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

Wang，Xi1,2; You，Xintian1,3; Langer，Julian D.4; Hou，Jingyi1; Rupprecht，Fiona4; Vlatkovic，Irena4; Quedenau，Claudia1; Tushev，Georgi4; Epstein，Irina4; Schaefke，Bernhard5,6; Sun，Wei5; Fang，Liang5,6; Li，Guipeng5,6; Hu，Yuhui5; Schuman，Erin M.4; Chen，Wei5,6

2019-12-01

10.1038/s41467-019-13037-0

Nature Communications   影响因子和分区

2041-1723

2041-1723

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.

SCI

英语

NI期刊

通讯

European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program[743216]

Science & Technology - Other Topics

Multidisciplinary Sciences

WOS:000493712700002

NATURE PUBLISHING GROUP

2-s2.0-85074361547

Scopus

1.Max Delbrück Center for Molecular Medicine,Berlin,13125,Germany
2.German Cancer Research Center,Heidelberg,69120,Germany
3.Max Planck Institute for Molecular Genetics,Berlin,14195,Germany
4.Max Planck Institute for Brain Research,Frankfurt,60438,Germany
5.Department of BiologySouthern University of Science and Technology,Shenzhen,518055,China
6.Medi-X InstituteSUSTech Academy for Advanced Interdisciplinary StudiesSouthern University of Science and Technology,Shenzhen,518055,China

Wang，Xi,You，Xintian,Langer，Julian D.,et al. Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus[J]. Nature Communications,2019,10(1).

Wang，Xi.,You，Xintian.,Langer，Julian D..,Hou，Jingyi.,Rupprecht，Fiona.,...&Chen，Wei.(2019).Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus.Nature Communications,10(1).

Wang，Xi,et al."Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus".Nature Communications 10.1(2019).