Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.

Ribosomal profiling is a promising approach with increasing popularity for studying translation. This approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides.In this study, we focused on ribosomal density profiles of mouse embryonic stem cells. Our analysi...

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Autores principales:	Alexandra Dana, Tamir Tuller
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/97aad5d08c184186b49e711005de3d60
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spelling	oai:doaj.org-article:97aad5d08c184186b49e711005de3d602021-11-18T05:52:44ZDeterminants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.1553-734X1553-735810.1371/journal.pcbi.1002755https://doaj.org/article/97aad5d08c184186b49e711005de3d602012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23133360/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Ribosomal profiling is a promising approach with increasing popularity for studying translation. This approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides.In this study, we focused on ribosomal density profiles of mouse embryonic stem cells. Our analysis suggests, for the first time, that even in mammals such as M. musculus the elongation speed is significantly and directly affected by determinants of the coding sequence such as: 1) the adaptation of codons to the tRNA pool; 2) the local mRNA folding of the coding sequence; 3) the local charge of amino acids encoded in the codon sequence. In addition, our analyses suggest that in general, the translation velocity of ribosomes is slower at the beginning of the coding sequence and tends to increase downstream.Finally, a comparison of these data to the expected biophysical behavior of translation suggests that it suffers from some unknown biases. Specifically, the ribosomal flux measured on the experimental data increases along the coding sequence; however, according to any biophysical model of ribosomal movement lacking internal initiation sites, the flux is expected to remain constant or decrease. Thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance.Alexandra DanaTamir TullerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 11, p e1002755 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Alexandra Dana Tamir Tuller Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
description	Ribosomal profiling is a promising approach with increasing popularity for studying translation. This approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides.In this study, we focused on ribosomal density profiles of mouse embryonic stem cells. Our analysis suggests, for the first time, that even in mammals such as M. musculus the elongation speed is significantly and directly affected by determinants of the coding sequence such as: 1) the adaptation of codons to the tRNA pool; 2) the local mRNA folding of the coding sequence; 3) the local charge of amino acids encoded in the codon sequence. In addition, our analyses suggest that in general, the translation velocity of ribosomes is slower at the beginning of the coding sequence and tends to increase downstream.Finally, a comparison of these data to the expected biophysical behavior of translation suggests that it suffers from some unknown biases. Specifically, the ribosomal flux measured on the experimental data increases along the coding sequence; however, according to any biophysical model of ribosomal movement lacking internal initiation sites, the flux is expected to remain constant or decrease. Thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance.
format	article
author	Alexandra Dana Tamir Tuller
author_facet	Alexandra Dana Tamir Tuller
author_sort	Alexandra Dana
title	Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
title_short	Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
title_full	Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
title_fullStr	Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
title_full_unstemmed	Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
title_sort	determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/97aad5d08c184186b49e711005de3d60
work_keys_str_mv	AT alexandradana determinantsoftranslationelongationspeedandribosomalprofilingbiasesinmouseembryonicstemcells AT tamirtuller determinantsoftranslationelongationspeedandribosomalprofilingbiasesinmouseembryonicstemcells
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Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.

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