MRNA-seq
Ontology highlight
ABSTRACT:
TISSUE(S): ['pancreatic Cancer']
SUBMITTER: Yizhi Cao
PROVIDER: OEX00024272 | NODE | 2023-07-09
REPOSITORIES: NODE
Similar Datasets
Project description:mRNAs are generally assumed to be loaded instantly with ribosomes upon entry into the cytoplasm. To measure ribosome density on nascent mRNA, we developed nascent Ribo-Seq (nRibo-Seq) by combining Ribo-Seq with progressive 4-thiouridine labelling. In mouse macrophages, we experimentally determined, for the first time, the lag between the appearance of nascent RNA and its association with ribosomes, which was calculated to be 20 - 22 min for bulk mRNA, and approximated the time it takes for mRNAs to be fully loaded with ribosomes to be 41 - 44 min. Notably, ribosomal loading time is adapted to gene function as rapid loading was observed with highly regulated genes. The lag and ribosomal loading time correlate positively with ORF size and mRNA half-life, and negatively with tRNA adaptation index. Similar results were obtained in mouse embryonic stem cells, where the lag in ribosome loading was even more pronounced with 35 - 38 min. We validated our measurements after stimulation of macrophages with lipopolysaccharide, where the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments. Uncoupling is stronger for mRNAs with long ORFs or half-lives, a finding we also confirmed at the level of protein production by nascent chain proteomics. As a consequence of the lag in ribosome loading, ribosome density measurements are distorted when performed under conditions where mRNA levels are far from steady state expression, and transcriptional changes affect ribosome density in a passive way. This study uncovers an unexpected and considerable lag in ribosome loading, and provides guidelines for the interpretation of Ribo-Seq data taking passive effects on ribosome density into account.
2021-06-22 | PXD026828 | Pride
Project description:mRNA-seq of SW837 USP22 knockdown cells
2025-01-16 | E-MTAB-8215 | ExpressionAtlas
Project description:mRNA-seq of MCF10A USP22 knockdown cells
2025-01-16 | E-MTAB-8247 | ExpressionAtlas
Project description:mRNA-seq of SW480 USP22 knockdown cells
2025-01-16 | E-MTAB-8214 | ExpressionAtlas
Project description:mRNA-seq of HCT116 USP22 knockdown cells
2025-01-23 | E-MTAB-7393 | ExpressionAtlas
Project description:mRNA-seq for HCT116 Parental and ARID1A knockdown cells, mRNA-seq for DLD1 Parental, ARID1A knockdown and ARID1A knockout cells, mRNA-seq for COLO320DM Parental and ARID1A knockdown and ARID1A knockout cells
2025-01-23 | E-MTAB-7791 | ExpressionAtlas
Project description:mRNA-Seq of head tissue from Drosophila melanogaster
2020-04-28 | E-GEOD-20348 | ExpressionAtlas
Project description:modENCODE: mRNA-seq of whole flies from Drosophila melanogaster
2020-01-13 | E-CURD-15 | ExpressionAtlas
Project description:Grad-seq in Enterococcus faecalis V583 and Enterococcus faecium AUS004.
2022-11-28 | PXD031577 | Pride