Une perte locale ou globale de l’information épigénétique est souvent un facteur significatif dans les désordres génétiques notamment dans les cancers car elle mène à une dérégulation de l’expression des gènes.Un couplage direct a été mis en évidence par mon équipe entre les mécanismes de transcription des récepteurs à l’acide rétinoïque (RAR) et de son corégulateur, la CREB Binding Protein (CBP) dans le cas de la méthylation des îlots CpG, via la réparation par excision de base (BER) par la Thymine DNA glycosylase (TDG) des mésappariements G : U/T. Ces mésappariements G : U/T, produits lors de la déamination des paires G: meC (cytosine méthylée) dans les îlots CpG, contribuent à une déméthylation de l’ADN. TDG possède une activité de cofacteur de transcription et peut aussi interagir avec le facteur de transcription RARα et avec le coactivateur transcriptionnel CBP. TDG joue donc un rôle essentiel dans les processus de différenciation et de développement. Le complexe formé par CBP, TDG et RAR constitue donc le premier lien entre la réparation d’ADN par excision de base, la transcription, et l’épigenèse et est ainsi une nouvelle voie de régulation de l'intégrité et de l'expression génomique. Mon projet de recherche a pour but une caractérisation fonctionnelle de la régulation du complexe CBP/TDG/RAR et de son rôle dans la régulation épigénétique de la transcription. En parallèle nous avons étudiés les mécanismes épigénomiques in vivo par l’utilisation d’un modèle du stress prénatal chez le rat. Par ailleurs, grâce à mon expertise en analyse transcriptomique, j’ai participé à cinq collaborations portant sur l’étude des mécanismes de défense innés de l’organisme face à une infection bactérienne à Streptococcus pneumoniae, l’exploration des gènes régulés par HMGA1 et par TAF6delta à l’échelle génomique. / The packaging of eukaryotic DNA into chromatin represents an essential organizational and an important regulatory feature. Chromatin structure can specifically contribute positively or negatively to the correct assembly of transcription factors (TFs) and their activity. So a local and/or global loss of epigenetic information is often a significant factor in genetic disorders including cancers because it leads to a deregulation of gene expression. Unfortunaly the modifications occurring at this level of the chromosome, are ample and only in part understood. Direct coupling has been highlighted by my team between mechanisms of transcription by retinoic acid receptor (RAR) and its coregulator, the CREB Binding Protein (CBP) and mechanisms of excision repair (BER) by the Thymine DNA Glycosylase (TDG). TDG acts as a coactivator of transcription factors RAR and also like a transcription factor. TDG thus playing an essential role in the process of differentiation and development.Furthermore, TDG has a potency to repair G: T mismatches, produced by deamination of G: meC (methylated cytosine) in CpG islands, to restore a G: C pair so TDG contributes to indirect demethylation of DNA. In addition, the malignant transformation associated with mutations of CBP and its homologue, p300, could be due to dysfunction of major signaling pathways that require CBP as coactivators, such as retinoic acid pathway. The CBP-RAR-TDG complex is the first link between DNA repair by base excision, transcription, and epigenetic and is thus a new way of regulating the integrity and gene expression. The aim of our work is to characterize functional complex CBP-TDG-RAR in transcriptional regulation and epigenetics. The ultimate aim of my work is the understanding of genomic plasticity induced by the CBP-TDG complex and its role in oncogenesis. I also studied the epigenomics mecanisms of prenatal stress in the rat. Moreover, I used my expertise in microarrays expereriment and transcriptome analyse to work on severals projects about the study of innate defense against Streptococcus pneumoniae bacterial infection, the study of HMGA1 regulated genes and TAF6delta regulated genes at wide genome level.

Mycobacterium tuberculosis is an exquisitely adapted intracellular pathogen that encounters hostile, host-derived reactive nitrogen and oxygen intermediates during the course of infection of its human host. These radicals cause DNA damage, which is repaired through various pathways to allow for the continued survival of the organism. Base excision repair (BER) is one such pathway, which depends on DNA glycosylases to identify and excise damaged DNA bases. Formamidopyrimidine DNA glycosylase (Fpg/ MutM/ FAPY) and Endonuclease VIII (Nei) are such enzymes, which both target oxidatively damaged DNA and together, form the Fpg family of DNA glycosylases. Bioinformatic analyses identified two copies each of Fpg and Nei-encoding genes in M. tuberculosis as well as in its non-pathogenic relative, Mycobacterium smegmatis. To understand the role of these multiple glycosylases in the maintenance of genomic integrity and survival of mycobacteria, the genes encoding the four Fpg/Nei glycosylases were individually deleted in M. smegmatis strain mc2155 by homologous recombination. In addition to the four single mutants, double and triple Fpg and Nei glycosylase knockout mutants were generated by sequential gene knockout. When compared to the parental strain, the single and double mutants showed no variation in growth kinetics, no increased sensitivity to hydrogen peroxide and no increase in spontaneous mutation rates. However, a slight increase in frequency of spontaneous C T transition mutations was observed in double knockout mutants compared to the wild type and single mutant strains. These results suggest that these enzymes may be part of an extensive network of enzymes which collectively work to enhance the overall survival of M. smegmatis through the repair of oxidatively damaged DNA.

