Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences

Area of Science:

• Molecular Biology
• Genomics
• Plant Science

Background:

• Polyadenylation is a crucial post-transcriptional modification affecting eukaryotic transcript fate.
• Alternative polyadenylation (APA) is prevalent in plants, with ~70% of genes possessing APA sites.
• A comprehensive map of polyadenylation events in maize is currently lacking despite available sequencing data.

Purpose of the Study:

• To create a comprehensive map of polyadenylation events in maize.
• To characterize poly(A) Clusters (PACs) and alternative polyadenylation (APA) sites across the maize genome.
• To investigate the genomic distribution and characteristics of PACs and APA sites.

Main Methods:

• Analysis of 9.48 billion RNA-Seq reads from maize.
• Identification and characterization of 95,345 Poly(A) Clusters (PACs) in 23,705 maize genes.
• Examination of genomic distribution, nucleotide composition, and associated motifs of PACs.

Main Results:

• Characterized 95,345 PACs in 51% of maize genes, with 76% exhibiting APA.
• Identified PACs in genic regions (78%), intergenic regions (21,264), 5'-UTR (735), CDS (2,542), and introns (12,841).
• Observed AT-richness around PACs and the common upstream motif AAUAAA, though only 2,830 genes retained this motif.

Conclusions:

• This large-scale study provides the first comprehensive map of polyadenylation events in maize.
• The findings reveal extensive APA and diverse PAC locations, offering insights into gene expression regulation.
• The generated data can serve as a valuable resource for validating transcript end annotations in maize.