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Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

Alaaddin Bulak Arpat, Angélica Liechti, Mara De Matos, René Dreos, Peggy Janich, David Gatfield
2020 Genome Research  
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]

Alaaddin Bulak Arpat, Luz Angelica Liechti, Mara De Matos, Rene Dreos, Peggy Janich, David Gatfield
2019 biorxiv/medrxiv   pre-print
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

Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Ji Hun Kim, Gahyeon Kim, Hyeseong Kim, Neung-Ho Ahn, Byoung-Hee Lee, Bernhard O. Palsson, Byung-Kwan Cho
2022 Frontiers in Bioengineering and Biotechnology  
, 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

Emad Bahrami-Samani, Dat T. Vo, Patricia Rosa de Araujo, Christine Vogel, Andrew D. Smith, Luiz O. F. Penalva, Philip J. Uren
2014 Wiley Interdisciplinary Reviews - RNA  
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

Yuanhui Mao, Leiming Dong, Xiao-Min Liu, Jiayin Guo, Honghui Ma, Bin Shen, Shu-Bing Qian
2019 Nature Communications  
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

Michael Y Pavlov, Gustaf Ullman, Zoya Ignatova, Måns Ehrenberg
2021 Nucleic Acids Research  
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]

Henry Miller, Daniel Montemayor, Jebriel Abdul, Simon Levy, Stella R Hartono, Anna Vines, Kumar Sharma, Bess Frost, Frederic Chedin, Alexander JR Bishop
2021 bioRxiv   pre-print
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

Xinlei Lian, Jiahui Guo, Wei Gu, Yizhi Cui, Jiayong Zhong, Jingjie Jin, Qing-Yu He, Tong Wang, Gong Zhang, Ronald B Gartenhaus
2016 PLoS Genetics  
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

Yinuo J. Wang, Pavanapuresan P. Vaidyanathan, Maria F. Rojas-Duran, Namrata D. Udeshi, Kristen M. Bartoli, Steven A. Carr, Wendy V. Gilbert, Jeff Coller
2018 PLoS Biology  
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

Nir Fluman, Sivan Navon, Eitan Bibi, Yitzhak Pilpel
2014 eLife  
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]

Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng
2016 bioRxiv   pre-print
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

Tao Liu, Mikhail E. Belov, Navdeep Jaitly, Wei-Jun Qian, Richard D. Smith
2007 Chemical Reviews  
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]

Shilpa Rao, Ian Hoskins, Daniela Garcia, Tori Tonn, Hakan Ozadam, Elif Sarinay Cenik, Can Cenik
2020 biorxiv/medrxiv  
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

Nahuel A. Paolini, Kat S. Moore, Franca M. di Summa, Ivo F. A. C. Fokkema, Peter A. C. 't Hoen, Marieke von Lindern, Eric Jan
2018 PLoS ONE  
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

Ahmed Ahmed, Christian J. Michel
2011 Journal of computer science and systems biology  
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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