Improved definition of the mouse transcriptome via targeted RNA sequencing.

摘要: Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding putative or annotated long noncoding (lncRNAs) 154,281 known splicing junction sites were selected targeted across five mouse tissues three brain subregions. The results illustrate that transcriptome is considerably more complex previously thought. assemble complete isoforms GENCODE, expand boundaries, connect interspersed islands mapped reads. describe a novel filtering pipeline identifies unannotated but high-quality isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded models. Additionally, 594 lncRNAs acquire an open reading frame (ORF) when their structure extended with CaptureSeq. Finally, we validate our observations using FANTOM Mouse ENCODE resources.