NKX2.2 and KLF4 cooperate to regulate α cell identity [aTC_klf4_KD_nkx2.2_ChIPseq]

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 α cells by directly activating α cell genes and repressing alternate islet cell fate genes. When compared to the known role of NKX2.2 in islet β cells, we demonstrate that NKX2.2 regulates novel α cell target genes, facilitated in part by α cell specific DNA binding at gene promoters. Furthermore, we have identified the reprogramming factor KLF4 as having enriched expression in α cells, where it co-occupies NKX2.2-bound α cell promoters and is necessary for NKX2.2 binding in α cells to co-regulate many NKX2.2 α cell transcriptional targets. Misexpression of Klf4 in β cells is sufficient to manipulate chromatin accessibility, increase binding of NKX2.2 at α cell specific promoters sites, and alter expression of NKX2.2-regulated cell specific targets. This study identifies KLF4 is a novel α cell identity factor that cooperates with NKX2.2 to regulate α cell identity. To charcterize the changes in genomic occupancy of NKX2.2 when Klf4 expression is knocked down in alphaTC alpha cells Chromatin immunoprecipication was performed on alphaTC6 alpha cell culture using an anti-NKX2.2 antibody that was transfected with either a Klf4 siRNA knockdown or siScramble control ChIP-seq was done on 3-4 biological replicates in both the klf4 knockdown and scramble control of the NKX2.2 ChIP and input samples. Csaw was used to perform the differential binding analysis.