A cross-platform genome-wide comparison of the relationship of promoter DNA methylation to gene expression.

Frontiers in Genetics
Jeffrey M PlumeRobert A Philibert

Abstract

Peripheral mononuclear cell preparations are commonly used as proxies for other tissues in studies of the role of gene expression and methylation in human disease. Whether changes in peripheral DNA methylation are associated with changes in peripheral blood or brain gene expression is not clear. In order to test the former hypothesis and determine which genome-wide methylation platform was most suitable for our studies of peripheral blood cells, we compared the results from two commercially available genome-wide methylation arrays with respect to genome-wide gene expression using lymphoblast DNA and RNA from eight individuals at the promoters of 5619 genes. We found that methylation signatures at these gene promoters were significantly correlated with one another across platforms and with genome-wide gene expression, but the extent of that relationship is dependent on choice of platform and degree of methylation. Taken in context with data from other studies, these data demonstrate that peripheral blood cell methylation is associated with gene expression and that further studies to clarify the extent of this relationship, and the relationship between central and peripheral DNA methylation are in order.

Citations

Jun 26, 2014·PloS One·Carrie V BretonUNKNOWN Asthma BRIDGE consortium
Oct 21, 2016·Molecular Psychiatry·B Ludwig, Y Dwivedi
Mar 2, 2013·The International Journal of Neuropsychopharmacology·Márcio Gerhardt Soeiro-de-SouzaRicardo Alberto Moreno
Oct 23, 2020·BMC Medical Genomics·Mai ShiYingying Wei

❮ Previous
Next ❯

Methods Mentioned

BETA
immunoprecipitation
methylation sequencing
affinity purification

Software Mentioned

Affymetrix
SPSS
Partek Genomic Suite
SAS
GenomeStudio
NimbleGen

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.