he aim of the present work was to improve the discriminatory potentia􀀋 and hence the probative value, ofY-STR based testing by extending the set ofY chromosome STR loci available for operational use. In accord with the requirements of a multiplex system developed for forensic use, also important was the maximiz.ation the number of loci that can be co-amplified, ensuring appropriate assay sensitivity (1-3 ng of input genomic DNA), balancing inter-locus signals and minimizing confounding female DNA artifacts. Two Y chromosome STR systems, multiplex I (MP I) and multiplex II (MP II), have been developed. These allow for the robust co-amplification of 18 Y STRs and their subsequent separation and detection using a standard capillary electrophoresis analytical platform. The two multiplex systems are robust over a wide range of primer, magnesium and DNA polymerase concentrations and perform well under a variety of cycling conditions. Complete male haplotypes can be obtained with as little as 100-250 pg of template DNA. MPI and MPII have been optimized such that few confounding female DNA artifacts are obtained at a female:male DNA ratio of 100:1. Thus it is often unnecessary to employ a differential extraction strategy to obtain a male haplotype ( or haplotypes in the case of multiple male donors) in cases of sexual assault.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

La chromatine sert de support à de multiples processus biologiques, cependant son organisation spatiale diffère fortement selon l'échelle considérée. L'expression des gènes est ainsi coordonnée par des éléments régulateurs dispersés dans le génome mais capables d'interagir entre eux. Chez les métazoaires, des expériences de capture de conformation de chromosome (3C) combinées au séquençage haut-débit (Hi-C) ont permis la découverte de domaines d'association topologique (TAD), à l'échelle de la mégabase. Puisque la résolution du Hi-C reste limitée, nous avons utilisé la 3C-qPCR pour explorer, dans des cellules souches embryonnaires murines, la dynamique chromatinienne à l'intérieur de ces domaines ainsi qu'à leurs bordures. Nous identifions ainsi une modulation des fréquences de contacts, sur quelques centaines de kilobases. Cette modulation est plus ou moins importante en fonction du contenu en gènes des domaines, mais elle semble néanmoins universelle. Des modèles dérivés de la physique des polymères permettent de décrire cette modulation sous la forme d'une hélice statistique, que la chromatine adopterait en moyenne et en l'absence d'interactions spécifiques, à l'intérieur des TAD. Cette hélice reflète certaines contraintes que la chromatine subit à l'échelle supranucléosomale. Elle est très affectée par les bordures, qui bloquent la modulation, mais elle l'est beaucoup moins par le contenu en histone de liaison H1. Par ailleurs, grâce à des résultats de Hi-C à haute résolution, nous montrons que la modulation observée chez les souris n'est pas retrouvée chez la drosophile, où les caractéristiques des TAD semblent avant tout liées au paysage épigénétique local. Pour ces deux organismes, la dynamique chromatinienne à l'intérieur des domaines est donc sous le contrôle de phénomènes différents / The chromatin hosts various biological processes. However, its organization differs considerably depending on the scale. For example, gene expression is coordinated by regulatory elements that are dispersed in the genome but that are able to interact within the tridimensional space of the nucleus. In the Metazoa, chromosome conformation capture (3C) assays combined with high-throughput sequencing (Hi-C) uncovered the existence of topologically associating domains (TADs), at the mégabase scale. Due to the limited resolution of Hi-C, we used the 3C-qPCR method to explore, in murine embryonic stem cells, the chromatin dynamics inside TADs as well as at their borders. We found that contact frequencies undergo a periodic modulation over large genomic distances (few hundred kilobases). This modulation is weaker in gene-deserts than in gene-containing domains but it seems nevertheless to be universal. Using models derived from polymer physics, we show that this modulation can be understood as a fundamental helix shape that chromatin tends to adopt statistically, when no strong locus-specific interaction takes place, within the TADs. This statistical helix reflects some constraints that the chromatin undergoes at the supranucleosomal scale. It is affected by TADs borders, which disrupt the modulation, but linker histone H1 depletion only leads to subtle changes in the helix characteristics. Furthermore, using high-resolution Hi-C data, we found that chromatin dynamics is unconstrained in Drosophila where it seems mainly linked to the local epigenetics landscape. Therefore, distinct genome organization principles govern chromatin dynamics within mouse and Drosophila topologically associating domains.

