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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Calviello, Lorenzo Mukherjee, Neelanjan Wyler, Emanuel Zauber, Henrik Hirsekorn, Antje Selbach, Matthias Landthaler, Markus Obermayer, Benedikt Ohler, Uwe |
| Description | Country affiliation: Germany Author Affiliation: Calviello L ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Mukherjee N ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Wyler E ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Zauber H ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Hirsekorn A ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Selbach M ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Landthaler M ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Obermayer B ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.); Ohler U ( Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.) |
| Abstract | RNA-sequencing protocols can quantify gene expression regulation from transcription to protein synthesis. Ribosome profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. We have developed RiboTaper (available at https://ohlerlab.mdc-berlin.de/software/), a rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from HEK293 cells to derive an extensive map of translation that covered open reading frame (ORF) annotations for more than 11,000 protein-coding genes. We also found distinct ribosomal signatures for several hundred upstream ORFs and ORFs in annotated noncoding genes (ncORFs). Mass spectrometry data confirmed that RiboTaper achieved excellent coverage of the cellular proteome. Although dozens of novel peptide products were validated in this manner, few of the currently annotated long noncoding RNAs appeared to encode stable polypeptides. RiboTaper is a powerful method for comprehensive de novo identification of actively used ORFs from Ribo-seq data. |
| File Format | HTM / HTML |
| ISSN | 15487091 |
| Issue Number | 2 |
| Volume Number | 13 |
| e-ISSN | 15487105 |
| Journal | Nature Methods |
| Language | English |
| Publisher | Nature Publishing Group |
| Publisher Date | 2016-02-01 |
| Publisher Place | United States |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Discipline Clinical Laboratory Techniques Ribosomes Metabolism Hek293 Cells Humans Open Reading Frames Protein Biosynthesis Genetics Transcriptome Journal Article Research Support, N.i.h., Extramural |
| Content Type | Text |
| Resource Type | Article |
| Subject | Cell Biology Biochemistry Molecular Biology Biotechnology |
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