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Global analysis of RAR-responsive genes in the Xenopus neurula

ABSTRACT: Retinoid signaling is important for patterning the vertebrate hindbrain and midaxial regions. We recently showed that signaling through retinoic acid receptors (RARs) is essential for anteroposterior patterning along the entire body axis. To further investigate the mechanisms through which RARs act, we employed microarray analysis to investigate the effects of modulating RAR activity on target gene expression. We identified 334 upregulated genes (92% of which were validated) including known RA responsive genes, known genes that have never been proposed as RA targets and many hypothetical and unidentified genes (n = 166). 67 validated downregulated genes were identified including known RA responsive genes and anterior marker genes. The expression patterns of selected upregulated genes (n = 45) were examined at neurula stages using whole mount in situ hybridization. We found that most of these genes were expressed in the neural tube and many were expressed in anterior tissues such as neural crest, brain, eye anlagen, and cement gland. Some were expressed in tissues such as notochord, somites, pronephros and blood islands, where retinoic acid (RA) plays established roles in organogenesis. Members of this set of newly identified RAR target genes are likely to play important roles in neural patterning and organogenesis under the control of RAR signaling pathways and their further characterization will expand our understanding of RA signaling during development. Keywords = retinoid Keywords = microarray Keywords = RAR Keywords = neurula Keywords = anteroposterior patterning Keywords = and organogenesis Keywords: repeat sample

ORGANISM(S): Xenopus laevis

PROVIDER: GSE2295 | GEO | 2005/03/05

SECONDARY ACCESSION(S): PRJNA91671

REPOSITORIES: GEO

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Project description:The development of massively parallel sequencing technologies has revolutionized transcriptome analysis. Sequencing of total cDNA (RNA-Seq) can determine the expression levels of known and novel transcripts with high sensitivity from various developmental stages or conditions. Here we report a robust method for RNA-Seq in Xenopus laevis and apply it to understanding how modulation of retinoic acid signaling alters the transcriptome in early Xenopus laevis development. Three biological conditions were tested: early blastula stage embryos were treated with 1. a retinoic acid receptor (RAR) agonist NRX204647 (4647) at a concentration that stimulated all 3 RAR subtypes (alpha, beta, and gamma); 2. The same agonist at an RAR[gamma] selective dose, and 3. vehicle control. Five single-clutch replicates were obtained for each chemical treatment group, and harvested at neurula stage. We found that single-clutch replicates reflect the stochastic variation of the general outbred population and contribute more statistical power to RNA-Seq experiments due to their feasibility of replication. Our RNA-Seq dataset identified 1590 up-regulated and 685 down-regulated unique genes differentially regulated by all RAR subtypes, and 160 up-regulated and 60 down-regulated genes likely to be regulated specifically by RAR[gamma]. Differential expression detected by RNA-Seq was validated for selected genes by QPCR, which demonstrated nearly 100% quantitative agreement with the deep sequencing data. We further validated RAR-responsive genes by comparison with two previous, published microarray datasets and found substantial agreement. Gene ontology analysis identified RAR targets which may underlie such developmental processes as axial elongation, neurogenesis/synaptogenesis, dorsoventral regulation of the retina, homeotic fate specification, and central nervous system development. We investigated RAR[gamma]-selective targets identified by RNA-Seq and inferred that transcriptional repression by unliganded RARs is of substantial importance to embryonic patterning events. Overall, this paper demonstrates the utility of RNA-Seq in Xenopus laevis, obviating the perceived requirement to use X. tropicalis for genomic analyses.

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Global analysis of RAR-responsive genes in the Xenopus neurula

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