ArticleRNA (New York, N.Y.)2018
PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data.
Article in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- 2'-O-Methylation maintains ribosome structural and translation integrity.Molecular cell · 2026Article
- Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis.bioRxiv : the preprint server for biology · 2026Article
- Integrative bioinformatics analysis identifies METTL1 as a regulator of immune infiltration and prognosis in breast cancer.Scientific reports · 2025Article
- mCell · 2025Article
- An ISR-independent role of GCN2 prevents excessive ribosome biogenesis and mRNA translation.Life science alliance · 2025Article
- EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences.Nature communications · 2024Article
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- Dissecting infectious bronchitis virus-induced host shutoff at the translation level.Journal of virology · 2024Article
- Ribosome Pausing Negatively Regulates Protein Translation in Maize Seedlings during Dark-to-Light Transitions.International journal of molecular sciences · 2024Article
- Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease.Nature cell biology · 2024Article
- RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update.Journal of molecular biology · 2023Article
- The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome.Nucleic acids research · 2023Article
- Comparative oxidation proteomics analyses suggest redox regulation of cytosolic translation in rice leaves upon Magnaporthe oryzae infection.Plant communications · 2023Article
- Velcrin-induced selective cleavage of tRNANature chemical biology · 2023Article
- Histone deacetylases control lysine acetylation of ribosomal proteins in rice.Nucleic acids research · 2021Article
- Mutant Huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease.Nature communications · 2021Article
- RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data.BMC bioinformatics · 2020Article
- Cyclic GMP-AMP synthase promotes the inflammatory and autophagy responses in Huntington disease.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Nucleic acids research · 2020Article
- XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.PLoS computational biology · 2020Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The process of translation is characterized by irregularities in the local decoding rates of specific mRNA codons. This includes the occurrences of long pauses that can take place when ribosomes decode certain peptide sequences, encounter strong RNA secondary structures, or decode "hungry" codons. Examples are known where such pausing or stalling is used for regulating protein synthesis. This can be achieved at the level of translation via direct alteration of ribosome progression through mRNA or by altering mRNA stability via NoGo decay. Ribosome pausing has also been implicated in the cotranslational folding of proteins. Ribosome profiling data often are used for inferring the locations of ribosome pauses. However, no dedicated online software is available for this purpose. Here we present PausePred (https://pausepred.ucc.ie/), which can be used to infer ribosome pauses from ribosome profiling (Ribo-seq) data. Peaks of ribosome footprint density are scored based on their magnitude relative to the background density within the surrounding area. The scoring allows the comparison of peaks across the transcriptome or genome. In addition to the score, PausePred reports the coordinates of the pause, the footprint density at the pause site, and the surrounding nucleotide sequence. The pauses can be visualized in the context of Ribo-seq and RNA-seq density plots generated for specific transcripts or genomic regions with the Rfeet tool. PausePred does not require input on the location of protein coding ORFs (although gene annotations can be optionally supplied). As a result, it can be used universally and its output does not depend on ever evolving annotations.
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