目前廣泛應用于胎兒醫學的唐氏綜合症篩查法，即結合早孕期胎兒頸項透明層的超聲檢查，及母體血清生化指標的綜合篩查法。頸項透明層是指在早孕期利用超聲檢測到的胎兒頸后的皮下積水，其作為預測胎兒異常的一項重要“軟指標，其臨床意義，尤其是與胎兒染色體異常及器官結構異常之間的關係，逐漸得到深入的認識，但其形成機制尚未明確。現在已知有一百餘種畸形及遺傳綜合征與胎兒頸項透明層增厚相關，但其染色體異常譜系，尤其是亞顯微的染色體異常仍有待明確。大部分頸項透明層增厚但核型正常的胎兒預後良好，但約3-10%的這部分胎兒會伴有畸形或出生后的神經智力發育缺陷。而傳統核型分析無法檢測到亞顯微的染色體異常，從而無法判斷這部分核型正常卻伴有缺陷的胎兒是否因為這類染色體異常而致病。 / 微陣列比較基因組雜交芯片作為檢測兒童發育遲緩者及器官結構異常原因的重要手段已廣泛應用于臨床。在染色體核型正常的胎兒中，若伴有器官結構異常的胎兒，5-12%被檢出與該畸形相關的微缺失及微重複；若僅伴有孕婦高齡或唐氏篩查高危，則微缺失及微重複檢出率約1%。 / 該課題旨在研究頸項透明層增厚但核型正常的胎兒中，染色體拷貝數變異發生的頻率及頻譜；評估微陣列比較基因組雜交芯片在協助臨床判斷胎兒預後中的作用。因此，我們開展該多中心隊列研究，通過納入449例頸項透明層厚度≧3.5 mm但正常核型胎兒的，檢測其染色體拷貝數變異，監測并記錄其圍產、產後及新生兒期情況。微陣列比較基因組雜交芯片總共檢出2.8%的異常拷貝數變異，其大小範圍為0.1 kb至18Mb。在伴有器官結構異常的胎兒組中，異常拷貝數變異檢出率達7.8%。對於頸項透明層厚度≧4.0 mm的胎兒，異常拷貝數變異檢出率可達7.3%。 / 對於頸項透明層增厚的胎兒，致病拷貝數變異暫未發現特定的頻譜。但，該研究中發現重複的致病拷貝數變異，如22號染色體長臂1區1帶的微重複或微缺失，2號染色體長臂2區2帶的微缺失。未在3號、7號、12號、13號、18號、20號、21號或Y染色體上發現與胎兒頸項透明層增厚相關的致病拷貝數變異。 / 頸項透明層增厚的胎兒79.3%預後良好；若經微陣列比較基因組雜交芯片未檢出致病拷貝數變異，則81.2%預後良好。如果僅頸項透明層增厚不伴有結構異常的胎兒，經微陣列比較基因組雜交芯片未檢出致病拷貝數變異，則93.5%預後良好。 / 綜上所述，微陣列比較基因組雜交芯片顯著提高了致病拷貝數變異的檢出率。可考慮將微陣列比較基因組雜交芯片作為頸項透明層厚度≧4.0 mm的胎兒染色體異常檢查的首要方法。對於僅頸項透明層增厚不伴有結構異常的胎兒，且經微陣列比較基因組雜交芯片未檢出致病拷貝數變異，絶大部分預後良好。對於頸項透明層增厚的胎兒，致病拷貝數變異暫未發現特定的頻譜，但發現重複出現的致病拷貝數變異。通過初步的基因本體分析及基因通路分析，神經嵴細胞的分化遷徙功能異常可作為今後研究頸項透明層增厚的病理生理機制的方向。 / Measurement of nuchal translucency (NT) has been recognized as a sensitive marker for fetal chromosomal disorders for more than a decade, and is presently used as a routine first-trimester screening test. Although over 100 abnormalities and genetic syndromes have been reported to be associated with increased NT, these associations have not been fully explored and the relevant spectrum of associated submicroscopic chromosomal abnormalities has not been sufficiently investigated. The majority of euploid fetuses with increased NT have a good outcome, but around 3-10% of fetuses present with structural or neurodevelopmental abnormalities postnatally. A range of genetic syndromes has been reported, many of which are linked to submicroscopic chromosomal abnormalities that are typically missed by conventional karyotyping. / Microarray-based comparative genomic hybridization (arrayCGH) has been applied as the first-tier diagnostic tool for the evaluation of developmental delay and structural malformations in children. In fetuses with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 5-12% with a structural anomaly and