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RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
2016
Bioinformatics
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In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed. ...
Results: We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. ...
(C) Comparison of the distribution of TE ratios of genes that were detected to have a significant change in translation efficiency by RiboDiff (w/ joint dispersion), Z-score based analysis and Babel. ...
doi:10.1093/bioinformatics/btw585
pmid:27634950
pmcid:PMC5198522
fatcat:u2db5p3usndehawqlnftgapzh4
RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints
[article]
2015
bioRxiv
pre-print
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In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed. ...
Results: We present a statistical framework and analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. ...
(C) Comparison of the distribution of TE ratios of genes that were detected to have a significant change in translation efficiency by RiboDiff (w/ joint dispersion), Z-score based analysis and Babel. ...
doi:10.1101/017111
fatcat:jm4dxiegrnasbhbw5lq6pwndge
Computational resources for ribosome profiling: from database to Web server and software
2017
Briefings in Bioinformatics
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This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. ...
Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution. ...
For example, FLOSS exploits the magnitude of disagreement between the overall size distributions of fragments derived from 80 S footprints and non-ribosomal sources; RRS exploits the changes in ribosome ...
doi:10.1093/bib/bbx093
pmid:28968766
fatcat:uq5zk3rkhvhvlkrbtfjevc5uim
Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection
2022
Viruses
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Here, we used simultaneous RNA sequencing and ribosome footprinting to define the transcriptional and translational dynamics of ZIKV and DENV infection in human neuronal progenitor cells (hNPCs). ...
The RNA translation data highlight activation of polyamine metabolism through changes in key enzymes and their regulators. ...
Acknowledgments: The content of this paper is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. ...
doi:10.3390/v14071418
pmid:35891396
pmcid:PMC9316442
fatcat:5tyfod3yyzcbdkyg242cjapwwy
Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
2021
Cells
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This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes. ...
We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/cells10020322
pmid:33557293
pmcid:PMC7914831
fatcat:lyqqtt3wjbd3niruaavauzfzry
Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii
2017
BMC Genomics
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The Roslin Institute receives strategic support from the Biotechnology and Biological Sciences Research Council (BBSRC). ...
TNS was funded by a Young Investigator Program of the Research Center for Infectious Diseases (ZINF) of the University of Würzburg, and The German Research Foundation DFG (grant SI 1610/3-1). ...
The basic concept of ribosome profiling is that actively translated mRNAs are protected from ribonucleases by the decoding ribosomes. ...
doi:10.1186/s12864-017-4362-6
pmid:29228904
pmcid:PMC5725899
fatcat:2creid5c4vdw5pkanphewkqncu
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock
[article]
2018
bioRxiv
pre-print
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The non-canonical initiation factor DENR (Density regulated protein) promotes translation reinitiation on mRNAs harbouring upstream open reading frames (uORFs). ...
We uncovered 240 transcripts with altered translation rate, and used linear regression analysis to extract uORF features predictive of DENR dependence. ...
We thank Angelica Liechti and Georgia Katsioudi who were involved in initial steps of reporter plasmid clonings. ...
doi:10.1101/407551
fatcat:aiwez357ufbd5eqk4d4lrziiza
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock
2019
Nucleic Acids Research
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The non-canonical initiation factor DENR promotes translation reinitiation on mRNAs harbouring upstream open reading frames (uORFs). ...
We uncovered 240 transcripts with altered translation rate, and used linear regression analysis to extract 5' UTR features predictive of DENR dependence. ...
We thank Angelica Liechti and Georgia Katsioudi who were involved in initial steps of reporter plasmid clonings. ...
doi:10.1093/nar/gkz261
pmid:30982898
pmcid:PMC6547434
fatcat:zh5brwttzjbu7oizf4na7t4c2a
c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma
2019
Journal of Experimental Medicine
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We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. ...
Moreover, we observe a striking shift in translation initiation site usage. For example, in low-MYC conditions, lymphoma cells initiate translation of the CD19 mRNA from a site in exon 5. ...
