Wei Sun

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

Publisher: Springer Science and Business Media LLC

Date: 11-2019

DOI: 10.1038/S41467-019-13037-0

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 hippoc us, 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 ersity in the rat brain and provide a rich resource for functional studies.

Extensive allele‐specific translational regulation in hybrid mice

Publisher: EMBO

Date: 08-2015

DOI: 10.15252/MSB.156240

Abstract: Translational regulation is mediated through the interaction between diffusible trans-factors and cis-elements residing within mRNA transcripts. In contrast to extensively studied transcriptional regulation, cis-regulation on translation remains underexplored. Using deep sequencing-based transcriptome and polysome profiling, we globally profiled allele-specific translational efficiency for the first time in an F1 hybrid mouse. Out of 7,156 genes with reliable quantification of both alleles, we found 1,008 (14.1%) exhibiting significant allelic ergence in translational efficiency. Systematic analysis of sequence features of the genes with biased allelic translation revealed that local RNA secondary structure surrounding the start codon and proximal out-of-frame upstream AUGs could affect translational efficiency. Finally, we observed that the cis-effect was quantitatively comparable between transcriptional and translational regulation. Such effects in the two regulatory processes were more frequently compensatory, suggesting that the regulation at the two levels could be coordinated in maintaining robustness of protein expression.

Virginia Tech

Location: United States of America

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University Of California, San Francisco

Location: United States of America

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Shanghai Jiao Tong University School Of Medicine

Location: China

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Max Delbrück Centrum Für Molekulare Medizin Berlin Buch

Location: Germany

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Shanghai Jiao Tong University

Location: China

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