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Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus

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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. and You, X. and Langer, J.D. and Hou, J. and Rupprecht, F. and Vlatkovic, I. and Quedenau, C. and Tushev, G. and Epstein, I. and Schaefke, B. and Sun, W. and Fang, L. and Li, G. and Hu, Y. and 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
Publisher:Nature Publishing Group
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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