Genomewide Methylation Analyses of Human Hematopoietic Progenitors

This Ancillary Project represents a mechanism to continue, and integrate within PCBC, the extremely productive collaboration between the Center for Epigenetics at Johns Hopkins, led by Andrew Feinberg, and the laboratories of Irving Weissman and Ravi Majeti at Stanford. The Feinberg laboratory has pioneered studies of the epigenetic basis of human development and disease, in an NHGRI-designated Center of Excellence in Genomic Science (CEGS), developing laboratory and statistical tools for the general analysis of epigenetic modifications in normal development and disease. Among these are two papers from our collaboration on hematopoiesis published recently in Nature The Aim of this Ancillary Project is to identify epigenomic differences in human hematopoietic stem and progenitor populations using comprehensive DNA methylation mapping methods at Johns Hopkins, and to relate such changes to differences in gene expression and cellular function on the same cell populations studied at Stanford. We will prospectively isolate human HSPC populations from normal bone marrow, including HSC, MPP, L-MPP, CLP, CMP, GMP, and MEP, and subject them to a rigorous analysis of differential epigenetic modifications and gene expression. We will use two analytical approaches, CHARM and whole-genome bisulfite sequencing. These data will be integrated with RNA expression data on the same samples, using regression models in an annotation-agnostic manner. Finally, we will provide all of these data to the PCBC with a powerful graphical user interface, making it a key resource for the Consortium as a whole.
We generated the first comprehensive DNA methylation map of mouse HSPC using Comprehensive High-Throughput Array-Based Relative Methylation (CHARM). Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands. This analysis validated genes known to be lineage-related as well as many examples of genes and pathways not previously known to be involved in the choice between lymphoid/myeloid differentiation. 

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