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (leaves 88-100).

Diss. (sammanfattning) Göteborg : Göteborgs universitet, 2010. / Härtill 4 uppsatser.

The DNA glycosylases function in the first step of the base excision repair (BER) process, that is responsible for removing base lesions resulting from oxidation, alkylation or deamination. The DNA glycosylases that recognize oxidative base damage fall into two general families: the Fpg/Nei family and the Nth superfamily. Based on protein sequence alignments, we identified four putative Fpg/Nei family members as well as a putative Nth protein in Mycobacterium tuberculosis H37Rv, the causative agent of tuberculosis. While Fpg proteins are widely distributed among the bacteria and plants, Nei homologs are sparsely distributed across phyla, and are only found in γ-proteobacteria, actinobacteria and metazoans. Interestingly, M. tuberculosis H37Rv harbors two proteins (Rv2464c and Rv3297) from the Nei clade and two (Rv2924c and Rv0944) from the Fpg clade. All four Fpg/Nei proteins were successfully overexpressed by using a novel bicistronic vector, which theoretically prevented stable mRNA secondary structure(s) surrounding the translation initiation region (TIR) thereby improving translation efficiency. Additionally, MtuNth (Rv3674c) was also overexpressed in soluble form. The substrate specificities of the purified enzymes were characterized in vitro with oligonucleotide substrates containing single lesions. Some were further characterized by gas chromatography/mass spectrometry (GC/MS) analysis of products released from γ-irradiated DNA. MtuFpg1 (Rv2924c) has a substrate specificity similar to that of EcoFpg and recognizes oxidized purines. Both EcoFpg and MtuFpg1 are more efficient at removing spiroiminodihydantoin (Sp) than 7,8-dihydro-8-oxoguanine (8-oxoG); however, MtuFpg1 has a substantially increased opposite base discrimination compared to EcoFpg. The Rv0944 gene encodes MtuFpg2, which contains only the C-terminal domain of an Fpg protein and has no detectable DNA binding activity or DNA glycosylase/lyase activity and thus appears to be a pseudogene. MtuNei1 (Rv2464c) recognizes oxidized pyrimidines not only on doublestranded DNA but also on single-stranded DNA. It also exhibits uracil DNA glycosylase activity as well as weak activity on FapyA and FapyG. MtuNth recognizes a variety of oxidized bases, such as urea, 5,6-dihydrouracil (DHU), 5-hydroxyuracil (5- OHU), 5-hydroxycytosine (5-OHC) and methylhydantoin (MeHyd) as well as FapyA, FapyG and 8-oxoadenine (8-oxoA). Both MtuNei1 and MtuNth excise thymine glycol (Tg); however, MtuNei1 strongly prefers the (5R) isomers of Tg, whereas MtuNth recognizes only the (5S) isomers. The other Nei paralog, MtuNei2 (Rv3297), did not demonstrate activity in vitro as a recombinant protein, but when expressed in Escherichia coli, the protein decreased the spontaneous mutation frequency of both the fpg mutY nei triple and nei nth double mutants, suggesting that MtuNei2 is functionally active in vivo recognizing both guanine and cytosine oxidation products. The kinetic parameters of the MtuFpg1, MtuNei1 and MtuNth proteins on selected substrates were also determined and compared to those of their E. coli homologs. Since pathogenic bacteria are often exposed to an oxidative environment, such as in macrophages, our data, together with previous observations, support the idea that the BER pathway is of importance in protecting M. tuberculosis against oxidative stress, as has been observed with other pathogens .

Thesis (Ph.D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 135 pages. Includes Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 115-127).

