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| Item Type: | Article |
|---|---|
| Title: | Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus |
| Creators Name: | Wang, X., You, X., Langer, J.D., Hou, J., Rupprecht, F., Vlatkovic, I., Quedenau, C., Tushev, G., Epstein, I., Schaefke, B., Sun, W., Fang, L., Li, G., Hu, Y., Schuman, E.M. and Chen, W. |
| Abstract: | 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. |
| Keywords: | Gene Expression Profiling, Genomics, High-Throughput Nucleotide Sequencing, Hippocampus, Molecular Sequence Annotation, Open Reading Frames, Protein Isoforms, Proteins, RNA, RNA Isoforms, Sprague-Dawley Rats, RNA Sequence Analysis, Transcriptome, Animals, Rats |
| Source: | Nature Communications |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 10 |
| Number: | 1 |
| Page Range: | 5009 |
| Date: | 1 November 2019 |
| Official Publication: | https://doi.org/10.1038/s41467-019-13037-0 |
| PubMed: | View item in PubMed |
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