Practical guidelines and consideration of using RRHP for 5hmC detection

Epigenomics
Xueguang SunAngela Kim

Abstract

5-hydroxymethylcytosine (5hmC) is an epigenetic modification, which has been associated with gene expression in many biological contexts. Reduced representation hydroxymethylation profiling was developed as an enzymatic-based method for genome-wide 5hmC detection. It exploits β-glucosyltransferase to inhibit enzymatic cleavage of adapters ligated to a genomic library, allowing only fragments with glucosylated 5hmC residues at adapter junctions to be amplified and sequenced. The simple workflow and high sensitivity make it an efficient assay for 5hmC mapping. In this review, we discuss some technical consideration in applying reduced representation hydroxymethylation profiling, such as the use of alternative restriction enzymes for increased genomic coverage in different species, application of control libraries and specifications for multiplexing, data processing and normalization.

References

May 26, 1976·Journal of Molecular Evolution·R M Kothari, V Shankar
Feb 1, 1972·The Biochemical Journal·N W PennR Yura
Dec 20, 1952·Nature·G R WYATT, S S COHEN
Apr 18, 2009·Science·Skirmantas Kriaucionis, Nathaniel Heintz
May 10, 2011·Nature·William A PastorAnjana Rao
Jul 21, 2011·Journal of Nucleic Acids·Weiwei Li, Min Liu
Jan 28, 2012·Nature Protocols·Adam B RobertsonArne Klungland
May 31, 2014·Nucleic Acids Research·Chunlei JinJean-Pierre J Issa
Dec 6, 2014·Mutation Research. Reviews in Mutation Research·Jingyu WangHonghe Zhang
Jul 18, 2015·Epigenetics : Official Journal of the DNA Methylation Society·Christian GrosserBernhard Horsthemke

❮ Previous
Next ❯

Citations

Mar 24, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Ying QingJiajie Diao
Jan 30, 2020·Journal of Cellular Physiology·Ling MaYinghui Huang
Apr 9, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Ioannis KonstantinidisJorge M O Fernandes
Jun 9, 2021·Nature Communications·Sarah MoyonPatrizia Casaccia

❮ Previous
Next ❯

Methods Mentioned

BETA
hydroxymethylation profiling
RRBS
glucosylation
PCR

Software Mentioned

Ion PGM

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.