues and we suggested the co-expression of younger SSDs. Our disease studies showed the younger SSD accumulation of mutations associated with brain diseases. We finally found that paralog co-expression and their tissue-specificity across brain regions could enrich information of known brain disease-associated genes.

No description available.

La maladie de Huntington (MH) est une maladie neurodégénérative fatale, causée par l’expansion des répétitions CAG du gène de Huntingtine. La longueur de l’expansion est instable et proportionnelle à la gravité de la maladie. L’instabilité varie selon les tissus, p.ex. le striatum est très instable et dégénère, alors que le cervelet a une instabilité limitée et est épargné par la maladie. Nous avons étudié le rôle des lésions oxydantes et du mécanisme de réparation par excision de base (BER) dans la sélectivité tissulaire de l'instabilité dans ces deux tissus de souris R6/1. Le niveau des lésions était similaire dans ces tissus, alors que les niveaux et les activités des principales protéines BER étaient globalement diminués dans le striatum. L’efficacité de réparation dépendait de la stoechiométrie de BER, la position de la lésion et la séquence d’ADN. Nos résultats suggèrent une faible coopération entre les activités BER associée à la spécificité tissulaire de l’instabilité de la MH. / Huntington’s disease (HD) is a neurodegenerative fatal disease caused by the expansion of CAG repeats in the Huntingtin gene. The expansion length is unstable and proportional to the disease severity. The instability affects differently several tissues, among which the striatum that shows a high instability and degenerates, whereas the cerebellum that shows limited instability is spared from the disease. We addressed the role of oxidative lesions and Base Excision Repair (BER) in the tissue-selectivity of the instability in striatum and cerebellum of R6/1 mouse model. Interestingly, we observed a similar level of oxidative lesions at both tissues. Levels and activities of main BER proteins were globally decreased in striatum relative to cerebellum. Moreover we found that repair outcome is dependent upon BER stoichiometries, lesion location and sequence. Our results suggest a poor cooperation between BER activities that could underlie tissue-specificity of somatic instability in HD.

La régulation transcriptionelle fine assurée par les Eléments Cis Régulateurs (ECR, eg. promoteurs et «enhancers») et les facteurs protéiques associés, est à la base de la mise en place et le maintien de l'identité tissulaire. Les modifications de la chromatine corrèlent avec l’activité d’ECRs et constituent l’épigénome de la cellule. Au cours de ma thèse, je me suis intéressée aux transitions des modifications des histones (H3K4me1/me2/me3, H3K36me3, H3K27me3 and H3K9me2) accompagnant le développement précoce de la cellule T. Pour cela, j’ai utilisé un modèle murin reproduisant une étape cruciale de la thymopoïèse - la sélection β - et la technique d’Immunoprecipitation de la chromatine couplée à des puces à ADN (ChIP-chip). Au sein des enhancer connus, nos analyses ont mis en évidence une nouvelle signature épigénétique liée à leur activité. De plus, nous montrons que l'étendue d'enrichissement d’H3K4me2 au sein des régions géniques des gènes exprimés, constitue une signature épigénétique des gènes tissus spécifiques. Tout ceci a permis de mieux comprendre le rôle de l’épigénétique dans l'établissement et le maintien de l'identité cellulaire.Le traitement anti-cancer moderne est basé sur les analyses de différents marqueurs d'agressivité (MA) et par la suite, de l’établissement de la thérapie personnalisée. Durant la dernière partie de ma thèse, j’ai participé à un projet collaboratif avec le laboratoire de Thérapie Cellulaire de l’Institut Paoli Calmettes à Marseille, qui visait l’isolation des MA des Leucémies Aiguës Myéloïdes à caryotype normal (LMAcn) grâce aux études de profilage épigénétique (H3K27me3) des blastes des patients atteints de LMAcn. / Precise transcriptional regulation underlies the establishment and maintenance of cell type specific identity and is governed by dedicated DNA sequences (i.e., cis regulatory elements (CREs): eg.: promoters, enhancers) and transcription factors. Chromatin modifications (eg.: histone modifications, DNA methylation) impinge on CREs activity and constitute the epigenome of the cell.During my PhD, I was interested in the transitions of a set of histone modifications (H3K4me1/me2/me3, H3K36me3, H3K27me3 and H3K9me2), during one of the major checkpoints of thymopoiesis - the β-selection. I used a dedicated mouse model and Chromatin Immunoprecipitation coupled with microarrays (ChIP-chip) technique. Our data evidenced a previously unappreciated epigenetic signature linked to enhancer activity. In parallel, computational analyses of the patterns of gene body enrichment of H3K4me2 highlighted an epigenetic signature linked to the regulation of the tissue specific gene expression. Altogether, this enabled to deepen the relationship between chromatin states and regulation of cell type specific identity.Modern anticancer treatment is based on the analyses of a number of cancer aggressiveness markers (CAM) and results in a highly personalized therapy. Epigenetic profiling can constitute a powerful tool for CAM’s isolation. In the second part of the presented work, I participate in a collaborative project (with Cellular Therapy Centre at the Paoli Calmettes Institut, Marseille) aiming to isolate new CAM for Acute Myeloid Leukemia with normal karyotype (AMLnc) patients. For this purpose I performed epigenetic (H3K27me3) profiling of blasts of AMLnc.

Mgr. Daniela Fornuskova PhD thesis Biochemical and molecular studies of cytochrome c oxidase and ATP synthase deficiencies ABSTRACT The mammalian organism fully depends on the oxidative phosphorylation system (OXPHOS) as the major energy (ATP) producer of the cell. Disturbances of OXPHOS may be caused by mutations in either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA). One part of the thesis is focused on the role of early and late assembled nuclear-encoded structural subunits of cytochrome c oxidase (CcO) as well as Oxa1l, the human homologue of the yeast mitochondrial Oxa1 translocase, in the biogenesis and function of the human CcO complex using stable RNA interference of COX4, COX5A, COX6A1 and OXA1L, as well as expression of epitope-tagged Cox6a, Cox7a and Cox7b, in HEK (human embryonic kidney)- 293 cells. Our results indicate that, whereas nuclear- encoded CcO subunits Cox4 and Cox5a are required for the assembly of the functional CcO complex, the Cox6a subunit is required for the overall stability of the holoenzyme. In OXA1L knockdown HEK-293 cells, intriguingly, CcO activity and holoenzyme content were unaffected, although the inactivation of OXA1 in yeast was shown to cause complete absence of CcO activity. In addition, we compared OXPHOS protein deficiency patterns in mitochondria from skeletal...