Chez les mammifères, la méthylation est une marque épigénétique ciblant la cytosine principalement dans un contexte CpG pour produire une 5mC. 5mC est très sensible à une déamination spontanée ou enzymatique, conduisant à la formation d'un mésappariement G/T. La 5mCpeut également être oxydée pour former successivement la 5hmC, la 5fC et la 5caC. Ces modifications de la 5mC participent aux processus actifs de déméthylation de l’ADN. Chez les mammifères, la thymine, dans le mésappariement G/T, est clivée par TDG et MBD4. TDG est également en mesure d'exciser 5fC et 5caC. Cette thèse avait pour but de clarifier la fonction de TDG et MBD4 dans la dynamique de la 5mC. Nous avons montré que MBD4 est associée aux protéines de réparation des mésappariements. Les tests enzymatiques, in vitro, montrent que le complexe MBD4/MMR a une activité bifonctionnelle (glycosylase/lyase) spécifique pour G/T, qui est régulée par la méthylation. Pour TDG, nous avons ciblé cette enzyme dans les cellules MEF et caractérisé la distribution des cytosines modifiées. Les résultats montrent des profils de méthylation/oxydation d'ADN qui sont régulés par TDG et surviennent principalement au niveau des répétitions de CA et dans les rétroéléments spécifiques de la lignée souris. / In mammals, methylation is an epigenetic mark targeting cytosine mainly in a CpG context, producing 5mC. 5mC is highly sensitive to a spontaneous or enzymatic deamination leading to G/Tmismatch. 5mC can also be oxidized to 5- 5hmC, 5fC and 5caC. These modifications of 5mC participate in the active demethylation processes. In mammals, the thymine in G/T mismatch is cleaved by TDG and MBD4 glycosylases. TDG is able also to excise the 5fC and 5caC.This thesis was to clarify the function of TDG and MBD4 in the dynamics of 5mC. We showed that MBD4 is associated with PMS2, MLH1, MSH2 and MSH6 proteins, four proteins involved in DNA mismatch repair (MMR). The in vitro enzymatic tests show that MBD4/MMR complex has a bifunctional glycosylase/lyase activity specific for G/T and is regulated by methylation.For TDG, we targeted this enzyme in MEF cells and characterized the distribution of modified cytosines. The results show that DNA methylation/oxidation patterns are regulated by TDG and occur mainly at CA repeats and at the mouse-lineage specific retro-elements.

LES METHODES CLASSIQUES DISPONIBLES POUR MESURER L'ACTIVITE ENZYMATIQUE DE REPARATION DES LESIONS DE L'ADN PAR DES ADN N-GLYCOSYLASES SONT LONGUES ET LABORIEUSES A METTRE EN ŒUVRE (ANALYSE PAR ELECTROPHORESE SUR GEL COUPLEE AU MARQUAGE PAR UN ISOTOPE RADIOACTIF OU ENCORE PAR CHROMATOGRAPHIE LIQUIDE HAUTE PERFORMANCE). NOUS AVONS DEVELOPPE DANS LE PRESENT TRAVAIL, UNE NOUVELLE METHODE DE QUANTIFICATION PRECISE ET AISEE DES ACTIVITES DE REPARATION BASEE SUR UNE DETECTION UTILISANT LE PRINCIPE PHYSIQUE DU FRET (TRANSFERT PAR RESONANCE D'ENERGIE DE FLUORESCENCE). POUR CE FAIRE, UN SUBSTRAT D'ADN ORIGINAL A ETE CONÇU : UNE STRUCTURE AUTOCOMPLEMENTAIRE CONTENANT DES LESIONS SPECIFIQUES DANS LA SEQUENCE DOUBLE BRIN DE L'EPINGLE A CHEVEUX ET, AYANT LES DEUX EXTREMITES MARQUEES PAR DES CHROMOPHORES. L'EXCISION DE LA LESION PAR DES ADN N-GLYCOSYLASES CONDUIT A LA SEPARATION DES BRINS COMPLEMENTAIRES, INDUISANT UNE DIMINUTION DU PROCESSUS DE « QUENCHING » DE FLUORESCENCE. L'EXCISION EST DONC DETECTEE ET QUANTIFIEE PAR L'AUGMENTATION DE L'INTENSITE DU SIGNAL D'EMISSION DU FLUOROPHORE. APRES AVOIR ETABLI LA LINEARITE DE LA REPONSE DU TEST, NOUS AVONS UTILISE CETTE APPROCHE EXPERIMENTALE POUR ACCEDER AUX PARAMETRES CINETIQUES CARACTERISTIQUES DES ENZYMES DE REPARATION. LA VALIDITE DE CES PARAMETRES A ETE CONTROLEE PAR COMPARAISON AVEC LES DONNEES OBTENUES PAR ANALYSE SUR GEL D'ACRYLAMIDE (EGPA). LES POSSIBLES APPLICATIONS DE NOTRE TEST EN TANT QU'OUTIL DE SCREENING POUR LA DETECTION D'ACTIVITE DE REPARATION OU D'INHIBITION ENZYMATIQUE, SUR ENZYMES PURIFIEES OU A PARTIR D'EXTRAITS CELLULAIRES ONT ETE INVESTIGUEES. ENFIN, UN PROJET DE MINIATURISATION DU FORMAT DE LECTURE DANS UN MICROSYSTEME DE TYPE « LAB-ON-A-CHIP » A ETE MENE. L'ENSEMBLE DES RESULTATS OBTENUS PROUVE LA PERTINENCE DE NOTRE METHODE D'ANALYSE EN PHASE HOMOGENE, EN VUE D'EXTENSIONS A L'ANALYSE PARALLELISEE HAUT DEBIT POUR DES APPLICATIONS EN RECHERCHE FONDAMENTALE, BIOMEDICALE ET PHARMACEUTIQUE.

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