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


  • X. Wang
  • X. You
  • J.D. Langer
  • J. Hou
  • F. Rupprecht
  • I. Vlatkovic
  • C. Quedenau
  • G. Tushev
  • I. Epstein
  • B. Schaefke
  • W. Sun
  • L. Fang
  • G. Li
  • Y. Hu
  • E.M. Schuman
  • W. Chen


  • Nature Communications


  • Nat Commun 10 (1): 5009


  • 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.