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Estimation of pepti...
Estimation of peptide elongation times from ribosome profiling spectra
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- Pavlov, Michael (författare)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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- Ullman, Gustaf (författare)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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- Ignatova, Zoya (författare)
- Univ Hamburg, Inst Biochem & Mol Biol, D-20146 Hamburg, Germany.
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- Ehrenberg, Måns (författare)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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(creator_code:org_t)
- 2021-04-22
- 2021
- Engelska.
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Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 49:9, s. 5124-5142
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Nyckelord
- Biology with specialization in Molecular Cell Biology
- Biologi med inriktning mot molekylär cellbiologi
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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