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RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
2016 Bioinformatics  
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]

Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin Thankam T Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
2015 bioRxiv   pre-print
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

Hongwei Wang, Yan Wang, Zhi Xie
2017 Briefings in Bioinformatics  
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

Kamini Singh, Maria Guadalupe Martinez, Jianan Lin, James Gregory, Trang Uyen Nguyen, Rawan Abdelaal, Kristy Kang, Kristen Brennand, Arnold Grünweller, Zhengqing Ouyang, Hemali Phatnani, Margaret Kielian (+1 others)
2022 Viruses  
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

Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
2021 Cells  
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

Musa A. Hassan, Juan J. Vasquez, Chew Guo-Liang, Markus Meissner, T. Nicolai Siegel
2017 BMC Genomics  
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]

Violeta Castelo-Szekely, Mara De Matos, David Gatfield
2018 bioRxiv   pre-print
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  
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

Kamini Singh, Jianan Lin, Yi Zhong, Antonija Burčul, Prathibha Mohan, Man Jiang, Liping Sun, Vladimir Yong-Gonzalez, Agnes Viale, Justin R. Cross, Ronald C. Hendrickson, Gunnar Rätsch (+2 others)
2019 Journal of Experimental Medicine  
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

Amanda W. Ernlund, Robert J. Schneider, Kelly V. Ruggles
2018 BMC Genomics  
, 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]

Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B Scharff
2020 bioRxiv   pre-print
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]

Ethan J Greenblatt, Allan C Spradling
2020 bioRxiv   pre-print
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]

Sohani Das Sharma, Jordan B. Metz, Hongyu Li, Benjamin D. Hobson, Nicholas Hornstein, David Sulzer, Guomei Tang, Peter A. Sims
2018 bioRxiv   pre-print
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

Nicholas Hornstein, Daniela Torres, Sohani Das Sharma, Guomei Tang, Peter Canoll, Peter A. Sims
2016 Genome Biology  
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

Sohani Das Sharma, Jordan B. Metz, Hongyu Li, Benjamin D. Hobson, Nicholas Hornstein, David Sulzer, Guomei Tang, Peter A. Sims
2019 Cell Reports  
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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