Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula

Abstract

RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the Xenopus laevis complete genome now available provides a powerful tool for unravelling cell-cell signaling pathways during embryonic induction.

Xenopus laevis FGF16 activates the expression of genes coding for the transcription factors Sp5 and Sp5l

“…The presence and activity of this class of FGF ligand in a distant chordate relative supports the notion that FG9/16/20 is a conserved factor for mesoderm specification (Davidson et al, 2006). Furthermore, an RNA-seq screen of X. laevis gastrula expression in dorsal and ventral lip tissue identified FGF16.S and FGF16.L as having moderate positive Pearson correlation coefficients of 0.48 and 0.25 respectively to chordin, indicating the two genes may share transcriptional regulation mechanisms and that FGF16 may be involved in dorsal-ventral patterning (Ding et al, 2017).…”

Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis

“…There were also 124 genes that were decreased by β-CatMO but not dorsally enriched, of which 34 bound β-catenin in ChIP experiments (Dataset S3) (4). The early dorsal signature includes many secreted factors and transcription factors known to be expressed in Spemann's organizer (2,24), as well as many previously undescribed dorsal genes. As shown in Fig.…”

“…2000 using standard methods to generate 100-bp single-end reads at the Broad Stem Cell Research Center at the University of California, Los Angeles (UCLA). RNA sequencing data were processed as described previously (2,53,54). All RNA-seq data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database (accession No.…”

“…ith the recent completion of the Xenopus laevis genome (1), it has now become practical to study global transcriptional changes at the earliest stages of development in this classical model organism: for example, by analyzing the transcriptomes of the dorsal and ventral regions of the gastrula embryo (2). Recent studies analyzed the zygotic Wnt pathway in X. laevis and Xenopus tropicalis embryos, defining late gene signatures transcriptionally activated by endogenous Wnt8 expressed in the ventro-lateral marginal zone (3,4).…”

Preparation of single-cell suspension from mouse breast cancer focusing on preservation of original cell state information and cell type composition

“…These genes usually consist of the stress induced or immediate early genes (IEGs). Interestingly, this set of genes is conserved in higher eukaryotes and has been observed after injury in mouse (Grose et al, 2002), fish (Ishida et al, 2010) and also during embryonic wound healing at the gastrula and tailbud stages in Xenopus embryos (Ding et al, 2017;Abaffy et al, in press). Usually the peak expression of these genes appears between 30 and 60 minutes after treatment/injury.…”