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Longitudinal gene expression profiling in Nodal-induced and control zebrafish embryonic explants

ABSTRACT: We report RNA-sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 (N), constitutively active Nodal receptor CA-acvr1b* (T), and uninjected (U) controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere (SR), 30% epiboly (30), 50% epiboly (50), shield (SH), 75% epiboly (75), 90% epiboly (90), and 2-somite (2S) (corresponding to 4, 4.7, 5.3, 6, 8, 9, and 11 hours post fertilization, respectively).

ORGANISM(S): Danio rerio

PROVIDER: GSE246158 | GEO | 2024/12/16

REPOSITORIES: GEO

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Project description:The B1 SOX transcription factors SOX1/2/3/19 have been implicated in various processes of early embryogenesis. However, their regulatory functions in stages from the blastula to early neurula remain largely unknown, primarily because loss-of-function studies have not been informative to date. In our present study, we systematically knocked down the B1 sox genes in zebrafish. Only the quadruple knockdown of the four B1 sox genes sox2/3/19a/19b, which are active in the early embryo, resulted in very severe developmental abnormalities, confirming that the B1 sox genes are functionally redundant. We characterized the sox2/3/19a/19b quadruple knockdown embryos in detail by examining the changes in gene expression through microarray analysis as well as in situ hybridization. Importantly, these phenotypic analyses of the quadruple knockdown embryos reveled that the B1 SOX proteins regulate the following distinct processes: (1) early dorsoventral patterning by controlling bmp2b/7; (2) gastrulation movements via the regulation of pcdh18a/18b and non-canonical wnt genes; (3) neural differentiation by regulating the Hes-class bHLH gene her3 and the proneural-class bHLH genes neurog1 (positively) and ascl1a (negatively), and regional transcription factor genes, e.g. hesx1, zic1 and rx3; and (4) neural patterning by regulating signaling pathway genes, cyp26a1 in RA signaling, oep in Nodal signaling, shh, and mdkb. These findings indicate that the B1 SOX proteins control a wide range of developmental regulators in the early embryo and suggest that the B1 sox functions are central to coordinating cell fate specification with patterning and morphogenetic processes occurring in the early embryo. Microarray analysis was carried out to compare gene expression profiles at the 30% epiboly (30%E), 75% epiboly (75%E) and tailbud (TB) stages between wild-type embryos and the sox2/3/19a/19b quadruple knockdown embryos. RNAs from two independent samples were analyzed for each embryonic stage.

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Longitudinal gene expression profiling in Nodal-induced and control zebrafish embryonic explants

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