Omics Technologies - Epigenomics


Epigenomics is concerned with all epigenetic changes in the whole genome of a cell. Epigenetic changes are reversible chemical modifications of the genomic DNA or histones that package the genomic DNA into chromatin. Epigenetic changes have profound and wide-spread effects on gene expression without altering the genomic DNA sequence. Thus, this kind of changes would not be detected by any regular genomics methods. 


What is the major result used in personalized medicine?


A single driver mutation on its own would not be able to completely reprogram a cell to become a tumor cells evading all growth control signals. This happens in a multistage process where driver mutations induce key epigenetic changes that turn many genes on or off. Epigenetic modifications come in two flavors: repressive and activating. While the tumor needs to activate the cellular growth cycle it also needs to turn off other signals that would put brakes on the process. The most frequently used epigenetic feature today is DNA-methylation usually at a Cytosine residue (base C). Heavy methylation of Cs indicates a shutdown of gene expression in most cases. Not less important but technically more difficult to handle are histone modifications. They indicate on a finer scale activation or depression of individual genes.  


Which body samples are required to carry out the experimental analysis?


We all have one genome (more or less) but almost every cells or at least tissue has its own epigenome. Therefore, blood samples e.g. of a tumor patient, can only yield accurate epigenetic data about the tumor when, for example, circulating tumor cells can be isolated. Biopsies are the most reliable sources for epigenetic analyses. 



Fig. 15 Epigenetics controls the transcription

Histone H3 is part of an octamer of histones forming a so-called nucleosome. The genomic DNA is wrapped around these nucleosomes. K4 and K27 are lysine amino acids at the respective positions within the H3 protein. The gene promoter is the central processing unit of a gene/transcript and is switched on or off by epigenetics. Genomic DNA is shown in blue, RNA in green-yellow.


Which basic technologies are behind this -omics?


DNA methylation is usually assessed by a variation of Next Generation Sequencing (NGS), bisulfite sequencing. Here methylated Cs are chemically changed so they read as Ts in the subsequent sequencing. Wherever a C in the reference genome is replaced by a T in the sample’s sequence this is where the C was methylated. Histone modifications are more complicated to detect. The method here is called ChIP-Seq, which stands for Chromatine-Immuno-Precipitation Sequencing. Special antibodies recognize ONE histone modification and can be used to pull out the corresponding small chromatin fragment, the DNA of which is then sequenced by NGS. However, each individual form of histone modification requires a ChIP-seq experiment of its own. 


What are the most likely next advances and how would they improve application for personalized medicine?


DNA methylation can already be read directly without bisulfite modification in so-called nanopore sequencing, where bases are called based on characteristic variations on electric resistance as the base slides though the pore. Methylated Cs have a different resistance than non-methylated Cs and can be directly detected. It is fair to expect more technological advances that will allow to read epigenetic changes with the the same effort and efficiency than reading genomic sequences. Once that happens epigenomics will become equally important as genomics if not even a bit more important. 


What’s coming up next?


Next week the field of transcriptomics will be introduced. This is where the actual regulation of transcribing DNA into RNA governed by the genome and the epigenome takes place.