Integrative genome-wide studies to elucidate regulation of lineage choice in hematopoiesis
Open Access
- Author:
- Mishra, Tejaswini
- Graduate Program:
- Cell and Developmental Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- December 09, 2013
- Committee Members:
- Ross Cameron Hardison, Dissertation Advisor/Co-Advisor
Michael Axtell, Committee Member
Benjamin Franklin Pugh, Committee Member
Robert Paulson, Committee Member
Debashis Ghosh, Committee Member - Keywords:
- hematopoiesis
genomics
gene regulation;RNA-seq;erythroblast;megakaryocyte - Abstract:
- Regulation of gene expression in multicellular eukaryotes allows their cells to express heterogeneous transcriptomes despite possessing the same genome, thus resulting in tissue-specific gene expression, which in turn drives cellular differentiation. Hematopoiesis in mouse is an ideal system in which to study specification of cell fate and cellular differentiation after lineage commitment. Differential gene expression drives lineage commitment and maturation during differentiation, but few studies have addressed changes in gene expression genome-wide across these processes. Much is known about the transcriptome landscape of differentiated erythroblasts and megakaryocytes; however, the transcriptome of the megakaryocyte-erythroid progenitor is relatively unexplored. Till date, comparative transcriptome studies elucidating the alteration in transcriptional output between bipotential progenitors and differentiated, monopotent erythroblasts and megakaryocytes have not been performed. Additionally, even though these sister lineages are regulated by a common set of well-studied transcription factors, it is still unclear as to how these factors exert lineage-specific actions. I have examined changes in the transcriptome during the commitment of the bipotential megakaryocyte-erythroid progenitor into its daughter lineages to infer models of how these changes drive commitment to either of two radically distinct lineage outcomes. I used RNA-seq to map the transcriptome of the bipotential megakaryocyte-erythroid progenitor (MEP) prior to commitment to its two daughter lineages and also the transcriptomes of maturing erythroblasts (ERY) and megakaryocytes (MEG) after commitment. Comparison of these transcriptome maps revealed that MEPs already express much of the MEG program while continuing to express genes associated parallel myeloid lineages such as granulocytes. In contrast, greater numbers of genes are induced in ERY than MEG, along with repression of pan-hematopoietic genes and genes involved in proliferation, signaling, and cell growth. These results suggest a model of broad expression of genes in MEPs that are both a memory of previous myeloid potential and permissive for MEG differentiation, while active induction and repression are needed to execute the erythroid program. This model is supported by genome-wide maps of transcription factor (TF) occupancy. Genes specifically expressed in MEG were preferentially occupied by TFs in early, multipotent hematopoietic progenitors and continue to maintain occupancy post-commitment, whereas erythroid genes were primarily occupied in committed erythroid cells. These results suggest that the default commitment outcome for MEP is MEG, and commitment to ERY requires a radical rewiring of transcription circuitry.