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Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
2020
Genome Research
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A distinct class of pause sites is indicative of deterministic pausing signals. ...
Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. ...
A-site of the paused, leading ribosome. ...
doi:10.1101/gr.257741.119
pmid:32703885
pmcid:PMC7397865
fatcat:tnrfcdkfqbcrvfzp72orq4ca7m
Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
[article]
2019
biorxiv/medrxiv
pre-print
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Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. ...
A distinct class of pause sites, independent of translation rate, is indicative of deterministic pausing signals. ...
D.G. acknowledges funding by the Swiss National Science Foundation through the National Centre of Competence in Research (NCCR) RNA and Disease (141735) ...
doi:10.1101/710061
fatcat:e525gul745dsxg6unw5pjd7x6y
System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
2022
Frontiers in Bioengineering and Biotechnology
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, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5′-UTR length, RNA structures at ribosome-bound sites ...
Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative ...
The ribosome pausing score for each A site codon was the sum of the pausing scores at the −1, 0, and +1 positions of the P site codon. ...
doi:10.3389/fbioe.2022.844200
pmid:35284422
pmcid:PMC8914203
fatcat:ybd5kvgg7vbknet4h5d7wyyenu
Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput
2014
Wiley Interdisciplinary Reviews - RNA
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High-throughput profiling of the constituent events and processes is achieved through a range of technologies that continue to expand and evolve. ...
Fully leveraging the resulting data is nontrivial, and requires the use of computational methods and tools carefully crafted for specific data sources and often intended to probe particular biological ...
Yao Z, Weinberg Z, Ruzzo WL. CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics 2006, 22:445-452. 73. Mathews DH, Turner DH. ...
doi:10.1002/wrna.1274
pmid:25515586
pmcid:PMC4397117
fatcat:2vuanntmg5duzizzmga5dwq4fa
m6A in mRNA coding regions promotes translation via the RNA helicase-containing YTHDC2
2019
Nature Communications
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Here, we found that CDS m6A leads to ribosome pausing in a codon-specific manner. Unexpectedly, removing CDS m6A from these transcripts results in a further decrease of translation. ...
A systemic analysis of RNA structural datasets revealed that CDS m6A positively regulates translation by resolving mRNA secondary structures. ...
This work was supported in part by US National Institutes of Health (R21CA227917, R01GM1222814) and HHMI Faculty Scholar (55108556) to S.-B.Q. ...
doi:10.1038/s41467-019-13317-9
pmid:31767846
pmcid:PMC6877647
fatcat:wmfheer3dfhiziiftcsn5d2use
Estimation of peptide elongation times from ribosome profiling spectra
2021
Nucleic Acids Research
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Using maximum likelihood statistics and data set from Escherichia coli we develop a robust method for neutralizing technical biases (e.g. base specific RNase preferences in ribosome-protected mRNA fragments ...
Our approach provides a solution to the long-standing problem of extracting reliable information about peptide elongation times from highly noisy and technically biased ribosome profiling spectra. ...
ACKNOWLEDGEMENTS We thank Irem Avcilar, Christian del Campo, and Anneli Borg for ribosome profiling libraries and growth curves, and Alexander Bartholomäus and Baban Kolte for helping with the mapping ...
doi:10.1093/nar/gkab260
pmid:33885812
pmcid:PMC8136808
fatcat:znkk76ldrjfjzhokiize3fk4oi
Quality-controlled R-loop meta-analysis reveals the characteristics of R-Loop consensus regions
[article]
2021
bioRxiv
pre-print
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We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called "R-loop regions" (RL regions). ...
In this study, we reprocessed 693 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. ...
ACKNOWLEDGEMENT We want to thank all those who contributed to the development of the software used during this study, particularly the contributors to "RLSuite." ...
doi:10.1101/2021.11.01.466823
fatcat:y7m4cj4m3rdlhomb6svd7kvtau
Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells
2016
PLoS Genetics
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Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the ...
In the process of translation, ribosomes first assemble on mRNAs (translation initiation) and then translate along the mRNA (elongation) to synthesize proteins. ...
We calculated the mRNA fold energy per base for low-EVI and high-TR genes, respectively, using the MFOLD algorithm [46] . ...
doi:10.1371/journal.pgen.1005901
pmid:26926465
pmcid:PMC4771717
fatcat:xixkqkddvrbcvfjt7dqmyetwcy
Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast
2018
PLoS Biology
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Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog coiled-coil domain containing 124 (CCDC124) recovered 25S ribosomal RNA in a region near the A site that overlaps the GTPase ...
Using quantitative mass spectrometry, we identified late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. ...
Acknowledgments We thank members of the Gilbert lab, Rachel Green, Laura Nevin, Colin Wu, Boris Zinshteyn, and members of the Gene-Wei Li lab for helpful discussions; Mary K. Thompson ...
doi:10.1371/journal.pbio.2005903
pmid:30208026
pmcid:PMC6135351
fatcat:clhtzxpz2neurb6hhzllzwonzy
mRNA-programmed translation pauses in the targeting of E. coli membrane proteins
2014
eLife
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The underlying mechanism is likely programmed into the coding sequence, where Shine–Dalgarno-like elements trigger elongation pauses at strategic positions during the early stages of translation. ...
In all living organisms, ribosomes translating membrane proteins are targeted to membrane translocons early in translation, by the ubiquitous signal recognition particle (SRP) system. ...
We thank the Pilpel lab and Maya Schuldiner for useful discussions. NF acknowledges the Clore Foundation for scholarship support. ...
doi:10.7554/elife.03440
pmid:25135940
pmcid:PMC4359368
fatcat:vgecfdr47zbrfjtry2lhoccfcu
ROSE: a deep learning based framework for predicting ribosome stalling
[article]
2016
bioRxiv
pre-print
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We present a deep learning based framework, called ROSE, to accurately predict ribosome stalling events in translation elongation from coding sequences based on high-throughput ribosome profiling data. ...
ROSE provides an effective index to estimate the likelihood of translational pausing at codon resolution and understand diverse putative regulatory factors of ribosome stalling. ...
During translation, the additional methyl group of an m 6 A site may act as a stumbling block to ribosomes and thus result in a translational pause. ...
doi:10.1101/067108
fatcat:a2rjx5sem5hppfoe3x337gscfu
Accurate Mass Measurements in Proteomics
2007
Chemical Reviews
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Our laboratories are located in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the DOE and located at PNNL, which is operated by Battelle Memorial Institute ...
Center for Research Resources (RR018522) for support of portions of the reviewed research. ...
To deisotope each peak, THRASH identifies its charge state by using a charge detection algorithm. ...
doi:10.1021/cr068288j
pmid:17649984
pmcid:PMC2713049
fatcat:c7t7zjqfvrcstmli2wvxa56eje
Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein
[article]
2020
biorxiv/medrxiv
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Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing NSP1. ...
Importantly, we also uncover potential mechanisms of preferential translation through the presence of shared sites for specific RNA binding proteins and a remarkable enrichment for 5′ terminal oligo-pyrimidine ...
Nucleotide Resolution Analyses of Ribosome Occupancy and Pause Site Detection For all nucleotide resolution and pause site detection analyses, we used the ribosome footprints mapping to the CDS (28 to ...
doi:10.1101/2020.09.13.295493
pmid:32995776
pmcid:PMC7523102
fatcat:hncwlgtc4jg4bkihixp65gvx3u
Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors
2018
PLoS ONE
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Ribosome profiling combined with RNA sequencing was used to determine translation initiation sites and ribosome density on individual transcripts. ...
Lack of iron, a critical component of heme and hemoglobin, activates Heme Regulated Inhibitor (HRI). ...
Author Contributions Conceptualization: Nahuel A. Paolini, Peter A. C. 't Hoen, Marieke von Lindern. ...
doi:10.1371/journal.pone.0193790
pmid:29634759
pmcid:PMC5892948
fatcat:eda3riofwbcyfeedd6rhiufrk4
Circular Code Signal in Frameshift Genes
2011
Journal of computer science and systems biology
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After the frameshift site, the majority of local peaks (y = 21, n = 34, y/n = 62%, α = 0.018% with Formula 4) are in frame 1 (squares). ...
Before the frameshift site, the majority of local peaks (y = 18, n = 34, y/n = 53%, α = 0.565% with Formula 4) are in frame 0 (rhombuses). ...
the normal distribution Z(F ) to the binomial distribution Y(F ) can be used as follows Table 3 . ( ) ( ) ( ) ( ) ( ) ( ) Y E Y Z V Y - = F F F F and ( ) In order to automate the reading frame identification ...
doi:10.4172/jcsb.1000069
fatcat:5pik3ws2ezeu3iwdppebprigzm
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