NKX2.2 and KLF4 cooperate to regulate a cell identity [aTC_klf4_KD_RNAseq]

Transcription factors (TF) are indispensable for maintaining cell identity through regulating cell specific gene expression. Distinct cell identities derived from a common progenitor are frequently perpetuated by shared TFs; yet the mechanisms that facilitate their cell specific regulatory targets are poorly characterized. We report that the TF NKX2.2 is critical for the identity of pancreatic islet a cells by directly activating a cell genes and repressing alternate islet cell fate genes. When compared to the known role of NKX2.2 in islet ß cells, we demonstrate that NKX2.2 regulates novel a cell target genes, facilitated in part by a cell specific DNA binding at gene promoters. Furthermore, we have identified the reprogramming factor KLF4 as having enriched expression in a cells, where it co-occupies NKX2.2-bound a cell promoters and is necessary for NKX2.2 binding in a cells to co-regulate many NKX2.2 a cell transcriptional targets. Misexpression of Klf4 in ß cells is sufficient to manipulate chromatin accessibility, increase binding of NKX2.2 at a cell specific promoters sites, and alter expression of NKX2.2-regulated cell specific targets. This study identifies KLF4 is a novel a cell identity factor that cooperates with NKX2.2 to regulate a cell identity. Overall design: To investigate the gene expression regulation by Klf4 in in vitro pancreatic alpha cells. Pancreatic alpha cell culture alphaTC6 we transfected with either Klf4 siRNA pool to KD Klf4 or a siScramble control RNAseq on 4 biological replicates were used per treatment group to perform differential gene expression analysis on this RNAseq were conducted using EdgeR with batch correction.