Journal article
Alternative polyadenylation analysis in animals and plants: newly developed strategies for profiling, processing and validation
International journal of biological sciences, Vol.14(12), pp.1709-1714
2018
Handle:
https://hdl.handle.net/2376/110818
PMCID: PMC6216028
PMID: 30416385
Abstract
Alternative polyadenylation is an essential RNA processing event that contributes significantly to regulation of transcriptome diversity and functional dynamics in both animals and plants. Here we review newly developed next generation sequencing methods for genome-wide profiling of alternative polyadenylation (APA) sites, bioinformatics pipelines for data processing and both wet and dry laboratory approaches for APA validation. The library construction methods LITE-Seq (Low-Input 3'-Terminal sequencing) and PAC-seq (PolyA Click sequencing) tag polyA
cDNA, while BAT-seq (BArcoded, three-prime specific sequencing) and PAPERCLIP (
oly(
) binding
rotein-mediated mRNA 3'
nd
etrieval by
ross
inking
mmuno
recipitation) enrich polyA
RNA. Interestingly, only WTTS-seq (Whole Transcriptome Termini Site sequencing) targets both polyA
RNA and polyA
cDNA. Varieties of bioinformatics pipelines are well established to pursue read quality control, mapping, clustering, characterization and pathway analysis. The RHAPA (RNase H alternative polyadenylation assay) and 3'RACE-seq (3' rapid amplification of cDNA end sequencing) methods directly validate APA sites, while WTSS-seq (whole transcriptome start site sequencing), RNA-seq (RNA sequencing) and public APA databases can serve as indirect validation methods. We hope that these tools, pipelines and resources trigger huge waves of interest in the research community to investigate APA events underlying physiological, pathological and psychological changes and thus understand the information transfer events from genome to phenome relevant to economically important traits in both animals and plants.
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Details
- Title
- Alternative polyadenylation analysis in animals and plants: newly developed strategies for profiling, processing and validation
- Creators
- Yunqi Zhang - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620Shane A Carrion - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620Yangzi Zhang - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620Xiaohui Zhang - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620Amy L Zinski - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620Jennifer J Michal - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620Zhihua Jiang - Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620
- Publication Details
- International journal of biological sciences, Vol.14(12), pp.1709-1714
- Academic Unit
- Animal Sciences, Department of
- Publisher
- Australia
- Grant note
- R21 HD076845 / NICHD NIH HHS
- Identifiers
- 99900547028001842
- Language
- English
- Resource Type
- Journal article