PAT-Seq – polyA-tagging and sequencing for tissue-specific expression analysis changes in an in vivo setting

Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. Now, researchers at Arizona State University have developed a new method: polyA-tagging and sequencing (PAT-Seq), to isolate high-quality tissue-specific mRNA from C. elegans intestine, pharynx, and body muscle tissues and study changes in their tissue-specific transcriptomes, and 3’UTRomes.

The researchers identified thousands of novel genes and isoforms differentially expressed between these three tissues. They have precisely mapped ~20,000 tissue-specific polyadenylation sites, and discovered that ~30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3’UTR isoforms significantly enriched with microRNA targets.


PAT-Seq allowed for the first time to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment. Precise tissue-specific transcriptome rearrangements are pinpointed and for the first time tissue-specific alternative polyadenylation is linked to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.

Blazie SM, Babb C, Wilky H, Rawls A, Park JG, Mangone M. (2015) Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. BMC Biology [Epub ahead of print]. [abstract]

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