Combining Genomic and Proteomic Approaches for Epigenetics Research

Abstract

Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromatin immunoprecipitation (ChIP) followed by sequencing and other ChIP-based techniques are powerful techniques for genome-wide profiling of DNA-binding proteins, histone post-translational modifications or nucleosome positions. However, mass spectrometry-based proteomics is increasingly being used in functional biological studies and has proved to be an indispensable tool to characterize histone modifications, as well as DNA–protein and protein–protein interactions. With the development of genomic and proteomic approaches, combination of ChIP and mass spectrometry has the potential to expand our knowledge of epigenetics research to a higher level.

KEYWORDS::

• approach
• chromatin immunoprecipitation
• DNA methylation
• epigenetic
• genomic
• histone modification
• mass spectrometry
• proteomic

Financial & competing interests disclosure

BA Garcia acknowledges funding from a National Science Foundation Early Faculty CAREER award grant, and the NIH New Innovator award grant (DP2OD007447) from the Office of the Director. 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

BA Garcia acknowledges funding from a National Science Foundation Early Faculty CAREER award grant, and the National Institutes of Health (NIH) New Innovator award grant (DP2OD007447) from the Office of the Director. 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.