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No description available.

Chromatin packages eukaryotic genomes via a hierarchical series of folding steps, encrypting multiple layers of epigenetic information, which are capable of regulating nuclear transactions in response to complex signals in environment. Besides the 1-dimensinal chromatin landscape such as nucleosome positioning and histone modifications, little is known about the secondary chromatin structures and their functional consequences related to transcriptional regulation and DNA replication. The family of chromosomal conformation capture (3C) assays has revolutionized our understanding of large-scale chromosome folding with the ability to measure relative interaction probability between genomic loci in vivo. However, the suboptimal resolution of the typical 3C techniques leaves the levels of nucleosome interactions or 30 nm structures inaccessible, and also restricts their applicability to study gene level of chromatin folding in small genome organisms such as yeasts, worm, and plants. To uncover the “blind spot” of chromatin organization, I developed an innovative method called Micro-C and an improved protocol, Micro-C XL, which enable to map chromatin structures at all range of scale from single nucleosome to the entire genome. Several fine-scale aspects of chromatin folding in budding and fission yeasts have been identified by Micro-C, including histone tail-mediated tri-/tetra-nucleosome stackings, gene crumples/globules, and chromosomally-interacting domains (CIDs). CIDs are spatially demarcated by the boundaries, which are colocalized with the promoters of actively transcribed genes and histone marks for active transcription or turnover. The levels of chromatin compaction are regulated via transcription-dependent or transcription-independent manner – either the perturbations of transcription or the mutations of chromatin regulators strongly affect the global chromatin folding. Taken together, Micro-C further reveals chromatin folding behaviors below the sub-kilobase scale and opens an avenue to study chromatin organization in many biological systems.

The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization. At a finer resolution within compartments, chromatin forms loop structures capable of regulating gene expression. Genome wide association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with the neuropsychiatric disease schizophrenia. When these SNPs are not located within a gene it is difficult to gain insight into disease pathology; however, in some cases chromatin loops may link these noncoding schizophrenia risk variants to their pathological gene targets. By generating 3D genome maps, we identified and analyzed loops of glial cells, neural progenitor cells, and neurons thereby expanding the set of genes conferring schizophrenia risk. The binding of T-cell receptors (TCRs) to foreign peptides on the surface of diseased cells triggers an immune response against the foreign invader. Utilizing available structural information of the TCR antigen interface, we developed computational methods for successful prediction of TCR-antigen binding. As this binding is a prerequisite for immune response, such improvements in binding prediction could lead to important advancements in the fields of autoimmunity and TCR design for cancer therapeutics.

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13566号 / 論医博第2293号 / 新制||医||1068(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 柊, 卓志, 教授 篠原, 隆司, 教授 後藤, 慎平 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

TAD-Grenzen sind genomische Regionen mit Isolatorpotenzial, die zwischen benachbarten Chromatindomänen liegen und deren Unterbrechung zu einer pathologischen Genexpression führen kann. Die meisten TAD-Grenzen werden durch das CTCF gebunden, ein Architekturprotein, das Chromatinschleifen bevorzugt zwischen distalen Paaren von CTCF-Bindungsstellen (CBS) mit einer konvergenten Motivausrichtung bildet. An TAD-Grenzen sind die CBS häufig geclustert, wobei die Motive eine divergente Ausrichtung aufweisen und Chromatinschleifen in Richtung der stromaufwärts und stromabwärts gelegenen Regionen projizieren. Wie die CTCF-Besetzung die Isolierung an TAD-Grenzen moduliert, ist immer noch nicht ganz klar. Hier habe ich die regulatorische Logik von CTCF-geclusterten TAD-Grenzen untersucht, indem ich genomweite Analysen und in vivo-Mausexperimente an der Epha4-Pax3-TAD-Grenze kombiniert habe. Analysen einzelner Deletionen zeigten einen deutlichen hierarchischen Beitrag von CBS zur Grenzfunktion. Im Gegensatz dazu zeigten kombinierte CBS-Deletionen ein gewisses Maß an funktioneller Redundanz und Kooperativität zwischen den Stellen. Diese Analysen zeigten auch, dass die abweichende Konfiguration der CBS, die immer wieder an TAD-Grenzen zu finden ist, für eine robuste Isolierung nicht unbedingt erforderlich ist. Genomweite Analysen haben gezeigt, dass es eine Untergruppe von CBS gibt, die unabhängig von der konvergenten Ausrichtung Chromatinschleifen bilden, wofür ich einen Mechanismus der "Schleifeninterferenz" vorschlage. Weitere Vergleiche ergaben, dass das Niveau der Genexpression von den Abständen zwischen Enhancer und Promoter im linearen Genom abhängen könnte. Durch die Quantifizierung der Isolierung der Grenzen, der Pax3-Fehlexpression und der Schwere der Gliedmaßenfehlbildungen konnte ich schließlich zeigen, dass die TAD-Grenzen die Genexpression und den Phänotyp quantitativ beeinflussen. / TAD boundaries are genomic regions with insulator potential located between adjacent chromatin domains, which disruption can cause pathological gene expression. Most TAD boundaries are bound by the CTCF, an architectural protein that forms chromatin loops preferentially between distal pairs of CTCF binding sites (CBSs) with a convergent motif orientation. At TAD boundaries, CBSs are frequently clustered, with motifs displaying a divergent orientation and projecting chromatin loops towards up and downstream regions. How CTCF occupancy modulates insulation at TAD boundaries still remains elusive. Here, I dissected the regulatory logic of CTCF-clustered TAD boundaries by combining genome-wide analysis and in vivo mouse experiments at the Epha4-Pax3 TAD boundary. Analyses of individual deletions revealed a distinct hierarchical contribution of CBS to boundary function. In contrast, combined CBSs deletions revealed a certain degree of functional redundancy and cooperativity between sites. These analyses also demonstrated that the divergent configuration of CBSs, recurrently found at TAD boundaries, is not strictly required for robust insulation. Genome-wide analysis highlighted the existence of a subset of CBSs that establish chromatin loops independently of the convergent orientation bias, for which I propose a mechanism of “loop interference”. This mechanism suggests that CBS forming a robust convergent loop can simultaneously form a non-convergent loop, by stalling Cohesin complexes extruded from both sides. Further comparisons revealed that gene expression levels might depend on enhancer-promoter distances in the linear genome. Finally, by quantifying boundary insulation, Pax3 misexpression and the severity of limb malformation, I demonstrate that TAD boundaries are quantitative modulators of gene expression and phenotypes. Overall, I highlight that TAD boundary composition and strength constitute a fundamental regulatory layer in developmental processes and disease.

Transcriptional regulation is the principal mechanism in establishing cell-type specific gene activity by exploring an almost infinite space of different combinations of regulatory elements, transcription factors with high precision. Recent efforts have mapped thousands of candidate regulatory elements, of which a great portion is cell-type specific yet it is still unclear as to what fraction of these elements is functional, what genes these elements regulate, or how they are established in a cell-type specific manner. In this dissertation, I will discuss methods and approaches I developed to better understand the role of regulatory elements and transcription factors in gene expression regulation. First, by comparing the transcriptome and chromatin landscape between mouse and human innate immune cells I showed specific gene expression programs are regulated by highly conserved regulatory elements that contain a set of constrained sequence motifs, which can successfully classify gene-induction in both species. Next, using chromatin interactions I accurately defined functional enhancers and their target genes. This fine mapping dramatically improved the prediction of transcriptional changes. Finally, we built a supervised learning approach to detect the short DNA sequences motifs that regulate the activation of regulatory elements following LPS stimulation. This approach detected several transcription factors to be critical in remodeling the epigenetic landscape both across time and individuals. Overall this thesis addresses several important aspects of cis-regulatory elements in transcriptional regulation and started to derive principles and models of gene-expression regulation that address the fundamental question: “How do cis-regulatory elements drive cell-type-specific transcription?”