in about 1% of those whose indications were advanced maternal age or positive screening results. / The objectives of this study were to delineate the frequency and spectrum of pathogenic chromosome copy number variants (CNVs) among fetuses with increased NT and normal karyotype; to evaluate the role of arrayCGH to predict the prognosis of the high NT fetuses; to explore the genotype-phenotype correlations of increased NT. Therefore, a multi-centre cohort of 449 fetuses with NT ≧3.5 mm and normal karyotype were further investigated by arrayCGH. Antenatal surveillance, pregnancy outcome and paediatric follow up were documented. ArrayCGH detected abnormal CNVs in 2.8% (14 of 449) of the fetuses with high NT; the size of CNVs ranged from 0.1 kb to 18Mb. Among fetuses with major congenital abnormalities the incidence of abnormal CNV reached 7.8% (4 of 51). By adjusting the NT to ≧4.0 mm as the referral indication, 7.3% (14 of 192) of the fetuses would have abnormal arrayCGH results. The spectrum of pathogenic CNVs found associated with increased NT was diverse. However, there were recurrent ones such as the deletions or duplications at chromosomal region 22q11, and deletions in ZEB2. There was no pathogenic CNV related with increased NT found in chromosomes 3, 7, 12, 13, 18, 20, 21, or Y. The total normal outcome rate of euploid fetuses with an increased NT was 79.3%; for fetuses with normal arrayCGH results 81.2% had a normal outcome. In fetuses with isolated increased NT, normal arrayCGH results predict a favorable prognosis of 93.5%. / In conclusion, arrayCGH significantly increased the diagnostic yield of pathogenic CNVs. In clinical practice arrayCGH may be considered as the first tier investigation in fetuses with an increased NT more than 4.0 mm. In cases with an isolated increased NT with normal arrayCGH results the pregnancy outcome is likely to be favorable. The spectrum of abnormal CNVs found by arrayCGH is diverse but there are recurrent cases such as del/dup 22q11 and del ZEB2. Our preliminary gene ontology and pathway analysis showed that gene pathways related to neural crest cells may be considered as a future study for physiopathologic mechanisms of NT. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Huang, Jin. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 106-120). / Abstracts also in Chinese.

