Epigenome

thumb|The function of DNA strands (yellow) alters depending on how it is organized around [[histones (blue) that can be methylated (green).]]

In biology, the epigenome of an organism is the collection of chemical changes to its DNA and histone proteins that affects when, where, and how the DNA is expressed; these changes can be passed down to an organism's offspring via transgenerational epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome. The human epigenome, including DNA methylation and histone modification, is maintained through cell division (both mitosis and meiosis). The epigenome is essential for normal development and cellular differentiation, enabling cells with the same genetic code to perform different functions. The human epigenome is dynamic and can be influenced by environmental factors such as diet, stress, and toxins.

The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome, which remains largely static within an individual, the epigenome can be dynamically altered by environmental conditions.

Types

The main types of epigenetic changes include:

DNA methylation

Addition of a methyl group to the DNA molecule, typically at cytosine bases. This modification generally leads to gene silencing by preventing the binding of transcription factors and other proteins necessary for gene expression.

Individuals differ with their epigenetic profile, for example the variance in CpG methylation among individuals is about 42%. On the contrary, epigenetic profile (including methylation profile) of each individual is constant over the course of a year, reflecting the constancy of our phenotype and metabolic traits. Methylation profile, in particular, is quite stable in a 12-month period and appears to change more over decades.

Methylation sites

CoRSIVs are Correlated Regions of Systemic Interindividual Variation in DNA methylation. They span only 0.1% of the human genome, so they are very rare; they can be inter-correlated over long genomic distances (>50 kbp). CoRSIVs are also associated with genes involved in a lot of human disorders, including tumors, mental disorders and cardiovascular diseases. It has been observed that disease-associated CpG sites are 37% enriched in CoRSIVs compared to control regions and 53% enriched in CoRSIVs relative to tDMRs (tissue specific Differentially Methylated Regions).

Most of the CoRSIVs are only 200 – 300 bp long and include 5–10 CpG dinucleotides, the largest span several kbp and involve hundreds of CpGs. These regions tend to occur in clusters and the two genomic areas of high CoRSIV density are observed at the major histocompatibility (MHC) locus on chromosome 6 and at the pericentromeric region on the long arm of chromosome 20.

Factors affecting methylation pattern

Quantification of the heritable basis underlying population epigenomic variation is also important to delineate its cis- and trans-regulatory architecture. In particular, most studies state that inter-individual differences in DNA methylation are mainly determined by cis-regulatory sequence polymorphisms, probably involving mutations in TFBSs (Transcription Factor Binding Sites) with downstream consequences on local chromatin environment. The sparsity of trans-acting polymorphisms in humans suggests that such effects are highly deleterious. Indeed, trans-acting factors are expected to be caused by mutations in chromatin control genes or other highly pleiotropic regulators. If trans-acting variants do exist in human populations, they probably segregate as rare alleles or originate from somatic mutations and present with clinical phenotypes, as is the case in many cancers.

The percentage of DNA methylation is different in oocytes and in sperm: the mature oocyte has an intermediate level of DNA methylation (72%), instead the sperm has high level of DNA methylation (86%). Demethylation in paternal genome occurs quickly after fertilisation, whereas the maternal genome is quite resistant at the demethylation process at this stage. Maternal different methylated regions (DMRs) are more resistant to the preimplantation demethylation wave.

On the sites of gene regulatory loci bound by transcription factors the random switching between methylated and unmethylated states of DNA was observed. This is also referred as stochastic switching and it is linked to selective buffering of gene regulatory circuit against mutations and genetic diseases. Only rare genetic variants show the stochastic type of gene regulation.

The study made by Onuchic et al. was aimed to construct the maps of allelic imbalances in DNA methylation, gene transcription, and also of histone modifications. 36 cell and tissue types from 13 participant donors were used to examine 71 epigenomes. The results of WGBS tested on 49 methylomes revealed CpG methylation imbalances exceeding 30% differences in 5% of the loci. The stochastic switching occurred at thousands of heterozygous regulatory loci that were bound to transcription factors. The intermediate methylation state is referred to the relative frequencies between methylated and unmethylated epialleles. The epiallele frequency variations are correlated with the allele affinity for transcription factors.

The analysis of the study suggests that human epigenome in average covers approximately 200 adverse SD-ASM variants. The sensitivity of the genes with tissue-specific expression patterns gives the opportunity for the evolutionary innovation in gene regulation.