Acknowledgments We thank Anne Quy Hoa Le Thi (Johns Hopkins University School of Medicine, Baltimore, MD) for providing the P493-6 cell line. We thank Renier J. ...
doi:10.1084/jem.20181726
pmid:31142587
pmcid:PMC6605752
fatcat:5puezebdvzbutmdxc3acp6w3ta
RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data
2018
BMC Genomics
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, as well translational efficiency. ...
RIVET can analyze either microarray or RNA sequencing data from polysome profiling and ribosome profiling experiments. ...
Funding This work has been supported by RO1CA178509 and RO1CA207893 from the National Institutes of Health and by BCRF-16-143 from the Breast Cancer Research Foundation. ...
doi:10.1186/s12864-018-5166-z
pmid:30409155
pmcid:PMC6225633
fatcat:vmxdb4sttvhn3jlyg76tmmhbve
Light-dependent translation change of Arabidopsis psbA correlates with RNA structure alterations at the translation initiation region
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
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This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes. ...
We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation ...
G, Change in translation efficiency (ratio footprints/transcript levels) of psbA mRNA in young leaves of 7-week-old plants(Figures 4, S12, and S13). ...
doi:10.1101/2020.06.11.145870
fatcat:ijsostzyebhq3mwgbvl4ypwa2i
Fmr1 translationally activates stress-sensitive mRNAs encoding large proteins in oocytes and neurons
[article]
2020
bioRxiv
pre-print
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Reanalysis of Fmr1 KO mouse cortex ribosome profiling data demonstrates that autism-associated mRNAs encoding large proteins exhibit a concordant reduction in ribosome footprints, consistent with a general ...
Our data thus identify a critical role for Fmr1 in promoting the translation of long, stress-sensitive, autism-associated mRNAs. ...
For translation efficiency analyses, foldchange and padj values were computed using RiboDiff software (Zhong et al. 2017) . Stressgranule enrichment data were obtained from (Khong et al. 2017) . ...
doi:10.1101/2020.06.27.174136
fatcat:u3vymequ5rbi3pmplzahszg66y
Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knock-Out Mice
[article]
2018
bioRxiv
pre-print
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We found a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP, and an increase for terminal oligo-pyrimidine ( ...
To elucidate the impact of Fmr1 loss on translation, we used ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of 24 day-old Fmr1 knock-out mice. ...
RiboDiff: detecting changes of mRNA translation efficiency from ribosome 491 footprints. Bioinformatics 33, 139-141.
492 Ishimura, R., Nagy, G., Dotu, I., Zhou, H., Yang, X. ...
doi:10.1101/319368
fatcat:2el7nj2tn5ga5ie2odklxgl7ou
Ligation-free ribosome profiling of cell type-specific translation in the brain
2016
Genome Biology
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Library construction for ligation-free ribosome profiling can be completed in one day with as little as 1 ng of purified RNA footprints. ...
We apply ligation-free ribosome profiling to mouse brain tissue to identify new patterns of cell type-specific translation and test its ability to identify translational targets of mTOR signaling in the ...
Availability of data and materials The dataset supporting the conclusions of this article is available on the Gene Expression Omnibus under accession GSE78163. ...
doi:10.1186/s13059-016-1005-1
pmid:27380875
pmcid:PMC4934013
fatcat:si24zn3xpff7rgx2uustu65nu4
Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice
2019
Cell Reports
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We find a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP and an increase for terminal oligopyrimidine (TOP ...
To elucidate the impact of Fmr1 loss on translation, we utilize ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of 24-day-old Fmr1 knockout mice. ...
D.S. was supported by R01DA07418 from NIH/NIDA, R01MH108186 from NIH/NIMH, and the JPB Foundation. G.T. was supported by W81XWH-16-1-0263 from DOD and K01MH096956 from NIH/NIMH. ...
doi:10.1016/j.celrep.2019.02.086
pmid:30893603
pmcid:PMC6457272
fatcat:qmq6kymkfzdfhmgbcrmypiuhrq
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