Le développement embryonnaire précoce des mammifères femelles s’accompagne de l’inactivation transcriptionnelle d’un de leurs deux chromosomes X. Cet évènement est initié suite à l’expression mono-allélique de l’ARN non codant Xist, qui est contrôlée par de nombreux éléments cis-régulateurs présents dans le centre d’inactivation du chromosome X (Xic) – tel son anti-sens répresseur Tsix. Mon travail de thèse a consisté à développer des approches permettant d’appréhender le paysage structural dans lequel s’exerce cette régulation. La caractérisation de l’architecture tridimensionnelle du Xic, par des techniques basées sur la capture de conformation chromosomique (3C) et l’hybridation in situ en fluorescence (FISH), m’a permis de mettre en évidence que les promoteurs respectifs de Xist et Tsix sont engagés dans des interactions physiques intimes avec des loci distaux, localisés au sein du Xic, et de montrer qu’au moins certaines de ces régions exercent un effets régulateurs à longue-distance. Les éléments du Xic contactés par les régions promotrices de Xist et de Tsix sont en outre fondamentalement différents, chacune engageant des associations chromosomiques sur plusieurs centaines de kilobases dans leur direction 5’ respective.Ce travail a également permis de révéler des propriétés insoupçonnées de l’architecture chromosomiques. En effet, le Xic apparaît scindé en plusieurs sous-régions, couvrant chacune entre 200kb et 1Mb, à l’intérieur desquelles les interactions chromosomiques sont préférentiellement établies. L’existence de ces domaines d’interaction s’intègre avec d’autres propriétés structurales du génome, tels la composition de la chromatine sous-jacente et l’association à la lamine nucléaire, mais n’apparaît pas en dépendre directement. En étudiant la dynamique de la conformation chromosomique du Xic au cours de la différenciation cellulaire, j’ai pu constater la robustesse de cette organisation, sauf sur le chromosome X inactif, qui se distingue par la perte des contacts chromosomiques préférentiels détectables sur son homologue actif.Enfin, j’ai pu mettre en évidence que la variabilité du repliement général du chromosome X amène à un instant donné chaque allèle de Tsix à contacter physiquement des jeux de séquences distales différents, suggérant que l’environnement structural instantané de chacun de ces allèles à l’orée de l’activation mono-allélique de Xist est différent. Ce travail, combinant des approches à l’échelle de la population cellulaire d’une part et de la fibre de chromatine unique d’autre part, apporte une nouvelle vision du paysage structural et régulateur dans lequel s’inscrit le contrôle de l’activité transcriptionnelle de Xist, et fourni de nouvelles perspectives concernant les principes fondamentaux de l’organisation topologique des chromosomes chez les mammifères. / Early development of female mammals is accompanied by transcriptional inactivation of one of their two X chromosomes. This event is initiated following mono-allelic expression of the Xist non-coding RNA – what is achieved by the interplay of numerous cis-regulatory elements present within the X inactivation center (Xic), such as its repressive antisense Tsix. Our work aimed at throwing light on the structural landscape that underlies such long-range regulation. Characterization of the three-dimensional architecture of the Xic, by the means of Chromosome Conformation Capture (3C)-based techniques and in situ fluorescence hybridization (FISH), revealed that the respective promoters of Xist and Tsix contact many distal genomic elements within the Xic, and that at least one of such interacting region exerts long-range cis-transcriptional control. Noticeably, Xist and Tsix promoters associate with different sets of elements in their respective 5’ direction that are spread out over several hundreds of kilobases These experiments also revealed unforeseen properties of chromatin architecture. Indeed, the Xic appears to be partitioned in several sub-regions, each spanning between 200kb and 1Mb, inside which chromosomal interactions are preferentially established. The existence of these interaction domains integrates with other structural features of the genome, such as underlying chromatin composition and association with the nuclear lamina, but does not seem to directly depend on them. By analyzing chromosome conformation of the Xic during cell differentiation we document the robustness of this organizational principle, with the noticeable exception of the inactive X chromosome that assumes a folding pattern that is more random than its active homolog. Finally we also bring evidence that variability in the folding pattern of the two X chromosomes in the same cell brings each Tsix allele in association with different sets of chromosomal partners at a given moment, suggesting that the instantaneous structural environment of each allele at the onset of mono-allelic Xist up-regulation is different.By combining approaches at the scale of cell populations on the one hand, and at the single chromatin fiber level on the other, this study provides a first vision of the structural landscape in which Xist regulation takes place, and brings new insights concerning fundamental properties of chromosome organization in mammals.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.

