This recent review on mapping transcriptional regulatory networks in hematopoietic stem cells (HSC) blood cells is very nice (1). Transcriptional regulatory networks are central to specifying context-specific gene expression patterns. Such networks specifying connections between transcription factor proteins and target genes, although, it is common to also include some upstream regulators such as signaling proteins, non-specific DNA binding proteins and chromatin remodelers as potential regulators. The review highlights the need to predict the connections between regulators and target genes. In particular for the HSCs about 50 or so regulators have been identified already. For several of these there are ChIP-seq/ChIP-chip data that have been measured. But our understanding of networks in this cellular state is still far from complete. While expression-based network inference methods including module networks have been applied to this lineage, there is still a lot to do to map these networks. The ability to measure single cell expression profiles opens up new opportunities because one can potentially discriminate causal and temporal dynamics on these networks. Furthermore, the ability to make more targeted perturbations using CRISPR offers even more opportunities to build more accurate pictures of such regulatory networks.
1. Göttgens, Berthold. “Regulatory network control of blood stem cells..” Blood 125 (April 2015): 2614-2620.