Abstract
E74‐like factor 5 (ELF5) and ETS‐homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three key cis‐regulatory elements (CREs) from the chr11p13 region and also activated multiple open chromatin sites with CRISPRa in airway epithelial cells. Deletion of the CREs caused subtle changes in chromatin architecture and site‐specific increases in EHF and ELF5. CRISPRa had most effect on ELF5 transcription. ELF5 levels are low in airway cells but higher in LNCaP (prostate) and T47D (breast) cancer cells. ATAC‐seq in these lines revealed novel peaks of open chromatin at the 5’ end of chr11p13 associated with an expressed ELF5 gene. Furthermore, 4C‐seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP‐seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6, and siRNA‐mediated depletion of ELF5 enhanced EHF expression. These results define a new role for ELF5 in lung epithelial biology.
Highlights
Many monogenic disorders have significant phenotypic variability that may be attributed to genetic elements outside the causative locus
E twenty‐six (ETS)‐homologous factor (EHF) has a direct role in CFTR regulation, as it binds to an airway selective enhancer element of CFTR and represses its expression.[13]
The deletion had no impact on interactions with the HB11.1485 viewpoint, while associations with the EHF promoter were modestly reduced. These data suggest that the 11.2521 cis‐regulatory elements (CREs) may inhibit E74‐like factor 5 (ELF5) promoter interactions with previously uncharacterized enhancer elements, and that its functions depend upon specific chromatin architecture at chr11p13
Summary
Many monogenic disorders have significant phenotypic variability that may be attributed to genetic elements outside the causative locus These sites (modifier loci) are often identified by genome-wide-association studies (GWAS).[1]. EHF has a direct role in CFTR regulation, as it binds to an airway selective enhancer element of CFTR and represses its expression.[13] For these reasons, EHF is a strong candidate CF modifier gene and a potential CF therapeutic target since elevated CFTR substrate may enhance the efficacy of correctors and potentiators.[14]. We pursued the predicted role of ELF5 in regulating EHF by investigating open chromatin and 3D architecture in cell types with different abundance of ELF5. These genomic context studies revealed a critical role for ELF5 in coordinating the complex regulatory environment at chr11p13. Our results are relevant to the involvement of both ELF5 and EHF in lung disease, since both genes are expressed in human bronchial epithelium
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