Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation

Gene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we perform perturbation-based massively parallel reporter assays at seven early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide cellular differentiation. By perturbing over 2,000 putative DNA binding motifs in active regulatory regions, we delineate four categories of functional elements, and observe that activity direction is mostly determined by the sequence itself, while the magnitude of effect depends on the cellular environment. We also find that fine-tuning transcription rates is often achieved by a combined activity of adjacent activating and repressing elements. Our work provides a blueprint for the sequence components needed to induce different transcriptional patterns in general and specifically during neural differentiation.

Automated summary

This study systematically characterizes the role of regulatory elements and motifs in guiding cellular differentiation. The researchers find that the sequence of DNA binding motifs determines the activity direction, while the magnitude of effect depends on the cellular environment. They also observe that fine-tuning transcription rates is often achieved through the combined activity of activating and repressing elements. This work provides insights into the components needed to induce different transcriptional patterns during neural differentiation.