Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification
Transcriptional profiling is a useful strategy to study development and disease. Approaches to isolate RNA from specific cell types, or from specific cellular compartments, would extend the power of this strategy. Previous work has shown that isolation of genetically tagged ribosomes (translating ri...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2014
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| Online Access: | http://hdl.handle.net/1721.1/87995 |
| _version_ | 1811089732351819776 |
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| author | Day, Daniel Sindt Zhou, Pingzhu Zhang, Yijing Ma, Qing Gu, Fei He, Aibin Zhou, Bin Li, Jing Stevens, Sean M. Romo, Daniel Pu, William T. |
| author2 | Whitaker College of Health Sciences and Technology |
| author_facet | Whitaker College of Health Sciences and Technology Day, Daniel Sindt Zhou, Pingzhu Zhang, Yijing Ma, Qing Gu, Fei He, Aibin Zhou, Bin Li, Jing Stevens, Sean M. Romo, Daniel Pu, William T. |
| author_sort | Day, Daniel Sindt |
| collection | MIT |
| description | Transcriptional profiling is a useful strategy to study development and disease. Approaches to isolate RNA from specific cell types, or from specific cellular compartments, would extend the power of this strategy. Previous work has shown that isolation of genetically tagged ribosomes (translating ribosome affinity purification; TRAP) is an effective means to isolate ribosome-bound RNA selectively from transgene-expressing cells. However, widespread application of this technology has been limited by available transgenic mouse lines. Here we characterize a TRAP allele (Rosa26[superscript fsTRAP]) that makes this approach more widely accessible. We show that endothelium-specific activation of Rosa26[superscript fsTRAP] identifies endothelial cell-enriched transcripts, and that cardiomyocyte-restricted TRAP is a useful means to identify genes that are differentially expressed in cardiomyocytes in a disease model. Furthermore, we show that TRAP is an effective means for studying translational regulation, and that several nuclear-encoded mitochondrial genes are under strong translational control. Our analysis of ribosome-bound transcripts also shows that a subset of long intergenic noncoding RNAs are weakly ribosome-bound, but that the majority of noncoding RNAs, including most long intergenic noncoding RNAs, are ribosome-bound to the same extent as coding transcripts. Together, these data show that the TRAP strategy and the Rosa26[superscript fsTRAP] allele will be useful tools to probe cell type-specific transcriptomes, study translational regulation, and probe ribosome binding of noncoding RNAs. |
| first_indexed | 2024-09-23T14:23:50Z |
| format | Article |
| id | mit-1721.1/87995 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:23:50Z |
| publishDate | 2014 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/879952022-09-29T09:13:25Z Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification Day, Daniel Sindt Zhou, Pingzhu Zhang, Yijing Ma, Qing Gu, Fei He, Aibin Zhou, Bin Li, Jing Stevens, Sean M. Romo, Daniel Pu, William T. Whitaker College of Health Sciences and Technology Harvard University--MIT Division of Health Sciences and Technology Day, Daniel Sindt Transcriptional profiling is a useful strategy to study development and disease. Approaches to isolate RNA from specific cell types, or from specific cellular compartments, would extend the power of this strategy. Previous work has shown that isolation of genetically tagged ribosomes (translating ribosome affinity purification; TRAP) is an effective means to isolate ribosome-bound RNA selectively from transgene-expressing cells. However, widespread application of this technology has been limited by available transgenic mouse lines. Here we characterize a TRAP allele (Rosa26[superscript fsTRAP]) that makes this approach more widely accessible. We show that endothelium-specific activation of Rosa26[superscript fsTRAP] identifies endothelial cell-enriched transcripts, and that cardiomyocyte-restricted TRAP is a useful means to identify genes that are differentially expressed in cardiomyocytes in a disease model. Furthermore, we show that TRAP is an effective means for studying translational regulation, and that several nuclear-encoded mitochondrial genes are under strong translational control. Our analysis of ribosome-bound transcripts also shows that a subset of long intergenic noncoding RNAs are weakly ribosome-bound, but that the majority of noncoding RNAs, including most long intergenic noncoding RNAs, are ribosome-bound to the same extent as coding transcripts. Together, these data show that the TRAP strategy and the Rosa26[superscript fsTRAP] allele will be useful tools to probe cell type-specific transcriptomes, study translational regulation, and probe ribosome binding of noncoding RNAs. American Heart Association National Heart, Lung, and Blood Institute (U01HL098166) National Heart, Lung, and Blood Institute (U01HL098188) National Heart, Lung, and Blood Institute (R01HL095712) 2014-06-16T14:33:05Z 2014-06-16T14:33:05Z 2013-09 2013-03 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/87995 Zhou, P., Y. Zhang, Q. Ma, F. Gu, D. S. Day, A. He, B. Zhou, et al. “Interrogating Translational Efficiency and Lineage-Specific Transcriptomes Using Ribosome Affinity Purification.” Proceedings of the National Academy of Sciences 110, no. 38 (September 17, 2013): 15395–15400. en_US http://dx.doi.org/10.1073/pnas.1304124110 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) National Academy of Sciences (U.S.) |
| spellingShingle | Day, Daniel Sindt Zhou, Pingzhu Zhang, Yijing Ma, Qing Gu, Fei He, Aibin Zhou, Bin Li, Jing Stevens, Sean M. Romo, Daniel Pu, William T. Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification |
| title | Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification |
| title_full | Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification |
| title_fullStr | Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification |
| title_full_unstemmed | Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification |
| title_short | Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification |
| title_sort | interrogating translational efficiency and lineage specific transcriptomes using ribosome affinity purification |
| url | http://hdl.handle.net/1721.1/87995 |
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