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BMC Genomics. 2013 Sep 11;14:615. doi: 10.1186/1471-2164-14-615.

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.

Author information

1
National Heart Lung Blood Institute, National Institutes of Health, Genetics and Development Biology Center, 9000 Rockville Pike, Bethesda, MD, 20892, USA. tingni@fudan.edu.cn.

Abstract

BACKGROUND:

Polyadenylation is a key regulatory step in eukaryotic gene expression and one of the major contributors of transcriptome diversity. Aberrant polyadenylation often associates with expression defects and leads to human diseases.

RESULTS:

To better understand global polyadenylation regulation, we have developed a polyadenylation sequencing (PA-seq) approach. By profiling polyadenylation events in 13 human tissues, we found that alternative cleavage and polyadenylation (APA) is prevalent in both protein-coding and noncoding genes. In addition, APA usage, similar to gene expression profiling, exhibits tissue-specific signatures and is sufficient for determining tissue origin. A 3' untranslated region shortening index (USI) was further developed for genes with tandem APA sites. Strikingly, the results showed that different tissues exhibit distinct patterns of shortening and/or lengthening of 3' untranslated regions, suggesting the intimate involvement of APA in establishing tissue or cell identity.

CONCLUSIONS:

This study provides a comprehensive resource to uncover regulated polyadenylation events in human tissues and to characterize the underlying regulatory mechanism.

PMID:
24025092
PMCID:
PMC3848854
DOI:
10.1186/1471-2164-14-615
[Indexed for MEDLINE]
Free PMC Article
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