Epigenetic regulation of cilia stability and kidney development by the chromatin remodeling SWI/SNF complexes [ATAC-seq]

Cilia are important subcellular organelles and are regulated by transcription factors including Foxj1 and Rfx proteins. Whether and how are cilia regulated at epigenetic level remains unknown. We addressed this question by knocking down or knocking out of chromatin remodeling genes. Interestingly, depletion of multiple components of the switch/sucrose non-fermentable (SWI/SNF) complexes lead to ciliopathy-like phenotypes in zebrafish embryos. Specifically, depletion of Actl6a, one of the components of the SWI/SNF complexes lead cilia disassembly and cystic kidney, but do not affect cilia motility. Omics studies show that in Actl6a-depleted embryos, a set of cilia genes including Foxj1a and Rfx2, the master regulators of cilia assembly, were downregulated at transcriptional level, chromatin accessibility and the SWI/SNF complexes binding. Thus, our study reveals that the SWI/SNF complexes regulate cilia stability and kidney development by direct modulating the expression Foxj1a and Rfx2. Overall design: In order to investigate which chromatin regions were affected by actl6a deficiency in protonephros of zebrafish, and ultimately determine which genes may have been affected in transcriptional regulation, we used morpholino microinjection to knock down actl6a in one-cell stage embryos (Tg (atp1a1a.4:EGFP), the transgenic line has GFP fluorescence in the pronephros). The 30hpf treated embryos were cleaved and the tissue of pronephric duct was isolated for ATAC-seq. Then, we collected 10000 to 20000 pronephric duct cells from ctrl and morphant, respectively, and constructed a library. Perform chromatin accessibility analysis on the data obtained from ATAC seq. Comparative chromatin accessibility analysis of ATAC-seq data for pronephric duct of 30 hpf ctrl and morphant.