TY  - GEN
N2  - Neuronal stimulation induces genome-wide transcriptomic and epigenomic changes modulating its synaptic function, structure and plasticity, with consequences on neurological disease etiology. Following membrane depolarization, calcium (Ca2+)-mediated signaling triggers the expression of immediate early genes (IEGs), a group enriched in transcription factors (TFs), including the AP-1 dimer. IEGs promote epigenetic changes regulating the activity-dependent response and drive the expression of late response genes (LRGs), which are crucial for neuronal function. This biphasic mechanism is conserved across rodents and humans. However, changes in cis-regulatory elements (CREs) are hypothesized to have modified the IEG/LRG transcriptional kinetics enabling the acquisition of superior cognitive abilities in our species. Throughout primate genome evolution, transposable elements (TEs) have been the biggest contributors to regulatory novelty. Among other strategies, the deleterious transposition activity of these repetitive loci can be repressed via their targeting by species-specific repertoires of Kru?ppel-associated box (KRAB) zinc finger (ZNF) proteins (KZFPs) and subsequent recruitment of heterochromatin-forming complexes. Beyond repression, KZFP-TE interactions are thought to have enabled the exaptation of TEs? raw regulatory potential for the establishment of human-specific gene regulatory networks (GRNs). The abundance of KZFPs among neuronal stimulation-modulated genes suggest KZFP-TE networks could have contributed to the regulatory innovation required in the human neuronal response. However, the function of TEs and KZFPs in this context is largely unknown.  
To address this gap in knowledge, in this thesis I established and optimized an in vitro model of human neuronal stimulation featuring hiPSC-derived glutamatergic neurons (hiGNs) in co-culture with mouse Astrocytes (mAstrocytes). Combining transcriptomic, epigenomic and imaging approaches together with CRISPRa/i perturbations and in depth bioinformatic analyses I characterized the hiGN response to membrane depolarization with a particular focus on studying the role of KZFPs and TEs in this response. My results revealed human neuron stimulation triggers global KZFP transcriptomic changes with temporally-defined dynamics. Among them, ZNF331, ZNF10 and ZNF184, show an IEG-like increase in expression, probably induced by Ca2+ signaling. Conversely, most KZFPs are downregulated upon stimulation at late timepoints. CRISPR perturbation of the activity-induced ZNF331, ZNF10 and ZNF184 showed that these KZFPs play a role in modulating the expression of ion transport genes, including Ca2+-transport. The KD of these three KZFPs in hiGNs modified the transcriptional and epigenomic responses of these cells to stimulation, as well as their Ca2+-transport kinetics. This underscored the relevance of ZNF331, ZNF10 and ZNF184 in fine-tuning the expression of LRGs key for neuronal function. While still under investigation, my preliminary data indicates KZFP repression could take place as a consequence of condensed chromatin re-location to Nucleolus-associated domains (NADs) following neuronal activation. At TEs, stimulation did not dramatically modify the distribution of the repressive H3K9me3 chromatin marks. However, it triggered significant increase of the active chromatin mark H3K27ac at loci enriched in bZIP-family TF motifs, especially for the AP-1 dimer, and falling within proximity of activity-relevant LRGs. A high proportion (i.e., 30 - 50 %) of AP-1 motif-bearing differentially-acetylated TEs (DA-TEs) are predicted binding sites of stimulation-repressed KZFPs. Thus, downregulation of KZFPs appears as a potential mechanism to facilitate the access to these TEs, which could be bound by AP-1 and used as CREs to regulate the expression of nearby activity-associated genes. However, unlike canonical activity-responsive CREs, DA-TEs are not enriched in neuropsychiatric disease-associated variants (daSNVs).
In conclusion, this study deepens our understanding of the activity-dependent transcriptomic and epigenomic responses in human neurons. My results suggest KZFPs and TEs are involved in the modulation of both gene expression and AP-1 activity in this context, ultimately fine-tuning the stimulation-induced transcriptional program. Finally, this data adds to the growing body of evidence describing regulatory functions for KZFPs and TEs, which could have potentially contributed to the regulatory innovation necessary to shape the human-specific response to neuronal stimulation.
AV  - restricted
KW  - KRAB zinc fingers
KW  -  Transcriptomics
KW  -  Epigenetics
KW  -  Transcription Factors
KW  -  Gene Regulation
A1  - Campos Fornés, Víctor
TI  - Re-wiring of KRAB zinc finger protein - transposable element regulatory networks in stimulated human neurons
Y1  - 2026///
ID  - heidok37311
CY  - Heidelberg
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/37311/
ER  -