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- Pavlov, MichaelUppsala universitet,Institutionen för cell- och molekylärbiologi (author)
Estimation of peptide elongation times from ribosome profiling spectra
- Article/chapterEnglish2021
Publisher, publication year, extent ...
- 2021-04-22
- Oxford University Press,2021
- electronicrdacarrier
Numbers
- LIBRIS-ID:oai:DiVA.org:uu-447936
- https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447936URI
- https://doi.org/10.1093/nar/gkab260DOI
Supplementary language notes
- Language:English
- Summary in:English
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- SwePubSwePub
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Notes
- Ribosome profiling spectra bear rich information on translation control and dynamics. Yet, due to technical biases in library generation, extracting quantitative measures of discrete translation events has remained elusive. 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 (RPF) generation), which allows for correct estimation of translation times at single codon resolution. Furthermore, we validated the method with available datasets from E. coli treated with antibiotic to inhibit isoleucyl-tRNA synthetase, and two datasets from Saccharomyces cerevisiae treated with two RNases with distinct cleavage signatures. We demonstrate that our approach accounts for RNase cleavage preferences and provides bias-corrected translation times estimates. 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.
Subject headings and genre
- NATURVETENSKAP Biologi Biokemi och molekylärbiologi hsv//swe
- NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology hsv//eng
- Biology with specialization in Molecular Cell Biology
- Biologi med inriktning mot molekylär cellbiologi
Added entries (persons, corporate bodies, meetings, titles ...)
- Ullman, GustafUppsala universitet,Institutionen för cell- och molekylärbiologi(Swepub:uu)gusul252 (author)
- Ignatova, ZoyaUniv Hamburg, Inst Biochem & Mol Biol, D-20146 Hamburg, Germany. (author)
- Ehrenberg, MånsUppsala universitet,Institutionen för cell- och molekylärbiologi(Swepub:uu)mansehre (author)
- Uppsala universitetInstitutionen för cell- och molekylärbiologi (creator_code:org_t)
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- In:Nucleic Acids Research: Oxford University Press49:9, s. 5124-51420305-10481362-4962
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