Comprehensive genome wide analysis of Satb2 function during vertebrate embryogenesis

In this study, we have addressed the involvement of chromatin organizer SATB2 in orchestrating zygotic genome activation and neural crest specification during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Comparative analysis with mouse embryos highlighted conserved molecular mechansisms for Satb2 during neural crest specification. To obtain insights into evolutionary conserved and zebrafish specific functions of Satb2, we performed stage dependent 3' mRNA analysis (80 % epiboly, 6 somite and 14 somites) on Wild type and Satb2 mutants in zebrafish (atleast in duplicates). We also performed stage dependent ChIPseq with anti-zebrafish Satb2 (512 cell, Dome stage, 80 % epiboly, 6 somite and 14 somites) in zebrafish and anti-human antibodies generated in this study (atleast in duplicates) in mouse embryos (E9.5 head, E9.5 trunk and E13.5 dorsal telencephalon) respectively. To get insights into chromatin modification status and accessibility upon loss or gain of function of Satb2, we performed ChIPseq for histone modifications (Dome stage) and ATAC-seq (Dome and 14 somites stage). Tg: SOX10:egfp line were utilized to isolate neural crest population and perform Satb2 ChIPseq (14 somites) to obtain neural crest specific occupancy of Satb2. scRNAseq analysis were utilized to understand cell autonomous regulation of Satb2 during ZGA (Dome stage) and neural crest specific function of Satb2 during organogenesis (14 somites).