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

• Published in: Nature communications Vol. 10; no. 1; pp. 5009 - 15
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.11.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/39; 38/88; 38/91; 631/114/2401; 631/1647/514/2184; 631/208/191/2018; 631/208/726/1912; 631/337/2019; 64/86; 82/58; Accuracy; Animals; Annotations; Computational neuroscience; Error correction & detection; Footprinting; Gene expression; Gene Expression Profiling - methods; Genomes; Genomics; Genomics - methods; High-Throughput Nucleotide Sequencing - methods; Hippocampus; Hippocampus - metabolism; Humanities and Social Sciences; Isoforms; Localization; Mass spectrometry; Mass spectroscopy; Medical research; Molecular Sequence Annotation; multidisciplinary; Neurosciences; Open reading frames; Open Reading Frames - genetics; Protein Isoforms - genetics; Protein Isoforms - metabolism; Proteins; Proteins - genetics; Proteins - metabolism; Proteomics; Rats, Sprague-Dawley; Ribonucleic acid; RNA; RNA - genetics; RNA - metabolism; RNA Isoforms - genetics; RNA Isoforms - metabolism; RNA processing; Science; Science (multidisciplinary); Scientific imaging; Sequence Analysis, RNA - methods; Transcriptome
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-13037-0

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. It is challenging to characterize diverse transcript isoforms by short-read sequencing. Here the authors report full-length transcriptomes in rat hippocampus by hybrid-sequencing, predict isoform-specific translational status, and reconstruct open reading frames validated by mass spectrometry.