Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data.
Ribosome profiling technology (Ribo-Seq) allowed to highlight more details of mRNA translation in cell and get additional information on importance of mRNA sequence features for this process. Application of translation inhibitors like harringtonine and cycloheximide along with mRNA-Seq technique helped to assess such important characteristic as translation efficiency. We assessed the translational importance of features of mRNA sequences with the help of statistical analysis of Ribo-Seq and mRNA-Seq data. Translationally important features known from literature as well as proposed by the authors were used in analysis. Such comparisons as protein coding versus non-coding RNAs and high- versus low-translated mRNAs were performed. We revealed a set of features that allowed to discriminate the compared categories of RNA. Significant relationships between mRNA features and efficiency of translation were also established.
* Laboratory of Gene Engineering, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, prosp. acad. Lavrentyeva, 10, Novosibirsk 630090, Russia.
Oxana A
OA
Volkova
† Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, The Siberian Branch of the Russian Academy of Sciences, ul. acad. Rzhanova, 6, Novosibirsk 630090, Russia.|‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia.
Yury V
YV
Kondrakhin
† Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, The Siberian Branch of the Russian Academy of Sciences, ul. acad. Rzhanova, 6, Novosibirsk 630090, Russia.|‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia.
Ivan S
IS
Yevshin
‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia.|§ Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems, The Siberian Branch of the Russian Academy of Sciences, prosp. acad. Lavrentyeva, 6, Novosibirsk 630090, Russia.
Tagir F
TF
Valeev
† Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, The Siberian Branch of the Russian Academy of Sciences, ul. acad. Rzhanova, 6, Novosibirsk 630090, Russia.|‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia.|¶ Specialized Educational Scientific Center, Novosibirsk State University, ul. Pirogova, 2, Novosibirsk 630090, Russia.
Ruslan N
RN
Sharipov
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000818:Animals; D018387:Codon, Initiator; D006801:Humans; D008322:Mammals / Q000235:genetics*; D051379:Mice; D014176:Protein Biosynthesis; D011506:Proteins / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D018387:Codon, Initiator; D011506:Proteins; D062085:RNA, Long Noncoding; D012333:RNA, Messenger
Mammalian mRNAs; Ribo-Seq; discriminant analysis; lncRNAs; mRNA-Seq; regression analysis; ribosome profiling; translation efficiency