Abstract
Purpose :
Mutations in the transcription factors CRX and NRL disrupt normal photoreceptor development and survival. Previous genome-wide assays provided insight into CRX/NRL target genes and regulatory roles, but did not address chromatin structure modulation. This study was designed to close this gap. We focused on developmental changes of gene activation-associated histone modifications in wild-type and Crx or Nrl deficient mice.
Methods :
Chromatin immunoprecipitation-sequencing (ChIPseq) assays were used to profile the genome-wide occupancy of two activation-associated histone H3 modifications: tri-methylation of Lysine 4 (H3K4me3) and acetylation of Lysine 27 (H3K27Ac), in the retinas of wild-type and Crx- or Nrl-deficient mice before and after photoreceptor differentiation. The results were analyzed alongside published RNAseq, ChIPseq and DnaseI hypersensitivity datasets to identify pathogenic epigenetic alterations that correlate with transcription misregulation.
Results :
The H3K4me3 and H3K27Ac marks on ChIPseq-identified CRX/NRL target genes in WT retinas significantly increased during postnatal photoreceptor differentiation, which was closely associated with gene activation. These dynamic changes of active histone marks were altered in Crx or Nrl deficient retinas. The prevalence and degree of the alterations correlated with gene expression changes and phenotype severity. Thus, dynamic epigenetic regulation is essential for appropriate expression of the genes necessary for photoreceptor cell fate and function, and CRX and/or NRL function is required for this to occur.
Conclusions :
CRX and NRL both act as positive chromatin modulators, as their presence is required for activation-associated epigenetic changes on target genes. Genome-wide profiling of epigenetic changes provides a deeper understanding of the mechanisms by which transcription factor mutations cause misregulation of gene expression and disease phenotype.
This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.