If you think the subway is crowded you haven’t seen what a TAL Effector (TALE) has to put up with when getting to work. In a new study involving the production of more than 200 TALE modulators, researches at Beijing University found the long sought explanation of why some TALEs effectively modulate transcription while others do not.
Hanshuo Zhang and colleagues started by systematically designing TALEs to cover the upstream regulatory sequences of 3 genes involved in cell migration. When testing the transcriptional activity of these TALE modulators by PCR and in cell migration assays they observed a “wave-like” pattern with alternating “peaks” and “valleys” along the upstream regulatory sequences.
This prompted them to take a closer look at the differences in chromatin topographies between transcriptionally permissive and non-permissive regions.
Here is what they found:
- Proximal core promoter regions are bad targets for TALEs as they tend to be occupied by the endogenous transcription factors
- Non-permissive regions exhibited a higher nucleosome occupancy preventing the TALE from binding to DNA
- Counter intuitively: the farther away from the transcriptional start site the better the TALE performs
- Tweaking the relative location of permissive sequences by TALE-TALE fusions results in efficient transcriptional repression
Armed with these new insights, the researchers performed gain-of function screening pinning down the role of Rho/ROCK and ERK pathway in cell migration and cancer development.
So next time you’re struggling with overcrowded public transport take a deep breathe and have a look at Nucleic Acids Research, June 2014.