At Fios Genomics, we regularly provide various epigenetics analysis services. One of our most popular solutions for epigenetics is gene expression analysis. In fact, this was one of the most popular bioinformatics services we provided in 2021. Therefore, if you are looking to learn about epigenetics, gene expression and bioinformatics, you are in the right place.

Epigenetics Bioinformatics

What is epigenetic analysis?

Epigenetics refers to studying how behavioural and environmental changes affect how genes work. Researchers can get great insight into heritable changes in gene activity due to epigenetic analysis. First, they will generate epigenetic data via technologies such as ChIP-seq, DNA Methylation, ATAC-seq and CLIP-seq.

Once the data has been gathered, this is when epigenetics bioinformatics comes in. A bioinformatics provider can generally provide analyses of these data types. For example, at Fios Genomics, we provide ChIP-seq analysis, CLIP-seq analysis, DNA Methylation analysis as well as ATAC-seq analysis.  Each of these analyses provides epigenetics researchers with different insights; these can be useful for understanding disease mechanisms or for developing therapies targeting the epigenome.

What is ChIP-seq analysis?

ChIP-seq refers to Chromatin immunoprecipitation sequencing. Analysis of ChIP-Seq data can be used for applications such as:

• histone modification assessment,
• DNA-protein interaction analysis,
• transcription factor determination.

What is CLIP-seq analysis?

CLIP-seq refers to Cross-linking immunoprecipitation sequencing. CLIP-seq analysis can locate RNA modification sites on a genome-wide scale; in addition, it can also analyse protein-RNA interaction and binding sites.

What is DNA Methylation Analysis?

DNA Methylation refers to the addition of a methyl group to the cytosine nucleotide in a cytosine-guanine (CpG) dinucleotide pairing.

What is ATAC-seq analysis?

ATAC-seq refers to Assay for Transposase-Accessible Chromatin using sequencing. Analysis of this type of sequencing data investigates genome-wide chromatin changes as well as chromatin-accessibility signatures.

For details of the analysis pipelines we use at Fios Genomics for each of these analysis types, visit our Epigenetics Data Analysis page.

Epigenetics: Gene Expression

What are the three major areas of epigenetics?

The three main types of epigenetics changes are DNA methylation, Histone modifications and changes to non-coding RNA. Each of these changes affects gene expression. This is why gene expression analysis is also a popular service with those conducting epigenetics research.

Epigenetics Gene Expression Analysis

Gene expression analysis provides an overall snapshot of a sample’s transcriptome, giving us an insight into the composition and activity of cells in that sample. Most gene expression data analyses aim to quantify changes in expression between sample groups that differ with respect to a treatment, experimental condition or outcome. Since epigenetics studies how behavioural and environmental changes affect genes, experimental conditions for this type of analysis may focus on certain lifestyle factors such as obesity, alcohol consumption or psychological stress.

What factors affect epigenetics? (What causes changes in gene activity?)

Epigenetics changes occur naturally and can also be influenced by disease or ageing. Additionally, other factors that affect epigenetics are behavioural and environmental. Behavioural factors can include, as mentioned above: obesity, alcohol consumption or psychological stress. Other behavioural factors which can affect epigenetics are diet, smoking tobacco, physical activity and working night shifts. Environmental factors which can cause changes in gene activity include exposure to metals or pollutants such as air pollution or organic pollutants; and diet can also be considered an environmental factor when choice (behaviour) is influenced by what’s available within an environment.

Further Learning

If you would like to learn more about epigenetics, its applications and the benefits of epigenetics bioinformatics, you will find our epigenetics whitepaper particularly useful. Also, if you are curious about what a bioinformatics analysis report for epigenetics looks like, you can request our bioinformatics analysis sample report for epigenetics using the form below. This analysis report evaluates publicly available methylation data from 110 liver samples, comprised of 15 fetal samples and 96 adult samples from organ donors as well as cancer patients. Three statistical comparisons were performed in order to identify differentially methylated features (DMFs) between certain groups within the samples.

Epigenetics, Gene Expression and Bioinformatics

We have provided clients with various bioinformatics services for epigenetics research, such as:

• Methylation analysis (Illumina 450k and 850k arrays and bisulfite sequencing)
• ChIP-seq analysis in order to identify DNA-protein interaction sites.
• Evaluation of methylation levels at baseline against age as a continuous variable, adjusting for disease status
• Metanalysis of disease vs healthy samples using methylation data generated from multiple studies
• Assessing sites of interest in human fibroblast cells following UV exposure and application of treatments.

Are you working on an epigenetics research project?  If you are interested in epigenetics gene expression analysis or another of our bioinformatics solutions for epigenetics research, then please get in touch.  We are always happy to discuss your current or upcoming projects in order to advise on bioinformatics solutions to help answer your research question.

Author: Breige McBride, Content and Social Media Manager, Fios Genomics
Reviewed by Fios Genomics Bioinformatics Experts to ensure accuracy

See also:

Bioinformatics and the Pharmaceutical Industry

Our Data Analysis Process (Video)

Supporting Biomarker Discovery With Bioinformatics