The STR markers linked to the X chromosome can be used for complement the analysis of autosomal markers, especially in complex cases of kinship testing, in cases of post-morten identification and in paternity testing, when the disputed child is a girl. The aim of this work was investigate five STR X-chromosome markers (DXS10079, DXS10074, DXS10075, DXS7424 and DXS101) in the population of Alagoas, Brazil and analyze their frequencies for forensic purposes. The sample was composed of 404 unrelated individuals, 203 males and 201 females. The DNA was extracted using Chelex procedure and amplification was performed by PCR in a pentaplex system and the fragments were separated by capillary electrophoresis. For the studied STR markers, it was calculated the allele and haplotype frequencies, the observed and expected Heterozygosity values, the Hardy Weinberg equilibrium (HWE), the genetic diversity, the Mean Exclusion Chance of trios involving daughters (MECT) as well as in father/daughter duos (MECD). Also, it was calculated Power of Discrimination in males (PDM) and in females (PDF) and the Polymorphism Information Content (PIC). The forensic efficiency values demonstrate that DXS101 is a highly informative marker, followed by DXS10074, DXS10079, DXS7424 and DXS10075. The polymorphism information content ranged from 0.7470 to 0.8858. For the pentaplex evaluated, the combined values of PDM and PDF were 0, 9998947 and 0, 9999998, respectively and the combined MEC in trios involving daughters and in father/daughter duos were 0,999817 and 0,998042, respectively. No deviations from the Hardy Weinberg equilibrium were observed. We concluded that the five ChrX STRs analyzed are highly informative markers for kinship testing and constitute a powerful tool for forensic practice in our population. / Fundação de Amparo a Pesquisa do Estado de Alagoas / Os marcadores STRs ligados ao cromossomo X podem ser utilizados para complementar as análises de marcadores autossômicos, especialmente em casos complexos de vínculo genético, em casos de identificação post-morten e em testes de paternidade, quando a criança analisada é uma menina. O objetivo desse trabalho foi investigar cinco marcadores STRs do cromossomo X (DXS10079, DXS10074, DXS10075, DXS7424 e DXS101) na população de Alagoas, Brasil, e analisar suas freqüências para propósitos forenses. A amostra foi composta de 404 indivíduos não aparentados, sendo 203 do sexo masculino e 201 do sexo feminino. O DNA foi extraído através do método Chelex-100 e a amplificação foi realizada por PCR em um sistema pentaplex, sendo os fragmentos separados por eletroferese de capilar. Para os marcadores STRs estudados, foram calculadas as freqüências alélicas e haplotípicas, Heterozigozidade esperada e observada, Equilíbrio de Hardy Weinberg (HWE), diversidade genética, Chance Média de Exclusão (MEC) em trios envolvendo filhas e em duplas de pai/filha. Também foram calculados Poder de Discriminação em homens (PDM) e mulheres (PDF) e Conteúdo de Informação Polimórfica (PIC). Os parâmetros forenses investigados demonstram que o STR DXS101 é o marcador mais informativo, seguido por DXS10074, DXS10079, DXS7424 e DXS10075. O Conteúdo de Informação Polimórfica variou de 0.7470 a 0.8858. Para o sistema pentaplex investigado, os valores combinados de PDM e PDF foram de 0,9998947 e 0, 9999998, respectivamente e o MEC combinado em trios envolvendo filhas e em duplas pai/filha foi de 0,999817 e 0, 998042, respectivamente. Nenhum desvio do Equilíbrio de Hardy Weinberg foi observado. Concluímos que os cinco marcadores analisados são altamente informativos para testes de parentesco e constituem uma poderosa ferramenta genética para a prática forense em nossa população.

