profit-seq

The high diversity and complexity of the eukaryotic transcriptome makes it difficult to effectively detect specific transcripts of interest. State-of-the-art targeted RNA-seq methods incorporate pre-sequencing enrichment steps that require complicated experimental treatment and compromise the characterization of the full transcriptome spectrum. Here, we describe an enriching by sequencing strategy called programmable full-length isoform transcriptome sequencing (PROFIT-seq) to enrich target transcripts with unbiased quantification of the whole transcriptome. We employ combinatorial reverse transcription to capture the whole transcriptome and implement a programmable control system for selective enrichment of target transcripts during sequencing. PROFIT-seq can achieve an over 300% increase in the yield of effective data and reduce the time required for detecting specific pathogens or key mutations by 75%. We further applied PROFIT-seq to explore the transcriptome changes during colorectal polyp development and revealed the complex association between immune responses and bacterial infection. The PROFIT-seq method enables accurate and efficient sequencing of target transcripts and provides unbiased quantification of both target and nontarget transcripts, which will undoubtedly facilitate its wide application in clinical diagnostic and targeted enrichment scenarios.