Miami researchers in plant biology, bioinformatics, show extensive role of APA in gene expression

A study by Miami University researchers and collaborators in the fields of plant biology and bioinformatics suggests that alternative polyadenylation plays a far greater role in gene expression in plants than previously expected.

“Our team developed a new strategy to sequence and tally the total polyadenylation profiles of the genome (collection of all genes in an organism) of the model plant Arabidopsis, using state-of-the-art DNA sequencing technology,” said Qingshun Quinn Li, professor of botany at Miami and one of the study authors. “Our research suggests that over two-thirds of plant genes are regulated through alternative polyadenylation (APA). Thus, APA plays a far greater role in gene expression in plants than previously expected.”

Polyadenylation (poly(A)) is needed for almost every protein coding gene in plants and animals — it is essential for gene expression. Alternative polyadenylation adds poly(A) in different locations of a gene’s transcripts, which may cause different expression resulting from the same gene, according to Li. This is called transcript diversity.

Transcript diversity can be used for regulating gene expression — one gene may now code for different messenger RNAs that may produce different proteins with altered functions.

“For example, our liver and lung have the exactly same set of genes, but differentially expressed, result in two organs with completely different morphologies and functions,” Li explained.

In addition, the study shows a “unique and unanticipated mode of polyadenylation that is directed to sites lying within protein-coding regions” in Arabidopsis, said the study authors.

Their results also support a potential new role of polyadenylation where it may regulate gene transcription activities.

The study, “Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation,” is published in the online, Early Edition of the Proceedings of the National Academy of Sciences (PNAS) USA the week of July 11, 2011.

Authors, from five laboratories in two countries, are Li, Xiaohui Wu, visiting doctoral student at Miami from Xiamen University, China; Chun Liang, associate professor of botany at Miami; Guoli Ji, Xiamen University; Man Liu, postdoctoral fellow at Miami; and Bruce Downie, associate professor, department of horticulture, and Arthur Hunt, professor, department of plant and soil sciences, both from the University of Kentucky.

The research was supported by grants from the National Science Foundation, the Kentucky Science and Engineering Foundation and the National Natural Science Foundation of China, among others.

Liang and Li, with John Karro, associate professor of computer science and software engineering, were recently awarded a $279,648 grant from the National Institute of General Medical Sciences for further research on APA, for the project “In-silico Exploration of APA using next generation sequencing.”