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Genome-wide Massive Sequencing in Embryonic Stem Cell Biology:Recent Insights and Challenges

Yaofeng Wang, Alex Chun Cheung, Jun-Tao Guo and Bo Feng

The discovery of pluripotent Embryonic Stem Cells (ESCs) in mammals has been vastly transforming stem cell research and regenerative medicine. To understand the molecular mechanism of pluripotency, massive sequencing technologies have been adopted with intense scientific interest due to their advantages, including high resolution, low noise, as well as their extensive coverage across the entire genome. Here we review the principles of genome wide massive sequencing technologies widely performed in ESCs studies, including ChIP-Seq, RNA-Seq and methylCSeq. Recent improvements and applications of these technologies will also be discussed. In addition, a summary of various methodologies used to integrate the massive genome wide sequencing data will be presented. Integrating the massive data that delineate different aspects of ESCs can prompt numerous innovations for understanding the transcription networks in maintaining pluripotency as well as gene regulations and epigenetic modifications in ESCs, which are important for research and clinical applications. Furthermore, we highlight the features that are worthy to pay attention from biologists due to current challenges in massive sequencing data analysis in bioinformatics and biostatistics.