Die räumliche Organisation des Chromatins im Zellkern ist für die Regulierung der Genexpression von großer Bedeutung. Genomische Varianten können die räumliche Organisation jedoch stören und Fehlbildungen und Krankheiten verursachen. In diploiden Genomen sind die meisten genomischen Varianten heterozygot und beeinflussen hauptsächlich das homologe Chromosom, auf dem sie sich befinden. Daher ist eine allelspezifische Analyse wichtig, erweist sich aber mit aktuellen Methoden zur Erfassung der Chromatinkonformation als äußerst schwierig. Erstens ist der Haplotyp, der die Verteilung unterschiedlicher Allele über die homologen Chromosomen beschreibt, oft unbekannt. Zweitens ist, insbesondere in Genomen mit geringer Variantendichte, wie dem menschlichen Genom, eine eindeutige Zuordnung der sequenzierten Genomabschnitte (Reads) zu ihrem Ursprungschromosom häufig nicht möglich, was die Erstellung haplotypspezifischer Chromatinkontaktmatrizen von guter Qualität verhindert. Genome Architecture Mapping (GAM) ist eine vielversprechende neue Methode mit dem Potential zur haplotypspezifischen Analyse der Chromatinkonformation. In dieser Dissertation zeige ich zunächst, dass GAM-Daten wertvolle Haplotypinformationen enthalten. Dann stelle ich GAMIBHEAR vor, einen graphenbasierten Ansatz, der die von GAM-Daten abgeleiteten Phaseninformationen nutzt, um genaue und vollständige Haplotypen zu rekonstruieren. Schließlich stelle ich Co-Phasing vor, eine neue Read-Phasing-Strategie, die erstmalig die eindeutige Zuordnung von variantenfreien Reads zu ihrem homologen Ursprungschromosom ermöglicht und somit auch die Erstellung detaillierter haplotypspezifischer Chromatinkontaktmatrizen in Maus und Mensch. Im Gegensatz zu früheren Erkenntnissen belegen meine Ergebnisse große Unterschiede in der räumlichen Organisation homologer Chromosomenkopien und ermöglichen erstmals einen sehr detaillierten Einblick in die haplotypspezifische Chromatinkonformation des menschlichen Genoms. / The spatial organization of chromatin in the nucleus plays an essential role in precise gene expression. Genomic variants can disrupt this spatial organization, potentially causing malformations and diseases. In diploid genomes, most genomic variants are heterozygous and mainly influence the homologous chromosome they reside on. Studying the effects of these variants in an allele-specific manner is crucial but has proven challenging using current state-of-the-art techniques. First, the haplotype describing the distribution of variant alleles over the homologous chromosomes is often unknown. Second, especially in genomes with a low variant density, such as the human genome, most sequencing reads map to genomic regions that are identical between homologous chromosomes, making it difficult to determine their origin. Thus, the read-phasing efficiency is insufficient to generate haplotype-specific chromatin contact matrices of good quality. Genome Architecture Mapping (GAM) is a promising new method for haplotype-specific analysis of chromatin conformation. In this thesis, I first demonstrate the ability of GAM data to provide valuable haplotype information. Then, I introduce GAMIBHEAR, a graph-based approach that leverages the GAM-derived phase information to infer accurate and complete haplotypes. Finally, building on GAMIBHEAR, I present Co-Phasing, a novel read-phasing strategy that allows for the unique assignment of variant-free reads to their homologous chromosome of origin and thus enables the creation of detailed haplotype-specific chromatin contact matrices in mouse and human. In contrast to previous findings, my results show significant differences in the spatial organization of homologous chromosomes and provide the first detailed view of haplotype-specific chromatin conformation in the human genome.

Malgré les vastes études démontrant le rôle de la conformation génomique dans le contrôle transcriptionnel, de nombreuses questions restent en suspens, et en particulier, comment ces structures chromatiniennes sont formées et maintenues. Pour mieux comprendre les liens entre l’état de la chromatine au niveau des éléments régulateurs, la topologie de la chromatine et la régulation de la transcription, nous utilisons la technique CHi-C basée sur la technologie de capture de la conformation chromosomique (3C). En utilisant deux stratégies de capture ciblant deux différentes structure chromatiniennes (les boucles chromatiniennes et les domaines topologiques), nous avons pu décrypter la structure chromatinienne associée à la différenciation des thymocytes et mettre en évidence des mécanismes de contrôle transcriptionnel de certains gènes. Les expériences futures de l’équipe vont consister à examiner les facteurs (hors transcription) qui peuvent influencer l'architecture de la chromatine, comme la liaison différentielle des CTCF, et comment ces facteurs peuvent être coordonnés par le contrôle de transcription. / Chromosome folding takes place at different hierarchical levels, with various topologies correlated with control of gene expression. Despite the large number of recent studies describing chromatin topologies and their correlations with gene activity, many questions remain, in particular how these topologies are formed and maintained. To understand better the link between epigenetic marks, chromatin topology and transcriptional control, we use CHi-C technique based on the chromosome conformation capture (3C) method. By using two capture strategies targeting two different chromatin structures (chromatin loops and topological domains), we have been able to decipher the chromatin structure associated with thymocyte differentiation and to highlight mechanisms for the transcriptional control of certain genes. Future experiments of the lab will examine mechanisms other than transcription which may influence chromatin architecture, such as differential binding of CTCF, and how these may interplay with transcriptional control and chromatin architecture.

No description available.