Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications

Molecular Genetics and Genomics : MGG
Thang T PhamJeremiah W Hanes

Abstract

A gene-level targeted enrichment method for direct detection of epigenetic modifications is described. The approach is demonstrated on the CGG-repeat region of the FMR1 gene, for which large repeat expansions, hitherto refractory to sequencing, are known to cause fragile X syndrome. In addition to achieving a single-locus enrichment of nearly 700,000-fold, the elimination of all amplification steps removes PCR-induced bias in the repeat count and preserves the native epigenetic modifications of the DNA. In conjunction with the single-molecule real-time sequencing approach, this enrichment method enables direct readout of the methylation status and the CGG repeat number of the FMR1 allele(s) for a clonally derived cell line. The current method avoids potential biases introduced through chemical modification and/or amplification methods for indirect detection of CpG methylation events.

References

Jan 13, 2000·American Journal of Human Genetics·F TassoneP J Hagerman
Nov 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Clyde A HutchisonJ Craig Venter
Jan 24, 2007·Lancet·Francis O Walker
Jun 22, 2007·Nature·Sergei M Mirkin
Oct 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Murim ChoiRichard P Lifton
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner
May 11, 2010·Nature Methods·Benjamin A FlusbergStephen W Turner
Jun 24, 2010·Nucleic Acids Research·Kevin J TraversStephen W Turner
Sep 23, 2010·Molecular Autism·Randi HagermanPaul Hagerman
May 10, 2011·Brain Research Reviews·Daniele Marmolino
May 18, 2011·Genes & Development·Aimée M Deaton, Adrian Bird
Jul 13, 2011·Journal of Neurology·Anne Gallagher, Brian Hallahan
Sep 22, 2012·Lancet Neurology·Bjarne Udd, Ralf Krahe
Oct 5, 2012·Nucleic Acids Research·Iain A MurrayRichard J Roberts
Oct 16, 2012·Genome Research·Erick W LoomisPaul J Hagerman
Oct 25, 2012·Current Opinion in Chemical Biology·Ye Fu, Chuan He
Mar 12, 2013·Neuron·David L NelsonStephen T Warren
Mar 19, 2013·Current Opinion in Cell Biology·Li Shen, Yi Zhang
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Jul 6, 2013·Science·Ryan ListerJoseph R Ecker
Aug 13, 2013·Trends in Biochemical Sciences·Chun-Xiao Song, Chuan He
Aug 21, 2013·Trends in Molecular Medicine·Marguerite V Evans-GaleaRichard Saffery

❮ Previous
Next ❯

Citations

May 28, 2019·Frontiers in Genetics·Tuomo MantereAlexander Hoischen
Aug 1, 2020·Progress in Retinal and Eye Research·Michael P FautschAlice E Davidson

❮ Previous
Next ❯

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.