Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers

Abstract

Transcription factors control the fate of a cell by regulating the expression of genes and regulatory networks. Recent successes in inducing pluripotency in terminally differentiated cells as well as directing differentiation with natural transcription factors has lent credence to the efforts that aim to direct cell fate with rationally designed transcription factors. Because DNA-binding factors are modular in design, they can be engineered to target specific genomic sequences and perform pre-programmed regulatory functions upon binding. Such precision-tailored factors can serve as molecular tools to reprogramme or differentiate cells in a targeted manner. Using different types of engineered DNA binders, both regulatory transcriptional controls of gene networks, as well as permanent alteration of genomic content, can be implemented to study cell fate decisions. In the present review, we describe the current state of the art in artificial transcription factor design and the exciting prospect of employing artificial DNA-binding factors to manipulate the transcriptional networks as well as epigenetic landscapes that govern cell fate.

Synthetic genome readers target clustered binding sites across diverse chromatin states

“…Such "pioneer" factors facilitate binding by other transcription factors and are usually necessary for the maintenance of cell identity. The forced overexpression of pioneer factors is often sufficient for cell-fate conversion (26). Our data suggest that polyamides, by virtue of being able to access repressive heterochromatin, could be harnessed to serve as pioneer factors, but the conditions under which they might do so will guide the next phase of polyamide design.…”

“…Indeed chromatin accessibility is a major barrier to binding by naturally occurring DNA-binding proteins as well as artificial DNA binders, such as zinc fingers, transcription activator-like effectors, and the RNA-guided CRISPR-Cas9 (26,27). Elegant biophysical and biochemical studies have demonstrated that polyamides bind to solvent-exposed cognate sites on nucleosomes without significant loss in affinity or specificity (28,29).…”

Reprogramming cell fate with artificial transcription factors

“…The majority of such challenges can be circumvented by artificial transcription factors (ATFs) that directly target key gene regulatory networks that govern cell fate changes(Fig. A) . Importantly, libraries of ATFs can also be used to screen thousands of genes in parallel to produce a phenotype of interest without prior knowledge of relevant natural TFs or gene regulatory networks .…”

SCNT versus iPSCs: proteins and small molecules in reprogramming

“…On the other hand, the origin of the cell type can also influence the immune properties of iPSCs, possibly due to differences in reprogramming memory (Polo et al, 2010). The difference in transcription and epigenetic landscape between ESCs and iPSCs is that the latter type bearing some memory of their original differentiated state (Eguchi et al, 2014). The memory of iPSCs can result in the partial retention of the transcriptional and epigenetic features of the source cells.…”