Poly(A)-seq – A method for direct sequencing and analysis of the transcriptomic poly(A)-tails

Poly(A) tails at the 3’ end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3ʹ-UTR length of gene transcripts have been extensively studied. However, poly(A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics.

Researchers at ABLife Inc have developed a straight forward NGS-method for poly(A) profiling, which applies a direct 3’-end adaptor ligation and the template switching for 5’-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3ʹ-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. The researchers next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3’ adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. The researchers hope that wide applications of Poly(A)-seq help facilitate the study of the development- and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.

Poly(A)-seq library construction and the NextSeq 500 sequencing profiles

A. Flowchart of Poly(A)-seq, TAIL-seq, PAL-seq, and PAT-seq library construction procedures. B. Distribution of four different sequenced bases in each of the 300 cycle of sequencing on Illumina NextSeq 500 for sample Hela_B1. C. Distribution of four different sequenced bases in each of the 300 cycle of sequencing on Illumina NextSeq 500 for sample Hela_B2. 

Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, et al. (2020) Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS ONE 15(6): e0234696. [article]

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