Orientador: Ana Silvia Alves Meira Tavares Moura / Banca: Luiz Lehmann Coutinho / Banca: Mônica Corrêa Ledur / Banca: Millor Fernandes do Rosário / Banca: José Roberto Sartori / Resumo: A partir de resultados de um estudo anterior, no qual foram mapeados QTLs para características de peso vivo, peso do coração e pulmões no GGA1, foi definida uma região no intervalo entre os marcadores ADL0234 e LEI0071, abrangendo 82,3 cM. Foram avaliadas três famílias de meios-irmãos paternos que compreendiam sete famílias de irmãos completos, num total de 652 F2 para as características: peso vivo aos 35 e 41 dias de idade, pesos do coração e pulmões e rendimentos de coração e pulmões. Os genótipos de seis marcadores microssatélites foram adicionados aos dez utilizados anteriormente. O mapa de ligação obtido da região compreendeu 110,8 cM com espaçamento médio entre os marcadores de 7,4 cM. Na análise de F2, em um único intervalo (LEI0146-LEI0174), compreendendo 28,8 cM, foram mapeados QTLs para todas as características estudadas, com exceção dos rendimentos de coração e pulmões. Neste intervalo estão localizados o gene IGF1 e o centrômero do cromossomo. A adição de seis marcadores confirmou os QTLs mapeados anteriormente, porém alguns em diferentes posições. A análise de meios-irmãos paternos indicou que os principais QTLs estavam segregando em apenas uma das famílias (7716), na qual cinco QTLs foram mapeados. Na análise de meios-irmãos maternos, duas famílias segregaram QTLs tanto na análise Individual como na Conjunta (7810 e 7971). As diferentes análises permitiram selecionar dois casais F1, que devem ser o alvo dos próximos estudos. Este estudo restringiu a busca por genes candidatos responsáveis pelas características de interesse a uma região de 28,8 cM (9,82 Mb) no GGA1. / Abstract: Based on the results from a previous study, in which QTL for body weight, heart and lungs weights and heart and lungs percentages were mapped to GGA1, a region was defined between markers ADL0234 and LEI0071, spanning 82.3 cM. Three paternal half-sib families, comprising seven full-sib families, totaling 652 F2 were evaluated for body weight at 35 and 41 days of age, heart and lungs weights and heart and lungs yields. Genotypes of six microsatellite markers were added to those of ten previously used. The linkage map of this region spanned 110.8 cM, with average spacing of 7.4 cM between markers. In a single interval (LEI0146-LEI0174), comprising 28.8 cM, QTLs for all traits, except for heart and lungs yields were mapped in the F2 analysis. In this same interval the IGF1 gene, and the chromosome centromere, are located. The use of six additional markers confirmed the same QTLs mapped previously, but some of them, in different positions. The paternal half-sib analysis indicated that the main QTLs were segregating in one of the families only (7716), in which five QTLs were mapped. In the maternal half-sib analysis, two families segregated QTLs both, in the across and within families analyses (7810 and 7971). These analyses allowed the selection of two F1 couples to be the target for future studies. This study restricted the search for candidate genes responsible for the traits of interest to a region of 28.8 cM (9.82 Mb) in GGA1. / Doutor

L'Indonésie a été l'objet de la dispersion Austronésienne qui a débuté il y a environ 5000 ans depuis Taiwan, se propager à travers les Philippines et l'Indonésie, puis toucher l'Océanie à l'est, et à Madagascar à l'ouest. Malgré de nombreuses recherches en génétique sur la dispersion Austronésienne vers l'est, il y a très peu de données sur la dispersion vers l'ouest, laissant sans réponse de nombreuses questions, liées notamment au peuplement de Madagascar. Reposant sur l'analyse des données culturelles et biologiques, les populations d'Indonésie semblent avoir joué un rôle majeur dans la colonisation de Madagascar, le premier millénaire de notre ère. Cependant, le peu de populations Indonésiennes étudiées à ce jour n'a pas permis jusqu'à présent d'identifier la population indonésienne source. Dans ce présent travail, j'ai réalisé des études en génétique des populations de 12 populations Indonésiennes, qui à priori devraient éclairer l'histoire des migrations austronésiennes dans l'Océan Indien. Parmi elles sont inclus le Ma'anyan du sud-est de Bornéo qui sont les plus proches linguistiquement des Malgaches. En utilisant différents marqueurs génétiques, ma recherche a amélioré nos connaissances de la diversité génétique Indonésienne, et du lien génétique entre