A high-throughput functional screening identifies non-canonical cis-regulatory sequences in the POU5F1 Locus

With less than 2% of the human genome coding for proteins, a major challenge confronting researchers today is to interpret the function of the non-coding DNA. Millions of regulatory sequences have been predicted in the human genome through the analyses of DNA methylation, chromatin modification, hypersensitivity to nucleases, and transcription factor binding, but few have been shown to regulate transcription in their native contexts. To begin to address this issue, we have developed a high throughput CRISPR/Cas9-based genome-editing strategy and used it to interrogate 174 candidate regulatory sequences within the 1Mbp POU5F1 locus in the human ES cells. We identified two classical regulatory elements - including a promoter and a proximal enhancer - that are essential for POU5F1 transcription in the ES cells. Unexpectedly, we also discovered a new class of cis elements that contribute to POU5F1 transcription in an unusual way: disruption of such sequences led to a temporary loss of POU5F1 transcription that is fully restored after a few rounds of cell division. These results demonstrate the utility of a high throughput screening for functional characterization of non-coding DNA, and reveal a previously unrecognized layer of gene regulation in human cells.