Molecular characterisation of the transcription factor – chromatin landscape interplay during neuronal cell fate acquisition
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Abstract
A multicellular organism consists of a huge variety of different cell types that are all derived from the totipotent zygote. In order to achieve the creation of such diversity from a single cell, a fine-tuned regulation of the genomic output is essential. With regard to gene regulation it is increasingly appreciated that cell fate changes are coordinated by multiple regulatory layers on both, the genetic as well as the epigenetic level. The concerted action of both layers integrates cell-intrinsic and cell-extrinsic cues during development to enable for dynamic cellular responses that become manifested in differential gene expression profiles.
This thesis focused on the molecular regulation of cell fate changes during embryonic neuronal differentiation in Mus musculus. Although several transcription factors and epigenetic mechanisms have been described in the context of embryonic neurogenesis, a full understanding yet remains elusive. In this thesis, molecular biology and neurobiology techniques were applied in addition to high-throughput sequencing technologies and computational analyses to explore the impact of two neuron-specific transcription factors on the developmental chromatin landscape. The first part of this thesis investigated the transcription factor NeuroD1. This protein was found to occupy cis-regulatory elements of neuronal genes in a sequence specific fashion. Interestingly, a significant fraction of such genomic loci were embedded in an inactive chromatin landscape prior to NeuroD1’s binding. NeuroD1’s occupancy of these sites initiated their conversion into an active euchromatin state and hence led to the induction of the neuronal developmental program. Several identified NeuroD1 target genes encompassed transcriptional regulators, suggesting that this protein initiated a cascade of nuclear factors that further mediated neuronal fate determination. Strikingly, the transient action of NeuroD1 was sufficient to induce a sustained shape of the neuronal chromatin landscape that persisted after its disappearance during later stages of development. This characterisation of NeuroD1’s molecular function suggested that it might act as a pioneer transcription factor. In the second part of this thesis Zfp354c was identified as a novel KRAB-zinc-finger protein that interacted with KAP1 to confer H3K9me3-mediated silencing of repetitive elements during neurogenesis. Both, its depletion in vitro and in vivo, impaired neuronal differentiation, possibly due to the de-repression of endogenous retroviral elements.
In summary, this thesis provides novel insights into coordinated chromatin landscape dynamics during neuronal cell fate acquisition and advocates for the importance of both, the coding as well as the non-coding genome, during this process. These findings open new avenues for the understanding of regulated cellular differentiation and their underlying transcriptome dynamics in the context of neurogenesis. This knowledge can potentially be used for therapeutic reprogramming attempts to ectopically restore degenerated neuronal cell populations.