Systems biology approaches to understanding hematopoiesis
Abraham, Brian J.
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Understanding gene expression and the regulation thereof that confer cell type-specific (CTS) functionality holds primary importance in devising therapeutics capable of emulating these functions, especially within blood. Hematopoiesis and further differentiation require epigenetic mechanisms to establish and maintain diverse cell identity and function, given constant genomic content. Gene expression and binding of chromatin-associated proteins coincide, and both change during differentiation from hematopoietic stem cells (HSCs) through progenitors with progressively restricted lineage capabilities to terminally differentiated cells. To understand the CTS expression patterns that underlie hematopoiesis, I investigated transcriptomes from discrete stages of blood progenitors, including human HSCs, B lymphocytes, T lymphocytes, and erythrocyte precursors as well as many stages of mouse T lymphocyte development and differentiation. Here, I identify hundreds of genes and numerous gene networks showing CTS expression. I next contextualize CTS expression within chromatin environments, including modified histones and other DNA-binding factors using genome-wide binding data. Specific histone modifications and chromatin proteins are enriched at the transcription start sites (TSSs) of CTS genes and correlate with expression. Surprisingly, certain chromatin marks remain at these CTS TSSs in other cell types. I show that TSSs of differentiation regulators are bivalently primed in HSCs, and become selectively activated in their specific cell type. I predict enhancers of CTS genes and show that their chromatin profiles act in mediating expression. To address regulation of epigenetic modifications during differentiation, I analyzed genome-wide binding profiles oftranscription factor GATA3, which (1) determines T cell lineage commitment, (2) is crucial for differentiation ofT lymphocytes into effector cells, and (3) promotes transcription ofmany T subset-specific genes. I show that GATA3 parsimoniously changes binding patterns during differentiation, and binds a core set of genes as well as T-subset-specific sets. Although GATA3 regulates a small percentage of genes in a cell-type-specific manner, histone modifications at a majority of GATA3-bound genes change significantly after Gata3 deletion, implicating GATA3 in regulatory chromatin organization. I further show that GATA3 binding and function may be mediated by co-binding factors in accord with the presence of their target DNA sequence motifs.
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