Lhx2 controls changes in chromatin accessibility in retinal progenitor cells during developmental competence transitions.

We profiled retinal progenitor cells by integrating next generation sequencing methods and interrogating changes in chromatin accessibility at embryonic and post-natal murine stages. We identified putative factors involved in the developmental progression of the retinal progenitors epigenome and we report Lhx2 role in the regulation of chromatin accessibility by coordinated action of developmentally regulated pioneer factors Overall design: Next generation sequencing methods were performed on RPCs that express the neuro-retinal transgene Chx10-Cre:eGFP. Chx10 positive (Chx10+ve) RPCs were separated from the post-mitotic pool by fluorescence activated cell sorting, isolated at embryonic day (E) 14 and postnatal day (P) 2 and they have been hereafter referred to as GFP+, whereas the post-mitotic pool as GFP-.Flow sorted cells were profiled by RNA-Seq and ATAC-Seq, relying on direct in vitro transposition of sequencing adapters into native chromatin. ChIP-Seq was then performed on the top transcription factor candidate, identified in the preliminary screening of the ATAC-Seq derived open chromatin regions. ChIP-Seq binding sites for the candidate factor were ultimately integrated and compared with the age-matched RNA-Seq and ATAC-Seq profiles from control and knock-out retinas.