eprintid: 34190
rev_number: 16
eprint_status: archive
userid: 7822
dir: disk0/00/03/41/90
datestamp: 2023-12-20 12:58:51
lastmod: 2023-12-21 10:44:03
status_changed: 2023-12-20 12:58:51
type: doctoralThesis
metadata_visibility: show
creators_name: Kremer, Lukas Peter Maria
title: Investigating the Molecular Basis of Adult Neurogenesis: Single-Cell Multi-Omics Unveils DNA Methylation as a Key Regulator of Astrocyte Stemness
subjects: ddc-004
subjects: ddc-500
subjects: ddc-570
divisions: i-140001
adv_faculty: af-14
keywords: single-cell sequencing, multi-omics, DNA methylation, adult neural stem cells, neural stem cells, astrocytes, adult neurogenesis, epigenetics, cell fate, stem cells, stemness, omics, single-cell bisulfite-sequencing, bioinformatics, computational biology
cterms_swd: Stammzelle
cterms_swd: Neurogenese
cterms_swd: Biomethylierung
cterms_swd: Glia
cterms_swd: Epigenetik
cterms_swd: Bioinformatik
abstract: The ventricular-subventricular zone (vSVZ) of adult mammalian brains harbors specialized astrocytes, called adult neural stem cells (NSCs), which are capable of generating both neurons and glial cells. In contrast, common parenchymal astrocytes perform a wide range of structural, metabolic, homeostatic and neurosupportive functions. Despite these distinct functions, studies employing immunostaining and single-cell RNA-sequencing have demonstrated that NSCs and astrocytes largely express the same set of genes, which raises the question how stem cell function is molecularly encoded. To address this question, I analyzed a single-cell triple-omic data set that contains information on gene expression, chromatin accessibility and DNA methylation for hundreds of cells of the adult NSC lineage, as well as common parenchymal astrocytes.

To enable this analysis, I developed "scbs", a Python software for the analysis of single-cell methylation data. I devised and implemented two major improvements over the current state of the art analysis workflow: First, instead of segmenting the genome into fixed intervals, I devised an approach to scan the entire genome for informative regions called variably methylated regions (VMRs). Second, instead of simply averaging methylation values within these tiles, I devised a more robust measure of DNA methylation.

By making use of these new methods, I demonstrated that adult NSCs possess a unique DNA methylation profile that is not found in common parenchymal astrocytes. This NSC methylome is characterized by hypomethylation of genes required for neurogenesis. I propose that this feature contributes to the neurogenic capabilities of NSCs by enabling the transcriptional activation of these genes. In
contrast, common parenchymal astrocytes are locked in their current astrocyte fate by DNA methylation. To test this hypothesis, I analyzed single-cell multi-omic data from mice that were subjected to ischemia, as ischemia is known to induce a neurogenic response in common parenchymal astrocytes and NSCs. My analysis suggests that this gain of neurogenic capabilities is accompanied by gain of an NSC
methylome, which supports the idea that a specific DNA methylome is required for stem cell function. Overall, my results demonstrate that DNA methylation is dynamic even in adult tissues and not just in embryonic development, and furthermore unveils DNA methylation as a crucial factor that constrains or enables alternative cellular fates.
date: 2023
id_scheme: DOI
id_number: 10.11588/heidok.00034190
fp7_project_id: 771376
ppn_swb: 1876774142
own_urn: urn:nbn:de:bsz:16-heidok-341900
date_accepted: 2023-12-04
advisor: HASH(0x55fc36cb60d0)
language: eng
bibsort: KREMERLUKAINVESTIGAT2023
full_text_status: public
place_of_pub: Heidelberg
citation:   Kremer, Lukas Peter Maria  (2023) Investigating the Molecular Basis of Adult Neurogenesis: Single-Cell Multi-Omics Unveils DNA Methylation as a Key Regulator of Astrocyte Stemness.  [Dissertation]     
document_url: https://archiv.ub.uni-heidelberg.de/volltextserver/34190/1/L_Kremer_PhD_thesis_PDFA-1b.pdf