Epigenome sequencing comes of age in development, differentiation and disease mechanism research

Abstract

In eukaryotic organisms, changes in cell phenotype are tightly associated with dynamic changes in the epigenome. Over the past few years, sequencing-based genome-wide approaches to generate, analyze, interpret and integrate epigenetic information have been applied to investigate the mechanisms behind the changes in cell status, such as those which are seen in differentiation, disease and reprogramming. This article focuses on the four types of epigenomic information (i.e., nucleosome positioning, histone modification, DNA methylation and chromatin higher-order structure). We summarize the distinct high-throughput sequencing applications used to generate the different types of epigenomic profiles and the bioinformatic software available for performing routine analysis. With the dramatic improvement of sequencing technology and bioinformatic analysis, epigenome sequencing has gradually become the common approach to study a variety of biological issues.

KEYWORDS::

• chromatin higher-order structure
• DNA methylation
• epigenomic dynamics
• high-throughput sequencing
• histone modification
• nucleosome positioning

Acknowledgements

The authors thank the peer reviewers for their critical comments and Kevin Boru for help with language editing.

Financial & competing interests disclosure

Research from the authors‘ laboratory is supported by funds from the National Basic Research Program of China (973 Program; No. 2010CB944904 and 2011CB965104), National Natural Science Foundation of China (31071114) and Shanghai Rising-Star Program (10QA1407300). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

Research from the authors‘ laboratory is supported by funds from the National Basic Research Program of China (973 Program; No. 2010CB944904 and 2011CB965104), National Natural Science Foundation of China (31071114) and Shanghai Rising-Star Program (10QA1407300). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.