l'Indonésie et Madagascar. Résultats L'analyse des marqueurs uniparentaux (chr-Y et ADNmt) suggère que les Malgaches proviennent de plusieurs régions d'Indonésie, avec un lien privilégié avec le sud-est de Bornéo, le sud de Sulawesi et les îles de la Sonde. Etonnamment, les Ma'anyan partagent un nombre limité de lignées paternelles et maternelles avec les Malgaches, malgré leur proximité linguistique. Par ailleurs, en combinant l'analyse de fréquences des SNPs et l'analyse haplotypique à partir des données autosomales, il a été confirmé que la diversité génétique des Ma'anyan ne correspond pas à l'ancestralité asiatique des Malgaches. Cependant, en centrant l'analyse sur les populations du sud-est de Bornéo, l'origine de l'ancestralité asiatique des Malgaches est ancrée dans la population Banjar, un mélange de population Ma'anyan et Malaise, résultat des activités commerciales de l'empire Malais dans le sud-est de Bornéo, qui se sont poursuivies à travers l'océan Indien. Par ailleurs nos résultats ont aussi permis d'accroitre notre compréhension de la diversité génétique de l'Indonésie en identifiant (1) une nouvelle composante génétique austronésienne présente chez les Ma'anyan, et retrouvée à faible fréquence à travers l'Asie du Sud-Est, suggérant une plus grande complexité du modèle d'expansion austronésien dans la région et (2) le rôle joué par les nomades de la mer dans la structuration de la diversité génétique et les échanges entre populations dans l'Indonésie, soulignant l'histoire génétique complexe de populations suivant un mode de vie nomade. / Indonesia hosts a wide range of linguistic, ethnic and genetic diversity, comprising ~600 ethnic groups and 700 living languages. Indonesia has facilitated the last substantial wave of human migration was the Austronesian dispersal ~5,000 years ago, which is thought to have originated in Taiwan. Its influence spread through Philippines and Indonesia, ultimately impacting a wide geographical area, from Remote Oceania in the east and to Madagascar in the west. Despite considerable genetic research on the eastward Austronesian expansion, there is little equivalent research on the western edge, leaving major issues unresolved regarding the settlement of Madagascar. Based on cultural and biological studies, it has been suggested that Indonesian peoples played a major role in the colonization of Madagascar from around the mid-first millennium CE (Current Era). However, poor geographical coverage of Indonesian populations has prevented the Indonesian source populations from being identified. Here, I performed human population genetic studies on 12 new Indonesian populations, which were a priori expected to shed light on the westward migration of Austronesians across the Indian Ocean. This includes the Ma'anyan ethnic group from Southeast Borneo, who are the closest linguistic siblings to modern Malagasy. Using different genetic markers (Y-chromosome SNPs, mitochondrial DNA and genome-wide SNPs), my research has improved the description of Indonesian genetic diversity, and investigated the genetic links between Indonesia and Madagascar. Results Uniparental markers (Y-chromosome and mtDNA) analyses suggest that Malagasy derive from multiple regional sources in Indonesia, with a focus on southeastern Borneo, southern Sulawesi and the Lesser Sunda islands. Interestingly, the Ma'anyan share limited paternal and maternal lineages with the Malagasy, despite their linguistic connection. Furthermore, combining SNP frequency and haplotype-based analyses from autosomal genome-wide data, it was confirmed that the genetic diversity of the Ma'anyan does not match the Asian ancestry of the Malagasy. However, by focusing on Southeast Borneo populations, strong support was found for an origin of the Asian ancestry of Malagasy among the people of Banjar, an admixed population of Ma'anyan and Malay, likely resulting from trading activities by the Malay Empire in Southeast Borneo, and later continuing across the Indian Ocean arena. These results increase our understanding of genetic diversity across Indonesia by 1) identifying the unique and undiscovered Austronesian genetic component carried by the Ma'anyan, which occurs at low levels across Island Southeast Asia and suggests a more complex model for the Austronesian expansion in this region, and 2) describing the role played by sea-nomads in structuring genetic diversity and exchanges in central Indonesia, thus revealing the complex genetic history of populations living this rare nomadic lifestyle.

