title: Deconvolution of Hematopoietic Commitment Decisions by Genome-wide Analysis of Progressive DNA Methylation Changes
creator: Stäble, Sina
subject: ddc-570
subject: 570 Life sciences
description: Hematopoietic stem cells (HSCs) are responsible for the life-long production of all mature blood cells. The classical hierarchical model of hematopoiesis has been revised based on single-cell transcriptome analyses to suggest a continuous rather than a step-wise differentiation process. While differentiation trajectories can be inferred from single-cell transcriptional snapshots, it remains a challenge to identify definitive points of lineage commitment. The molecular characterization of such commitment decisions is required to accurately model the hematopoietic system.  The analysis of 5-methylcytosine may facilitate the identification of such molecular commitment marks due to the progressive nature of how DNA methylation is programmed during differentiation. In this doctoral thesis, a genome-wide DNA methylome map of murine hematopoiesis was generated using tagmentation-based whole genome bisulfite sequencing, encompassing 26 hematopoietic cell populations. Across all populations, 147,232 differentially methylated regions (DMRs) were identified and grouped into coordinately regulated regions by hierarchical clustering. These dynamically regulated regions showed progressive and unidirectional DNA methylation programming during normal hematopoietic differentiation. The DNA methyltion programs can be interpreted as pan-hematopoietic, lineageand cell type-specific, indicating a molecular mechanism of cell fate restriction. The lineage specificity of the DNA methylation programs was confirmed by the enrichment of hematopoietic transcription factor binding motifs and lineage-specific enhancer programs. Strikingly, lineage-specific DMRs were already identified within the multipotent hematopoietic stem and progenitor compartment, supporting the concept of early lineage restriction. Furthermore, a model of murine hematopoiesis could be inferred in form of a diffusion map that is purely based on DNA methylation dynamics during hematopoietic differentiation. To gain further insights into how DNA methylation dynamics relate to the regulation of gene expression, a single-cell transcriptome map of the entire murine hematopoietic system was generated. The integration of DNA methylation dynamics with single-cell gene expression patterns provided evidence for an anti-correlation between DNA methylation and cell-type specific gene expression patterns. However, loss of DNA methylation was not invariably associated with an increase in gene expression. This suggests that DNA methylation has more a permissive rather than an instructive role in regulating lineage-specific transcriptional programs.  Finally, the DNA methylome map was used as a resource to investigate epigenetic patterns that underlie the myeloid and megakaryocytic lineage bias observed in aged mice. By comparing the DNA methylomes of young and aged HSCs, 3,275 DMRs were identified, which were predominantly associated with a loss of DNA methylation in genes involved in integrin signaling, platelet activation, and platelet aggregation. Notably, 46% of these DMRs overlapped with DNA methylation patterns identified in normal hematopoietic differentiation and significantly affected DNA methylation programs showing low DNA methylation levels in megakaryocyte-primed cell populations. Together, these findings suggest that HSC aging alters the DNA methylome in vivo, in a manner that is associated with a increased differentiation towards the megakaryocytic lineage.  In summary, the DNA methylome map of murine hematopoiesis generated in this thesis provides novel insights into the epigenetic regulation of hematopoietic differentiation and complements recent findings from single-cell transcriptome studies. Furthermore, it represents a rich resource to investigate DNA methylation patterns in hematopoiesis across a broad range of conditions.
date: 2019
type: Dissertation
type: info:eu-repo/semantics/doctoralThesis
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserver/27453/1/PhDThesis_Sina.pdf
identifier: DOI:10.11588/heidok.00027453
identifier: urn:nbn:de:bsz:16-heidok-274535
identifier:   Stäble, Sina  (2019) Deconvolution of Hematopoietic Commitment Decisions by Genome-wide Analysis of Progressive DNA Methylation Changes.  [Dissertation]     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/27453/
rights: info:eu-repo/semantics/openAccess
rights: http://archiv.ub.uni-heidelberg.de/volltextserver/help/license_urhg.html
language: eng