GSE119623
RNA-seq of zebrafish embryo dorsal forerunner cells lacking Vestigial like 4 like (Vgll4l) or Yes associated protein 1 (Yap1)/ WW domain containing transcription regulator 1 (Wwtr1/Taz) activities
Purpose: The goals of this study are to compare control Dorsal Forerunner Cells (DFCs)  transcriptome (RNA-seq) to the one of embryos depleted for either Vgll4l or Yap/Taz (Yap1 and Wwtr1) and to evaluate the transcriptional contribution of these transcription cofactors to the formation of the zebrafish left right organizer Methods: Knockdown (KD) of Vgll4l and Yap/Taz were performed by injection of morpholinos in Tg(sox17:GFP) embryos at the one cell stage. Single DFCs cluster were dissected out at 90% epiboly. Extraction of Total RNA and cDNA libraries construction were done using SMART-Seq®  v4 Ultra® Low Input RNA Kit for Sequencing from clontech and NEB DNA Ultra library construction kit. Whole genome sequencing was done on illumina Hiseq 2000 sequencer. Results/Conclusions: Vgll4l and Yap/ Taz play and essential role in the formation of  the left right organizer. They regulate a large number of genes important for differentiation of the organ. They are required for proper expression of major transciprition factors involved in Kupffer vesicle formation as well as for genes involved in ciliogenesis. Both Vgll4l and Yap/Taz  act upstream of major pathways known to regulate the formation of the left right organizer.  Additionally, Vgll4l is required for the spatio-temporal expression of writters and readers of DNA methylation marks (DNA methylation enzymes and methyl CpG binding proteins) during Kupffer's vesicle differentiation Overall design: Trancriptome of single cluser of control Dorsal Forerunner Cells were compared to the ones of Dorsal Forerunner cells depleted for either Vgll4l or Yap/Taz. Quadrupicates were analyzed for each experimental condtion.