Project description:Pumilio proteins are RNA-binding proteins that control mRNA translation and stability by binding to the 3' UTR of target mRNAs. Mammals have two canonical Pumilio proteins, PUM1 and PUM2, which are known to act in many biological processes, including embryonic development, neurogenesis, cell cycle regulation and genomic stability. Here, we characterized a new role of both PUM1 and PUM2 in regulating cell morphology, migration, and adhesion in T-REx-293 cells, in addition to previously known defects in growth rate. Gene ontology analysis of differentially expressed genes in PUM double knockout (PDKO) cells for both cellular component and biological process showed enrichment in categories related to adhesion and migration. PDKO cells had a collective cell migration rate significantly lower than that of WT cells and displayed changes in actin morphology. In addition, during growth, PDKO cells aggregated into clusters (clumps) due to an inability to escape cell-cell contacts. Addition of extracellular matrix (Matrigel) alleviated the clumping phenotype. Collagen IV (ColIV), a major component of Matrigel, was shown to be the driving force in allowing PDKO cells to monolayer appropriately, however, ColIV protein levels remained unperturbed in PDKO cells. This study characterizes a novel cellular phenotype associated with cellular morphology, migration, and adhesion which can aid in developing better models for PUM function in both developmental processes and disease.

2023-01-01 | GSE207836 | GEO

Post-Transcriptional Regulation of Mouse Neurogenesis by Pumilio Proteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-08-15 | GSE95197 | GEO

Transcriptome-wide identification and target analysis of the Pumilio family of RNA binding proteins

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

Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase

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

Mus musculus

Project description:Post-Transcriptional Regulation of Mouse Neurogenesis by Pumilio Proteins [RNA-Seq]

| PRJNA376283 | ENA

Mus musculus

Project description:Post-Transcriptional Regulation of Mouse Neurogenesis by Pumilio Proteins [RIP-Seq]

| PRJNA376400 | ENA