D Miranda-Saavedra et al.
University of Cambridge
Haematopoiesis is blood development – one cell type differentiating into ~14 cell types. BloodExpress, a database of gene expression in mouse haematopoiesis, is mentioned. TFs involved in HSC specification and their regulatory relationships. The vast majority are essential, and malfunctions are implicated in diseases like leukemias. Scl-ChIP sequencing is used. They'd like to know what genes are regulated by SCL. They've used HPC-7 cells in their experiments, which are a haematopoietic cell line, stem cell factor dependent, and multipotential.
The candidate SCL genes were those next to the 228 high-confidence bound regions. They did some in vivo assays (transgenic analyses), looking at the resulting embryos after 2 weeks. He then showed a series of microscopy images of cross-sections under different conditions. They then performed some bioinformatics analyses to explore the regulatory nodes. In one case, they selected genes specifically shut down in the progenitors. They found a series of motifs, motif classes, and candidate factors for those motifs. This is motif discovery.
Haematopoiesis is a powerful stem cell system where transcriptional regulation is the key in driving blood development. Using the BloodExpress database and ChIP-seq on SCL/TAL1 they have extended the known HSC regulatory netowrk. They have a paper in "Blood" that is currently in press.
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