REAPseq

REAPseq (RNA Expression and Processing sequencing) is a high-throughput sequencing technique designed to analyze both the expression and processing of RNA molecules within a cell. Developed as an extension of traditional RNA sequencing (RNA-seq), REAPseq provides insights into RNA splicing, polyadenylation, and other post-transcriptional modifications by capturing full-length RNA transcripts.

The method involves capturing RNA molecules using a unique adapter that binds to the poly(A) tail of mature mRNA. This adapter contains a random hexamer sequence, allowing for the amplification of full-length transcripts during library preparation. By sequencing these adapter-ligated RNA fragments, researchers can map the entire transcript, including exons, introns, and untranslated regions (UTRs), while also identifying alternative splicing events and polyadenylation sites.

REAPseq offers several advantages over conventional RNA-seq. Since it preserves the full-length structure of RNA, it enables more accurate quantification of transcript isoforms and detection of rare splicing variants. Additionally, the technique can be applied to low-input samples, making it suitable for studies involving limited biological material, such as single cells or small tissue biopsies.

The workflow of REAPseq begins with RNA extraction, followed by adapter ligation and reverse transcription to generate cDNA. The cDNA is then amplified, fragmented, and sequenced on a high-throughput platform. Bioinformatics analysis involves aligning reads to a reference genome, quantifying transcript abundance, and identifying splicing and polyadenylation patterns.

REAPseq has been widely used in various biological and medical research areas, including cancer genomics, developmental biology, and infectious disease studies. Its ability to provide comprehensive RNA profiling makes it a valuable tool for understanding gene regulation and functional genomics. However, like other sequencing methods, REAPseq requires careful experimental design and computational analysis to ensure reliable and reproducible results.