Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies.
Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced. [BMB Reports 2017; 50(4): 201-207].
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Hsin-Sung
HS
Yeh
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Wei
W
Zhang
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
Jeongsik
J
Yong
D020413:3' Untranslated Regions; D000465:Algorithms; D000818:Animals; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007075:Immunoglobulin M / Q000235:genetics / Q000378:metabolism; D026723:Polyadenylation; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
D020413:3' Untranslated Regions; D007075:Immunoglobulin M; D012333:RNA, Messenger; D013762:Tetrahydrofolate Dehydrogenase