- New Preprint: Dissecting the epigenome dynamics in human immune cells upon viral and chemical exposure by multimodal single-cell profiling
Together with the Greenleaf and Ecker labs, we characterize the multimodal epigenome and regulatory dynamics in human immune cells in response to pathogen exposure.
Abstract:
Pathogen and chemical exposures lead to profound remodeling of the gene-regulatory landscape across human immune cell populations. Exposure-induced epigenetic signatures in cell states can provide insights into gene regulation driven by these cell-extrinsic stimuli. Here, we present a single-nucleus chromatin accessibility atlas of human immune cells of individuals exposed to HIV, COVID-19, Influenza, organophosphates as well as healthy controls. This atlas comprises 271,299 cells and 319,420 candidate regulatory elements that exhibited dynamic accessibility associated with gene regulation across immune cell states. Our longitudinal HIV cohort revealed epigenetic signatures of T cell exhaustion, manifested in changes in the accessibility of binding sites for the FOXP transcription factor family. We further identified changes in the accessibility of candidate regulatory elements in CD14 monocytes upon SARS-CoV-2 exposure that are associated with a switch in NF-κB to AP-1-based regulation of cytokine networks. By integrating single-cell profiles of DNA methylation from matched samples, we create a multimodal epigenome atlas of human immune cells across various exposure states using the accessibility-derived candidate regulatory elements. Both modalities reveal complementary epigenetic signatures at transcription factor binding sites associated with cell state, as exemplified in the process of memory formation in T-cells. Finally, by linking potentially regulatory DNA methylation signatures to changes in chromatin in monocytes, we identify AP1 motifs exhibiting epigenetic dynamics, indicating selective remodeling in TF networks in cases of severe COVID-19. - Teaching: Computational Methods for Epigenome Analysis (2025)
We will be teaching workshop (special lecture in bioinformatics (5 CPs)) on the practical analysis of epigenome data. WIn this workshop you will gather hands-on exprience in the analysis of sequencing data for profiling gene expression, DNA methylation, histone modifications and chromatin accessibility. More details can be found on the lecture website.
- Teaching: Single-Cell Bioinformatics
We will be teaching a special lecture in bioinformatics (9 CPs) on the hot topic of computational methods for single-cell analyses. We will be covering methods and topics from the fields of single-cell transcriptomics, genomics, and epigenomics. Together with the Thomas Hentrich and Fabian Kern we are offering the lecture “Single-cell Bioinformatics”. More details can be found on the lecture website.
- Job Opportunity
Interested in a PhD or post-doc in bioinformatics? Eager to engage in cutting-edge research in computational epigenomics in a starting lab at Saarland University? Check out this opportunity!
Job posting (English)
Stellenausschreibung (deutsch) - Functional Epigenomics Conference
We are excited to be part of the organizing team for the “Functional Epigenomics Conference” (May 27-28, 2024) in Saarbrücken. Registration and Details can be found on the conference website.
