Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. By relocating promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the native Sox2 gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. Surprisingly, the confining effect of the Sox2 gene is partially conferred by its ~1 kb coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain the realm of influence of its enhancer.

This repository contains:

• PDF exports of all lab notebook entries related to this manuscript
• PDF exports of the FACS sorting from all hopping experiments (FACS_sorting_pdfs.zip)
• All gated or ungated fcs files used to generate the manuscript figures, split into zip files per experiment number (E2096 - E2555, as used in the lab notebook entries and the file references in the published plotting scripts)
• Called CTCF motifs (6764_2_ME_E2_CGATGT_S2_R1_001_peaks_motifs.bed)

Raw sequencing data is deposited to GEO (GSE275427), data analysis pipelines and scripts to create all manuscript figures are deposited in the affiliated GitHub release on Zenodo.