Chez les Mammifères femelles, l’extinction transcriptionnelle d’un des deux chromosomes X pendant l’embryogénèse précoce compense le déséquilibre de dose des gènes liés à l’X entre les sexes. L’inactivation aléatoire du chromosome X est mise en place dans la masse cellulaire interne du blastocyste et maintenue jusqu’à l’âge adulte dans le soma. Chez certains Euthériens incluant la souris, les tissus extra-embryonnaires (trophectoderme et endoderme primitif) montrent une inactivation soumise à empreinte du X paternel. Le statut inactif du Xp peut être étudié ex vivo dans les cellules souches trophoblastiques (TS) dérivées du trophectoderme. Nous avons pu sélectionner des cellules TS montrant une réactivation partielle du Xp ou bien une inversion complète du profil d’inactivation. Ceci révèle une plasticité épigénétique accrue de l’inactivation dans le trophectoderme par au soma.L’inactivation aléatoire du chromosome X est récapitulée pendant la différenciation des cellules souches embryonnaires (ES), qui servent de modèle cellulaire. Ce processus est déclenché par l’accumulation en cis du long ARN non codant Xist qui crée un domaine nucléaire répresseur autour du futur chromosome X inactif. Avant la différenciation, l’accumulation de Xist est réprimée par un autre long ARN non codant, Tsix, qui est transcrit en antisens de Xist. Afin d’adresser la dynamique fonctionnelle des ARN Xist et Tsix, nous avons inséré différents motifs d’étiquetage au locus Xist/Tsix endogène. Incorporés dans l’ARN sens ou antisens, ces étiquettes sont reconnues spécifiquement par des molécules fluorescentes, permettant ainsi la visualisation de ces transcrits dans les cellules vivantes. / In female Mammals, the transcriptional silencing of one of the two X chromosomes during early embryogenesis compensates the dosage disequilibrium of X-linked genes between sexes. Random X chromosome inactivation occurs in the inner cell mass of the blastocyst and is maintained through adult life in the soma. In some Eutherian species including mice, extraembryonic tissues (trophectoderm and primitive endoderm) exhibit imprinted inactivation of the paternal X. The inactive state of the Xp can be extensively studied ex vivo in Trophoblast Stem (TS) cells derived from the trophectoderm. We were able to select from the general cell population, TS cells exhibiting partial reactivation of the Xp or showing a complete switch of imprinted X-inactivation pattern. This reveals an accrued epigenetic plasticity of imprinted X-inactivation in the trophectoderm as compared to random X-inactivation in the soma.Random X-chromosome inactivation is recapitulated during the differentiation of female Embryonic Stem (ES) cells – which serves as cellular model. This process is triggered by the cis-accumulation of Xist long non coding RNA molecules which create a nuclear repressive domain around the future inactive X chromosome. Before differentiation, the accumulation of Xist is repressed by another lncRNA, Tsix, that is transcribed antisense to Xist. In order to address the functional dynamics of Xist and Tsix RNAs, we inserted different types of tag sequences in the endogenous Xist/Tsix locus. Incorporated in the sense or antisense RNA, these tags are specifically recognized by fluorescent molecules, thereby allowing live cell imaging of these transcripts.