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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. This guide provides an overview of epigenetic regulation and how to study these critical players.
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.
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 CUT&RUN and CUT&Tag
The Henikoff lab has recently developed two new chromatin profiling methods: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and Cleavage Under Targets and Tagmentation (CUT&Tag) which provide an exciting advance because they overcome many of the drawbacks of 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.