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Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus
Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstru...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825209/ https://www.ncbi.nlm.nih.gov/pubmed/31676752 http://dx.doi.org/10.1038/s41467-019-13037-0 |
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author | Wang, Xi You, Xintian Langer, Julian D. Hou, Jingyi Rupprecht, Fiona Vlatkovic, Irena Quedenau, Claudia Tushev, Georgi Epstein, Irina Schaefke, Bernhard Sun, Wei Fang, Liang Li, Guipeng Hu, Yuhui Schuman, Erin M. Chen, Wei |
author_facet | Wang, Xi You, Xintian Langer, Julian D. Hou, Jingyi Rupprecht, Fiona Vlatkovic, Irena Quedenau, Claudia Tushev, Georgi Epstein, Irina Schaefke, Bernhard Sun, Wei Fang, Liang Li, Guipeng Hu, Yuhui Schuman, Erin M. Chen, Wei |
author_sort | Wang, Xi |
collection | PubMed |
description | Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies. |
format | Online Article Text |
id | pubmed-6825209 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-68252092019-11-04 Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus Wang, Xi You, Xintian Langer, Julian D. Hou, Jingyi Rupprecht, Fiona Vlatkovic, Irena Quedenau, Claudia Tushev, Georgi Epstein, Irina Schaefke, Bernhard Sun, Wei Fang, Liang Li, Guipeng Hu, Yuhui Schuman, Erin M. Chen, Wei Nat Commun Article Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies. Nature Publishing Group UK 2019-11-01 /pmc/articles/PMC6825209/ /pubmed/31676752 http://dx.doi.org/10.1038/s41467-019-13037-0 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Wang, Xi You, Xintian Langer, Julian D. Hou, Jingyi Rupprecht, Fiona Vlatkovic, Irena Quedenau, Claudia Tushev, Georgi Epstein, Irina Schaefke, Bernhard Sun, Wei Fang, Liang Li, Guipeng Hu, Yuhui Schuman, Erin M. Chen, Wei Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
title | Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
title_full | Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
title_fullStr | Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
title_full_unstemmed | Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
title_short | Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
title_sort | full-length transcriptome reconstruction reveals a large diversity of rna and protein isoforms in rat hippocampus |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825209/ https://www.ncbi.nlm.nih.gov/pubmed/31676752 http://dx.doi.org/10.1038/s41467-019-13037-0 |
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