Computational analysis of transcriptional regulation and chromatin assembly
Kumulative Dissertation
Datum der mündl. Prüfung:2022-12-09
Erschienen:2023-12-07
Betreuer:Dr. Ufuk Günesdogan
Gutachter:Dr. Ufuk Günesdogan
Gutachter:Prof. Dr. Argyris Papantonis
Gutachter:Prof. Dr. Patrick Cramer
Gutachter:Dr. Nico Posnien
Gutachter:Dr. Johannes Soeding
Gutachter:Prof. Dr. Ernst A. Wimmer
Dateien
Name:Dissertation_XiaojuanLi_2023rev.pdf
Size:96.8Mb
Format:PDF
Zusammenfassung
Englisch
Primordial germ cells (PGCs), the precursors of gametes, are specified from post-implantation epiblast cells in response to bone morphogenetic protein (BMP) signaling at the onset of gastrulation in mouse. Followed by specification, a population of 30-40 PGCs are formed, and they migrate into the genital ridge. The migrating PGCs reprogramming, i.e. extensive changes on the transcriptional level accompanied by epigenetic changes including reorganized enhancer landscape. The reprogramming is required to remove epigenetic signatures and somatic memories acquired during development so that germ cells can generate totipotency. Enhancers play a central role in regulating spatio-temporal transcriptional dynamics. Enhancers can be located at a distance from their target promoter and regulate gene transcription. Indeed, the 3D organization of chromatin enables the establishment of long-range enhancer-promoter interactions. How enhancer-promoter interactions control the transcription dynamics, how they contribute to germline competence and whether they can be influenced by transcription during PGC differentiation remain unclear. Also, it is not clear whether enhancer-non promoter interactions participate in gene control. To gain insights into this, I investigated the role of enhancer-promoter interactions in transcriptional dynamics control during PGC differentiation using an in vitro PGC differentiation approach, in which mouse embryonic stem cells (ESCs) are induced into epiblast-like cells (EpiLCs) and then PGC-like cells (PGCLCs). By integrating Promoter Capture Hi-C (PCHi-C), Enhancer Capture Hi-C (ECHi-C), as well as transcriptome and epigenome data in ESCs, EpiLCs and PGCLCs, I uncovered genome-wide enhancer and promoter chromosomal interactions form large spatial cis regulatory networks that undergo extensive 3D rewiring upon cell state transitions. and the results indicate that both enhancer-promoter and enhancer-enhancer interactions constitute an important mechanism of transcriptional control during in vitro PGC differentiation. In contrast to reprogramming, during PGCs proliferation, DNA needs to be faithfully replicated with an epigenetic inheritance of gene expression states to help maintain PGC identity. Changes in histone posttranslational modifications (PTMs) are associated with epigenetic states that define activation or repression of gene expression. However, it is not well understood whether parental histones decorated with distinct PTMs are recycled and how epigenetic states are inherited in daughter cells during DNA replication. To understand this, I investigated how parental histone is assembled and whether parental histone with their PTMs is inheritable during embryonic DNA replication by using a Drosophila homozygous HisC mutant, which exhibits a deletion of all canonical histone genes (encoding histone H1, H2A, H2B, H3, and H4). The absence of newly synthesized histones in HisC mutant enables tracking the redistribution of parental histones and their PTMs during DNA replication. By integrating RNA-seq, ATAC-seq, CUT&Tag and CUTAC data of histones and their modifications, I found the parental histones are recycled to assembly nucleosomes and maintain the epigenetic landscape despite of the lack of newly synthesized histones. However parental histones are not sufficient to fully re-establish the chromatin structure during DNA replication, as revealed by reduced nucleosome occupancy, increased chromatin accessibility, and possible assembly of hexisome, which leads to increased transcription activity including cryptic transcription from gene bodies.
Keywords: transcription regulation; enhancer interaction; epigenetic inheritance; nucleosome assembly