Esophageal squamous cell carcinoma is a leading cause of
cancer death. Mapping the transcriptional landscapes such as
isoforms, fusion transcripts, as well as long noncoding RNAs have played a central role to understand the regulating mechanism during malignant processes. However, canonical methods such as short-read
RNA-seq are difficult to define the entire
polyadenylated RNA molecules. Here, we combined single-molecule real-time sequencing with
RNA-seq to generate high-quality long reads and to survey the transcriptional program in esophageal squamous cells. Compared with the recent annotations of human transcriptome (Ensembl 38 release 91), single-molecule real-time data identified many unannotated transcripts, novel
isoforms of known genes and an expanding repository of long intergenic noncoding RNAs (
lincRNAs). By integrating with annotation of
lincRNA catalog, 1,521
esophageal-cancer-specific
lincRNAs were defined from single-molecule real-time reads. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that these
lincRNAs and their target genes are involved in a variety of
cancer signaling pathways.
Isoform usage analysis revealed the shifted alternative splicing patterns, which can be recaptured from clinical samples or supported by previous studies. Utilizing vigorous searching criteria, we also detected multiple transcript fusions, which are not documented in current gene fusion database or readily identified from
RNA-seq reads. Two novel fusion transcripts were verified based on real-time PCR and Sanger sequencing. Overall, our long-read single-molecule sequencing largely expands current understanding of full-length transcriptome in esophageal cells and provides novel insights on the transcriptional diversity during oncogenic transformation.