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Epigenetic signals that direct cell type specific interferon beta response in mouse cells

Muckenhuber, Markus

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Interferon beta (IFNβ) triggers the JAK-STAT signaling cascade to induce IFN-stimulated genes (ISGs), which is a hallmark of innate immune response against viral infections. The transcription factors STAT1 and STAT2 become activated and, together with IRF9, assemble into the ISGF3 complex. This complex translocates to the nucleus and activates ISGs by binding to its DNA recognition motif. Most cell types have the potential to activate ISGs upon IFNs signaling but embryonic stem cells (ESC) have a very different response compared to differentiated cells. However, the exact molecular mechanisms that drive this cell type specific interferon signaling are poorly characterized.

In this thesis, the cell type specific IFNβ response was compared between mouse ESCs and differentiated cells like mouse embryonic fibroblasts (MEFs) that carry the same genome. I tested the hypothesis that the cell type specific differences in IFNβ response originate from distinct epigenetic states by applying a genome-wide multiomics approach: (i) A differential gene expression analysis by RNA-seq of IFNβ stimulation defined a total of 513 ISGs and allowed it to identify cell type specific ISG signatures. The bulk sequencing analysis was complemented with single cell RNA-seq to resolve heterogeneity of gene expression response. (ii) By TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) the STAT1 and STAT2 binding sites were mapped across cell types. (iii) Active chromatin regions were detected with the assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq). Single cell ATAC-seq was used to identify coregulated enhancers and promoters. (iv) ChIP-seq of histone acetylation (ac) and mono- and tri-methylation (me1, me3) marks at histone lysine residues for H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K9me3 and H3K27me3 was conducted.

The analysis of this comprehensive data set yielded cell type specific patterns of ISGs, ISGF3 binding and chromatin features. The overall stronger IFNβ response in MEFs could be rationalized by factors from the JAK/STAT signaling cascade being constitutively more strongly expressed. In addition, 33 ISGs in ESCs and 305 ISGs in MEFs were found to be cell type specific and thus candidates for epigenetic regulation. To characterize the underlying mechanism, the genomic location, chromatin context and target genes of ISGF3 were characterized. While 92 ISGF3 sites were shared between ESCs and MEFs, 116 and 184 sites were specific for one cell type and found at promoters and putative enhancers. Based on a co-regulation analysis of single cell ATAC-seq data, many of these enhancers could be linked to specific ISGs. Furthermore, the analysis revealed that a pre-existing enrichment of H3K4me1 and open chromatin loci at ISGF3 sites was positively correlated with ISGF3 binding while H3K27me3 showed the opposite effect.

In summary, this thesis characterizes the contribution of epigenetic gene regulation mechanisms to the cell type specific IFNβ response and rationalizes how chromatin features direct cell type specific ISGF3 binding. The insight gained opens up new possibilities for targeted interference with interferon response in anti-viral drug development by accounting for the contribution of chromatin to this process.

Item Type: Dissertation
Supervisor: Rippe, Prof. Dr. Karsten
Place of Publication: Heidelberg
Date of thesis defense: 14 December 2020
Date Deposited: 10 Feb 2021 16:10
Date: 2022
Faculties / Institutes: The Faculty of Bio Sciences > Dean's Office of the Faculty of Bio Sciences
Subjects: 500 Natural sciences and mathematics
570 Life sciences
610 Medical sciences Medicine
Controlled Keywords: Epigenetik, Genregulation, Genom, Interferon beta, STAT1/2
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