Why is epigenetics so important?

Completion of the human genome project and advances in next-generation sequencing technologies have revealed that genomic DNA has much less control over biological processes and disease states than initially thought. Instead, epigenetic factors dictate how DNA is translated, tightly regulating DNA structure to control which genes to express at what times.

Many of these epigenetic factors work together to orchestrate essential cellular programs, from developmental processes to cell death pathways. Dysfunction of any of these factors can upset genomic regulation, causing cellular processes to go awry, resulting in disease from cancers and autoimmune disorders to neurological conditions, infertility, and everything in between.

To understand any aspect of biology or disease, it is essential to examine epigenetic factors that may contribute.

How to study epigenetics?

Epigenetic regulation occurs on many interacting levels, and it is essential to examine all of these levels in parallel to understand epigenetics contributions to biological processes. Tackling epigenetic studies from multiple angles with redundancy is key to ensuring accurate results.

Here we focus on five essential aspects of epigenetic regulation.

1. Chromatin architecture and accessibility

Genomic DNA is packaged and organized into chromatin to fit into the nucleus of each cell. Some regions of the genome are tightly packaged and inaccessible for transcription, resulting in gene silencing. Other areas are in an open conformation, allowing transcription factors and machinery to bind for active gene transcription. Understanding which genomic regions are active vs inactive across the genome in different cellular or disease states can help to identify critical pathways and associated genes

2. Histone modifications

Histones are proteins responsible for packaging DNA. A variety of mechanisms and modify histones, including acetylation, methylation, and phosphorylation, to control their interactions with DNA and therefore DNA structure and gene activation. Examining histone modifications, and the activity of enzymes that control these modifications can reveal mechanisms of epigenetic regulation and dysregulation at specific gene sites or across the genome at large

3.  ChIP guide

Many different types of proteins bind to DNA to either directly or indirectly to regulate chromatin conformation and gene transcription. Identifying the presence or absence of such proteins in specific regions or across the genome can provide help build a complete picture of epigenetic regulation and dysregulation, as well as point to particular players and pathways involved. We can study these aspects of epigenetic regulation with chromatin immunoprecipitation (ChIP).

4. Chromatin profiling using ChIC/CUT&RUN

The Henikoff lab has recently developed a new chromatin profiling method: Cleavage Under Targets and Release Using Nuclease (CUT&RUN), which provides an exciting advance over conventional and widely used chromatin immunoprecipitation (ChIP) methods.

5. DNA modifications

Throughout the DNA sequence, many chemical modifications exist. The most well-studied of these is 5-methylcytosine (5mC), a modification most commonly recognized as a stable, repressive regulator of gene expression. There is a large body of research that shows 5mC and other chemical modifications within DNA to have epigenetic roles in gene regulation. Identifying these marks and their function in biology is a fascinating area of epigenetics right now.

6. RNA modifications

Scientists are continually discovering new RNA modifications and new functions for existing modifications. Many RNA modifications thought only to exist in bacteria are being found in eukaryotic cells while others presumed only to exist on certain RNA, species such as tRNAs, are now being found to have crucial roles in mammalian mRNA translation. RNA modifications are very hot right now, and there is still a lot to explore in this field of research.