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

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You,  Xintiang
Max Delbrück Center for Molecular Medicine, Berlin, Germany;
Max Planck Institute for Molecular Genetics, Max Planck Society;

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Langer,  Julian David
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;
Max Planck Institute for Brain Research, Max Planck Society;

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Rupprecht,  Fiona
Max Planck Institute for Brain Research, Max Planck Society;

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Vlatkovic,  Irena
Max Planck Institute for Brain Research, Max Planck Society;

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Tushev,  Georgi
Synaptic Plasticity Department, Max Planck Institute for Brain Research, Max Planck Society;

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Epstein,  Irina
Synaptic Plasticity Department, Max Planck Institute for Brain Research, Max Planck Society;

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Schuman,  Erin Margaret
Synaptic Plasticity Department, Max Planck Institute for Brain Research, Max Planck Society;

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Citation

Wang, X., You, X., Langer, J. D., Hou, J., Rupprecht, F., Vlatkovic, I., et al. (2019). Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus. Nature Communications, 10: 5009. doi:10.1038/s41467-019-13037-0.


Cite as: http://hdl.handle.net/21.11116/0000-0007-9071-6
Abstract
ene 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.