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RNA-seq profiling of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish hair cell IP vs. whole fish IN

ABSTRACT: We have developed and tested the efficiency of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells (IP) compared to the whole fish transcriptome (IN). We show through RNA-seq that HA-tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts.

ORGANISM(S): Danio rerio

PROVIDER: GSE102861 | GEO | 2018/04/24

REPOSITORIES: GEO

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Pervasive changes of mRNA splicing in upf1 deficient zebrafish identify rpl10a as a regulator of T cell development

Project description:The transcriptome of eukaryotic cells is constantly monitored for errors to avoid the production of undesired protein variants. The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway degrades aberrant mRNAs, but also functions in the regulation of transcript abundance in response to changed physiological states. As a result of its essential functions, only few animal models of impaired NMD activity have been developed. Here, we describe a zebrafish mutant of upf1, encoding the central component of the NMD machinery. Fish homozygous for the upf1t20450 allele (Y163X) survive until day 10 after fertilization, presenting with impaired T cell development as one of the most conspicuous features of the mutant phenotype. Analysis of differentially expressed genes identified dysregulation of the pre-mRNA splicing pathway, accompanied by perturbed auto-regulation of canonical splicing activators (SRSF) and repressors (HNRNP). In upf1-deficient mutants, NMD-susceptible transcripts of ribosomal proteins that are known for their role as non-canonical splicing regulators were greatly increased, most notably, rpl10a. When the levels of NMD-susceptible rpl10a transcripts were artifically increased in zebrafish morphants, T cell development was significantly impaired, suggesting that perturbed autoregulation of rpl10a splicing contributes to failing T cell development in upf1 deficiency. Our results identify an extra-ribosomal tissue-specific function to rpl10a in the immune system, and thus exemplify the advantages of the zebrafish model to study the effects of upf1-deficiency in the context of a vertebrate organism.

2020-07-13 | GSE136669 | GEO

Danio rerio

Project description:RNA-seq profiling of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish hair cell IP vs. whole fish IN

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A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production

Project description:Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.

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Whole-genome hypothalamic transcriptome data collected from wild-type and ob/ob Pdyn-eGFP-RPL10a mice using BAC TRAP procedure

Project description:Prodynorphine-expressing neurons were targeted by eGFP-RPL10a, a transgene that is expressed under the control of the Pdyn promoter in a BAC containing the Pdyn backbone. Trangenic mice were made with FvB embryos via pro-nuclear injection. Transgene-positive progenies were bred to C57BL/6J for more than five generations before being used in the current experiment. Triplicates of 6-8 hypothalami were collected per sample from wild-type and ob/ob adult mice. Polysomal IP RNA and total Input RNA were purified from each sample. Affymetrix GeneChip Mouse 430 2.0 arrays (900495) were used to identify transcripts that are specifically expressed in Pdyn neurons with a fold change (IP vs. Input) of >=2 in wild-type mice. The same microarrays were also used to identify Pdyn-specific transcripts that are differentially regulated transcriptionally by leptin deficiency with a fold change (ob IP vs. wt IP) of >=1.5.

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Pervasive changes of mRNA splicing in upf1 deficient zebrafish identify rpl10a as a regulator of T cell development

Project description:Pervasive changes of mRNA splicing in upf1 deficient zebrafish identify rpl10a as a regulator of T cell development

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Transcriptional profiling of cells in the dorsal striatum and accumbens nucleus of older Drd1-TRAP (CP73) mice: immunopurified (IP) data

Project description:Using translational profiling we obtained RNA-Seq data from total RNA present in the dorsal striatum and accumbens nucleus of older Drd1-EGFP/Rpl10a (CP73) mice

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Whole-genome hypothalamic transcriptome data collected from wild-type and ob/ob Pdyn-eGFP-RPL10a mice using BAC TRAP procedure

2014-12-25 | GSE61436 | GEO

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Transcriptomic profiling of Tg(fabp10a:hUHRF1-EGFP)high zebrafish livers and control siblings at 5 dpf

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Ethanol induced transcriptional and translational changes in Aldh1l1-EGFP/Rpl10a cortical astrocyte cultures

Project description:The role astrocytes play in brain development and function has come under increased focus as the diversity of roles they are involved in has become apparent. We have previously shown ethanol exposed astrocytes alter neuronal neurite outgrowth in an in vitro co-culture system and that ethanol alters the astrocyte produced extracellular matrix (ECM) in vitro, with similar alterations in vivo. Here we utilize the translating ribosome affinity purification (TRAP) procedure in Aldh1l1-EGFP/Rpl10a transgenic mouse primary cortical astrocyte cultures to transcriptionally and translationally profile the astrocyte response to ethanol. We found large differences in the total RNA pool in comparison to the translating RNA pool while the ethanol response within each pool showed a large degree of overlap. Comparisons to published datasets indicate the in vitro model used here are most similar to PD1-PD7 in vivo cortical astrocytes and the ethanol regulated genes showed significant overlap with models of chronic ethanol exposure in astrocytes and a model of third-trimester ethanol exposure in the hippocampus and cerebellum. These findings will further our understanding of the effects of ethanol on astrocyte gene expression and protein translation and how these changes alter brain development.

2023-06-21 | GSE227891 | GEO

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