Computational Biology of Embryonic Stem Cells

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Computational biology in combination with large-scale biology has played a critical role in exploring the great potentials of embryonic stem cells, resulting in significant discoveries. This e-book ...
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Computational Analysis of Alternative Polyadenylation in Embryonic Stem Cells and Induced Pluripotent Cells

Pp. 133-146 (14)

Zhe Ji, Mainul Hoque and Bin Tian


The 3’ untranslated region (3’UTR) of mRNA plays important roles in posttranscriptional control of gene expression. Over half of the human genes have multiple polyadenylation sites in 3’UTRs, leading to 3’UTR isoforms containing different cis elements. Alternative polyadenylation (APA) has been found to be dynamically regulated in different tissue types and under various cellular conditions. Embryonic stem (ES) cells have the ability to self-renew and differentiate into any cell type in the adult body. Posttranscriptional gene regulation through cis elements in 3’UTRs is increasingly found to be important for these functions. In addition, various methods have recently been developed to induce differentiated cells to ES-like cells, called induced pluripotent stem (iPS) cells. Here we show a computational method to examine regulation of 3’UTR by APA using DNA microarray data. We applied this method to ES cells and iPS cells derived from different cell types.


mRNA processing, alternative polyadenylation, 3' end formation, embryonic stem cells, induced pluripotent cells, 3'UTR, microRNA, development, proliferation, differentiation, mRNA isoform, post-transcriptional gene regulation.


Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences and New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA