Tired of not knowing what really turns an enhancer on? You’re not alone, but luckily an inquisitive team of researchers out of Cambridge spent some serious time targeting enhancers by throwing some genome editing wizardry at them.
The team, led by Pentao Liu, systematically compared how the TALE effectors and CRISPR targeting tools fare in turning gene expression up or down when targeting enhancer regions, demonstrating the distinct strengths of each tool.
They specifically targeted activators (VP64 activation domain) or repressors (KRAB domain) to the enhancer sites of two pluripotency genes (Oct4 and Nanog) using TALE effectors or CRISPR/dCas9 guides.
You might be surprised with the results:
CRISPR vs. TAL Effectors in Gene activation
The authors found that CRISPR/dCas9 seemed weaker in activating gene expression compared to TALE effectors.
Specifically, they noted:
- While both CRISPR/dCas9 and TALE effectors appeared to be equally effective at activation of a luciferase reporter, TALE effectors targeted activation outshined CRISPR/Cas9 in activation of endogenous Oct4 and Nanog loci.
- CRISPR/dCAS9 targeting of the Oct4 and Nanog enhancers led to lower enrichment of activating components (p300) and of active histone markers (H3K27Ac) at the enhancer regions compared to TALE targeting.
- The authors suggest that dCas9 binding is a weak activator of expression because it obstructs binding of native transcription factors (NANOG, KLF4) at the enhancer region, unlike the TAL effectors.
Tempting Fate: CRISPR vs. TAL Effectors in Cellular Reprogramming
But surely one wonders, how good is such ‘designed gene reactivation’, for studying biological processes such as enhancer usage or cell fate decision?
To assess such suitability, Liu’s team used TALE or CRISPR/dCas9 driven upregulation of Oct4 or Nanog to test if such activation is as competent as transgene driven upregulation in reprograming of somatic cells or EpiSCs to iPSCs.
They found that TALE directed activation of Oct4 and Nanog was tremendously more potent at achieving somatic cell/EpiSC to iPSC transformation compared to CRISPR/dCas9. The researchers suggest you use a combined TALE and CRISPR/dCas9 approach to achieve efficient simultaneous activation and repression of distinct genomic loci.
Read the TALE of the two tools Nucleic Acids Research, 2014