Transcript profiling by 3'-untranslated region sequencing resolves expression of gene families

Area of Science:

• Plant Biology
• Genomics
• Molecular Biology

Background:

• Gene expression differences are fundamental to plant biology, but resolving closely related genes (alleles, gene families) is difficult.
• Genome-wide expression analysis is hampered by sequence similarity and incomplete genome data.

Purpose of the Study:

• To develop and validate a novel expression-profiling strategy using 3 -untranslated regions (UTRs) for high-throughput sequencing.
• To enable gene- and allele-specific transcript resolution independent of a fully sequenced genome.

Main Methods:

• Utilized long-read, high-throughput sequencing to capture 3 -UTRs of messenger RNAs (mRNAs).
• Constructed multiplexed cDNA libraries from maize ovaries, labeling samples with unique key codes.
• Sequenced pooled samples and quantified transcript abundance by sequence read frequency.

Main Results:

• Identified 14,822 unique transcripts from approximately 229,000 3 -anchored sequences in maize ovaries.
• Detected over 202 unique transcripts with significant abundance differences between wild-type and mutant samples.
• Resolved 12 cellulose synthase (CesA) transcripts, identified new histone H1 family members, and distinguished nearly identical paralogs (Arda transcripts).

Conclusions:

• 3 -UTR profiling is a powerful strategy for resolving gene- and allele-specific transcripts.
• This method overcomes limitations of sequence similarity and incomplete genomes for expression analysis.
• The approach has broad applications in understanding gene function, evolution, and quantitative traits in plants.