Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
available in PMC 2011 November 01.
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Nature Publishing Group
2012
|
| Online Access: | http://hdl.handle.net/1721.1/74540 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1811097903327870976 |
|---|---|
| author | Rabani, Michal Levin, Joshua Z. Fan, Lin Adiconis, Xian Raychowdhury, Raktima Garber, Manuel Gnirke, Andreas Nusbaum, Chad Hacohen, Nir Friedman, Nir Amit, Ido Regev, Aviv |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Rabani, Michal Levin, Joshua Z. Fan, Lin Adiconis, Xian Raychowdhury, Raktima Garber, Manuel Gnirke, Andreas Nusbaum, Chad Hacohen, Nir Friedman, Nir Amit, Ido Regev, Aviv |
| author_sort | Rabani, Michal |
| collection | MIT |
| description | available in PMC 2011 November 01. |
| first_indexed | 2024-09-23T17:06:48Z |
| format | Article |
| id | mit-1721.1/74540 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T17:06:48Z |
| publishDate | 2012 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/745402022-10-03T10:29:22Z Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells Rabani, Michal Levin, Joshua Z. Fan, Lin Adiconis, Xian Raychowdhury, Raktima Garber, Manuel Gnirke, Andreas Nusbaum, Chad Hacohen, Nir Friedman, Nir Amit, Ido Regev, Aviv Massachusetts Institute of Technology. Department of Biology Regev, Aviv available in PMC 2011 November 01. Cellular RNA levels are determined by the interplay of RNA production, processing and degradation. However, because most studies of RNA regulation do not distinguish the separate contributions of these processes, little is known about how they are temporally integrated. Here we combine metabolic labeling of RNA at high temporal resolution with advanced RNA quantification and computational modeling to estimate RNA transcription and degradation rates during the response of mouse dendritic cells to lipopolysaccharide. We find that changes in transcription rates determine the majority of temporal changes in RNA levels, but that changes in degradation rates are important for shaping sharp 'peaked' responses. We used sequencing of the newly transcribed RNA population to estimate temporally constant RNA processing and degradation rates genome wide. Degradation rates vary significantly between genes and contribute to the observed differences in the dynamic response. Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation. Human Frontier Science Program (Strasbourg, France) Howard Hughes Medical Institute Burroughs Wellcome Fund (Career Award at the Scientific Interface) 2012-11-01T15:58:41Z 2012-11-01T15:58:41Z 2011-04 2010-12 Article http://purl.org/eprint/type/JournalArticle 1087-0156 1546-1696 http://hdl.handle.net/1721.1/74540 Rabani, Michal et al. “Metabolic Labeling of RNA Uncovers Principles of RNA Production and Degradation Dynamics in Mammalian Cells.” Nature Biotechnology 29.5 (2011): 436–442. Web. https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.1038/nbt.1861 Nature Biotechnology Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Nature Publishing Group PMC |
| spellingShingle | Rabani, Michal Levin, Joshua Z. Fan, Lin Adiconis, Xian Raychowdhury, Raktima Garber, Manuel Gnirke, Andreas Nusbaum, Chad Hacohen, Nir Friedman, Nir Amit, Ido Regev, Aviv Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells |
| title | Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells |
| title_full | Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells |
| title_fullStr | Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells |
| title_full_unstemmed | Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells |
| title_short | Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells |
| title_sort | metabolic labeling of rna uncovers principles of rna production and degradation dynamics in mammalian cells |
| url | http://hdl.handle.net/1721.1/74540 https://orcid.org/0000-0001-8567-2049 |
| work_keys_str_mv | AT rabanimichal metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT levinjoshuaz metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT fanlin metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT adiconisxian metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT raychowdhuryraktima metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT garbermanuel metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT gnirkeandreas metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT nusbaumchad metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT hacohennir metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT friedmannir metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT amitido metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells AT regevaviv metaboliclabelingofrnauncoversprinciplesofrnaproductionanddegradationdynamicsinmammaliancells |