Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Ribosomal biogenesis genes play an essential and p53-independent role in pancreas development

ABSTRACT: Analysis of transcriptional profiles in Sbds(ATG) MO-injected embryos with and without coinjection of p53(ATG) MO. We identified a large number of changes in transcript abundance associated with loss of Sbds. Among the 24,278 annotated zebrafish genes in the platform, 4,892 significantly differentially expressed genes were identified. Embryos were carefully staged at 24 hpf and RNA was extracted from approximately 50 embryos per condition in Trizol, followed by purification using RNA miniprep columns (Qiagen). Four independent experiments were extracted. cDNA microarrays were performed at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Microarray Core Facility using 4x44K Zebrafish gene expression microarray slides (Agilent, Santa Clara, CA).

ORGANISM(S): Danio rerio

SUBMITTER: Steven Leach

PROVIDER: E-GEOD-39399 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The basic helix-loop-helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes, including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets, in particular fast twitch muscle differentiation genes, thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast-twitch muscle-specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber-type regulator, Prdm1a, a SET-domain DNA-binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype, early and increased fast muscle differentiation, is the opposite of the Pbx-null phenotype, delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes, we used RNA-seq analysis to globally assess gene expression in zebrafish embryos with single- and double-losses-of-function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4-MO;prdm1a-/- embryos, suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However, other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus, our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program. Total RNA samples were genotyped and pooled for 4 sample types: control-MO;prdm1+/+; control-MO;prdm1-/-; pbx2/4-MO;prdm1+/+; and pbx2/4-MO;prdm1-/- embryos at the 10 somite (s) stage from three independent sets of egg collections/injections.

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Ribosomal biogenesis genes play an essential and p53-independent role in pancreas development

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