Novel Sequencing Approaches for the High-Throughput Identification of Full-length Poly(A) RNA Transcripts at the Single-cell Level

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandlingForskning

  • Zhe XIE
RNA poly(A) tails play a significant role in the post-transcriptional regulation of eukaryotic mRNA, mRNA stability, and translational efficiency. However, the mechanisms underlying these functions have remained elusive. In recent years, poly(A) tails regulatory roles are becoming more apparent due to the fast development of next-generation and third-generation sequencing technologies for reliable reading of poly(A) tails in bulk samples. Despite these advances, the assessment of poly(A) tail-containing transcripts in batches at a single-cell level remains a considerable hurdle. This project aimed to develop new sequencing methods to extensively profile single-cell transcriptomes maintaining poly(A) tail length in hundreds to thousands of cells (singlecell poly(A)-tail length sequencing; scPAL-seq). We combined an end-extension approach to extend RNA poly(A) tails with a matching single-cell gel beads primer with droplet-based singlecell library preparation to produce high-quality single-cell data, including poly(A) tail lengths. Our results show that scPAL-seq provides an easy and efficient workflow and can detect RNA isoforms while getting poly(A) tail lengths inside individual cells. We also devised a low-cost, high-detection 3'-end RNA sequencing technique (Easy-RNA-seq). This approach takes advantage of the Tn5 transposase unique feature of direct tagmentation of RNA/DNA hybrids. Easy-RNA-Seq avoids mRNA enrichment and rRNA consumption, completes library construction within 3 hours, and generates strand-specific libraries. Also, data within <10M still maintain data quality, standard generation, and gene expression quantification comparable to conventional RNA-seq. We further improved the Easy-RNA-seq method to allow the sequencing of transcripts retaining poly(A) tail length information during transcription, which we named Easy-PA-seq. Easy-PA-seq facilitates the detection of expressed genes' poly(A) tails and reliably detects poly(A)-tailed transcripts in different replicates. This improved method simplifies the way to identify transcripts with poly(A) tail information. Finally, we created sc3PAL-seq, which identifies information from numerous single-cell 3' transcriptomes and poly(A) tails by combining Easy-PA-seq with a microfluidic droplet producer. However, the sc3PAL-seq method is still not fully efficient in monitoring the dynamic changes and expression differences of poly(A) tails in single cells. These novel technologies may pave the way to comprehensively characterize the complexity of RNA transcripts, their dynamic regulation, and gene expression.
OriginalsprogEngelsk
ForlagDepartment of Biology, Faculty of Science, University of Copenhagen
Antal sider88
StatusUdgivet - 2022

ID: 370743582