Rhabdomys pumilio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA399358 | ENA |
REPOSITORIES: ENA
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Project description:Circadian clocks are essential for generating and coordinating rhythms in animals’ physiology, behaviour, and metabolism. These activities are regulated by intracellular molecular clocks that operate with a ~24 hour periodicity. The African striped mouse, Rhabdomys pumilio, is notable for undergoing temporal niche switching from ancestrally nocturnal to diurnal, although the molecular components of its’ circadian organization remain unknown. We undertook transcriptome profiling of daily rhythms in the suprachiasmatic nucleus (SCN) and in the liver, lung and retina of Rhabdomys stably housed under a stable 12h:12h light:dark cycle with bright (n=10) or dim (n=10) daytime light intensity. Tissues were collected at two time points: two hours after lights on (Zeitgeber Time (ZT2)) coinciding with high behavioural activity, or two hours after lights off (ZT14) during the animal’s resting/sleep period, and RNA-sequencing performed.
2023-07-31 | E-MTAB-12024 | biostudies-arrayexpress
Project description:Oophaga pumilio Genome sequencing and assembly
| PRJNA550263 | ENA
Project description:Chlamydomonas pumilio var pumilio Cytochromome oxydase 1 (COI)
| PRJEB43352 | ENA
Project description:In this study, we identified the transcriptome-wide direct RNA target sites of the entire family of Pumilio proteins in the budding yeast Saccharomyces cerevisiae by deep sequencing of RNA regions bound by each of six Pumilio proteins. As a family, the Pumilio proteins of yeast interact with over half of the entire transcriptome. Computational analysis of Pumilio target sites reveal striking differences in mRNA stability, gene set categories, and response to nutrient deprivation conditions based on features of Pumilio binding. Some of these features include variations in primary sequence motif and presence of predicted structured RNA hairpins. Puf6p also binds snoRNAs.
2017-05-31 | GSE67064 | GEO
Project description:Purpose: PUMILIO proteins are known to repress target genes by specifically binding to PUMILIO response elements (PREs) in target mRNAs. NORAD is a noncoding RNA that negatively regulates PUMILIO activity. The goal of this study was to determine the gene expression changes that result from knockout of NORAD or overexpression of PUMILIO and to test whether NORAD knockout causes PUMILIO hyperactivity. Methods: RNA-seq libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat Sample Preparation kit (Illumina) and sequenced using the 100 bp paired-end protocol on an Illumina HiSeq 2000. For comparing NORAD+/+ and NORAD-/- HCT116 cells, 3 biological replicates per genotype were sequenced. For PUM overexpression experiments, 3 replicates of GFP-expressing HCT116 cells (negative control) and 2 independent PUM1- or PUM2-overexpressing clones (2 replicates each) were sequenced. Results: Gene expression profiles show that PUMILIO target genes are downregulated in both NORAD knockout cells and PUMILIO overexpressing cells. Conclusions: These data indicate that NORAD sequesters PUMILIO, preventing excessive repression of PUMILIO target genes that are important for maintaining genomic stability.
2015-12-03 | GSE75440 | GEO
Project description:The sequence-specific RNA-binding protein Pumilio controls development of Drosophila; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells. We also used an improved RNA co-immunoprecipitation method to identify Pumilio bound mRNAs in Drosophila embryos. Integration of these datasets with the content of Pumilio binding motifs across the transcriptome revealed novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. Additionally, we identified the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pumilio-mediated repression, and observed concordant regulation of Pumilio:CCR4-NOT target mRNAs. Computational modeling revealed that Pumilio binding site location, number, density, and context are important determinants of regulation. Moreover, the content of optimal synonymous codons exhibits a striking functional relationship to Pumilio and CCR4-NOT regulation, indicating that the inherent translation efficiency and stability of the mRNA modulates their response to these trans-acting regulatory factors. Together, the results of this work provide new insights into the Pumilio regulatory network and mechanisms, and the parameters that influence the efficacy of Pumilio-mediated regulation.
2023-09-03 | GSE241940 | GEO