Histone modification

Post-translational modifications of histone proteins, which include methylation, acetylation, phosphorylation, ubiquitination, and sumoylation. These modifications can either activate or repress gene expression by altering chromatin structure and accessibility of the DNA to transcriptional machinery.

The epigenetic profiles of human tissues reveals the following distinct histone modifications in different functional areas:

Methylation

Can lead to activation or repression of gene expression depending on the specific amino acids that are methylated.

Non-coding RNA gene silencing

Non-coding RNA (ncRNA) gene silencing involves various types of non-coding RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and small interfering RNAs (siRNAs). These RNA molecules can modulate gene expression by various mechanisms, including mRNA degradation, inhibition of translation, and chromatin remodeling.

The structural modifications that these projects aim to study can be divided into five main groups:

Nucleosome occupancy to detect regions with regulatory genes;
Chromatin interactions and domains;

Topological domains in humans, like in other mammalians, have many functions regarding gene expression and transcriptional control process. Inside these domains, the chromatin shows to be well tangled, while in the boundary regions chromatin interactions are far less present. These boundary areas in particular show some peculiarity that determine the functions of all the topological domains.

Firstly, they contain insulator regions and barrier elements, both of which function as inhibitors of further transcription from the RNA polymerase enzyme. Such elements are characterized by the massive presence of insulator binding proteins CTCF.

Secondly, boundary regions block heterochromatin spreading, thus preventing the loss of useful genetic informations. This information derives from the observation that the heterochromatin mark H3K9me3 sequences clearly interrupts near boundary sequences.

Thirdly, transcription start sites (TSS), housekeeping genes and tRNA genes are particularly abundant in boundary regions, denoting that those areas have a prolific transcriptional activity, thanks to their structural characteristics, different from other topological regions.

Finally, in the border areas of the topological domains and their surroundings there is an enrichment of Alu/B1 and B2 SINE retrotransposons. In the recent years, those sequences were referred to alter binding site of CTCF, thus interfering with expression of some genomic areas.

Further proofs towards a role in genetic modulation and transcription regulation refers to the great conservation of the boundary pattern across mammalian evolution, with a dynamic range of small diversities inside different cell types, suggesting that these topological domains take part in cell-type specific regulatory events. is an experimental method used to map the connections between DNA fragments in three-dimensional space on a genome-wide scale. This technique combines chemical crosslinking of chromatin with restriction enzyme digestion and next-generation DNA sequencing.

This kind of studies are currently limited by the lack or unavailability of raw data. In recent decades, evidence has accumulated supporting the additional idea that DNA damage and repair elicit widespread epigenome alterations that also contribute to aging (e.g.). Such epigenome changes include age-related changes in the patterns of DNA methylation and histone modification. Advances in sequencing technology now allow for assaying genome-wide epigenomic states by multiple molecular methodologies. Micro- and nanoscale devices have been constructed or proposed to investigate the epigenome.

An international effort to assay reference epigenomes commenced in 2010 in the form of the International Human Epigenome Consortium (IHEC). IHEC members aim to generate at least 1,000 reference (baseline) human epigenomes from different types of normal and disease-related human cell types.

Roadmap epigenomics project

One goal of the NIH Roadmap Epigenomics Project is to generate human reference epigenomes from normal, healthy individuals across a large variety of cell lines, primary cells, and primary tissues. Data produced by the project, which can be browsed and downloaded from the Human Epigenome Atlas, fall into five types that assay different aspects of the epigenome and outcomes of epigenomic states (such as gene expression):

Histone Modifications – Chromatin Immunoprecipitation Sequencing (ChIP-Seq) identifies genome wide patterns of histone modifications using antibodies against the modifications.
DNA Methylation – Whole Genome Bisulfite-Seq, Reduced Representation Bisulfite-Seq (RRBS), Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq), and Methylation-sensitive Restriction Enzyme Sequencing (MRE-Seq) identify DNA methylation across portions of the genome at varying levels of resolution down to basepair level.
Chromatin Accessibility – DNase I hypersensitive sites Sequencing (DNase-Seq) uses the DNase I enzyme to find open or accessible regions in the genome.
Gene Expression – RNA-Seq and expression arrays identify expression levels or protein coding genes.
Small RNA Expression – smRNA-Seq identifies expression of small noncoding RNA, primarily miRNAs.

Reference epigenomes for healthy individuals will enable the second goal of the Roadmap Epigenomics Project, which is to examine epigenomic differences that occur in disease states such as Alzheimer's disease.