DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform

DNA modifications are small covalent chemical groups that modify nucleotides to regulate DNA readout. Anomalous abundance and genome-wide localization of these modifications can negatively tune gene expression and propagate into unbalanced epigenetics regulation, which is known to be associated with...

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Autores principales:	Yan Sun, Stephanie Stransky, Jennifer Aguilan, Michael Brenowitz, Simone Sidoli
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Direct injection mass spectrometry (DI-MS) Science Q
Acceso en línea:	https://doaj.org/article/16d6779d59b84a6590e5787db987fe67
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spelling	oai:doaj.org-article:16d6779d59b84a6590e5787db987fe672021-11-22T04:26:09ZDNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform2215-016110.1016/j.mex.2021.101585https://doaj.org/article/16d6779d59b84a6590e5787db987fe672021-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2215016121003757https://doaj.org/toc/2215-0161DNA modifications are small covalent chemical groups that modify nucleotides to regulate DNA readout. Anomalous abundance and genome-wide localization of these modifications can negatively tune gene expression and propagate into unbalanced epigenetics regulation, which is known to be associated with multiple conditions such as cancer, diabetes and aging. We present a direct injection mass spectrometry (DI-MS) platform that offers fast, accurate and precise quantitation of global levels of DNA cytidine methylation (mC) and hydroxymethylation (hmC) in less than one minute per sample. On the contrary to most methods adopting mass spectrometry for the analysis of nucleotide modifications, in this DI-MS approach we eliminate the use of liquid chromatography, increasing throughput, eliminating issues of carryover and batch effects caused by column contamination across samples. In addition, potential biases in detection efficiency of modified nucleotides with different binding efficiency to stationary phases is eliminated, as no chromatographic separation is adopted. This method can analyze >1000 samples per day, overcoming the throughput of next-generation sequencing. • Direct injection mass spectrometry improves throughput and precision compared to liquid chromatography. • Direct injection can be used to quantify in less than one minute global levels of DNA methylation and hydroxymethylation. • The unbiased acquisition can be potentially utilized to analyze other nucleotide modifications.Yan SunStephanie StranskyJennifer AguilanMichael BrenowitzSimone SidoliElsevierarticleDirect injection mass spectrometry (DI-MS)ScienceQENMethodsX, Vol 8, Iss , Pp 101585- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Direct injection mass spectrometry (DI-MS) Science Q
spellingShingle	Direct injection mass spectrometry (DI-MS) Science Q Yan Sun Stephanie Stransky Jennifer Aguilan Michael Brenowitz Simone Sidoli DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
description	DNA modifications are small covalent chemical groups that modify nucleotides to regulate DNA readout. Anomalous abundance and genome-wide localization of these modifications can negatively tune gene expression and propagate into unbalanced epigenetics regulation, which is known to be associated with multiple conditions such as cancer, diabetes and aging. We present a direct injection mass spectrometry (DI-MS) platform that offers fast, accurate and precise quantitation of global levels of DNA cytidine methylation (mC) and hydroxymethylation (hmC) in less than one minute per sample. On the contrary to most methods adopting mass spectrometry for the analysis of nucleotide modifications, in this DI-MS approach we eliminate the use of liquid chromatography, increasing throughput, eliminating issues of carryover and batch effects caused by column contamination across samples. In addition, potential biases in detection efficiency of modified nucleotides with different binding efficiency to stationary phases is eliminated, as no chromatographic separation is adopted. This method can analyze >1000 samples per day, overcoming the throughput of next-generation sequencing. • Direct injection mass spectrometry improves throughput and precision compared to liquid chromatography. • Direct injection can be used to quantify in less than one minute global levels of DNA methylation and hydroxymethylation. • The unbiased acquisition can be potentially utilized to analyze other nucleotide modifications.
format	article
author	Yan Sun Stephanie Stransky Jennifer Aguilan Michael Brenowitz Simone Sidoli
author_facet	Yan Sun Stephanie Stransky Jennifer Aguilan Michael Brenowitz Simone Sidoli
author_sort	Yan Sun
title	DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
title_short	DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
title_full	DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
title_fullStr	DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
title_full_unstemmed	DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
title_sort	dna methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/16d6779d59b84a6590e5787db987fe67
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_version_	1718418207441682432

DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform

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