Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles

Sang Yun Yeom, Choong Hyun Son, Byung Sun Kim, Sung Hyun Tag, Eunjoo Nam, Hyogeun Shin, So Hyun Kim, Haemin Gang, Hyunjoo J. Lee, Jungkyu Choi, Heh In Im, Il Joo Cho, Nakwon Choi

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Epigenetic alterations in gene expression are influenced by experiences and environment, resulting in significant variation of epigenetic markers from individual to individual. Therefore, it is imperative to measure various epigenetic markers simultaneously from samples of individual subjects to accurately analyze the epigenetic markers in biological samples. Moreover, the individualized genome-wide analysis has become a critical technology for recent trends in clinical applications such as early diagnosis and personalized medicine screening of numerous diseases. The array-based detection of modified histones, conventionally used for multiplexed analysis of epigenetic changes, requires pooling of samples from many subjects to analyze population-wise differences in the expression of histone markers and does not permit individualized analysis. Here, we report multiplexed detection of genome-wide changes in various histone modifications at a single-residue resolution using quantum dot (QD)-encoded polyethylene glycol diacrylate (PEGDA) hydrogel microparticles. To demonstrate the potential of our methodology, we present the simultaneous detection of (1) acetylation of lysine 9 of histone 3 (Ac-H3K9), (2) dimethylation of H3K9 (2Me-H3K9), and (3) trimethylation of H3K9 (3Me-H3K9) from three distinct regions in the brain [nucleus accumbens (NAc), dorsal striatum (DSt), and cerebellum (Cbl)] of cocaine-exposed mice. Our hydrogel-based epigenetic assay enabled relative quantification of the three histone variants from only 10 μL of each brain lysate (protein content = ∼ 1 μg/μL) per mouse. We verified that the exposure to cocaine induced a significant increase of acetylation while a notable decrease in methylation in NAc.

Original languageEnglish
Pages (from-to)4259-4268
Number of pages10
JournalAnalytical Chemistry
Volume88
Issue number8
DOIs
Publication statusPublished - 2016 May 3

Fingerprint

Hydrogel
Histones
Semiconductor quantum dots
Acetylation
Cocaine
Brain
Genes
Methylation
Gene expression
Lysine
Medicine
Assays
Screening
Proteins

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Yeom, S. Y., Son, C. H., Kim, B. S., Tag, S. H., Nam, E., Shin, H., ... Choi, N. (2016). Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles. Analytical Chemistry, 88(8), 4259-4268. https://doi.org/10.1021/acs.analchem.5b04190

Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles. / Yeom, Sang Yun; Son, Choong Hyun; Kim, Byung Sun; Tag, Sung Hyun; Nam, Eunjoo; Shin, Hyogeun; Kim, So Hyun; Gang, Haemin; Lee, Hyunjoo J.; Choi, Jungkyu; Im, Heh In; Cho, Il Joo; Choi, Nakwon.

In: Analytical Chemistry, Vol. 88, No. 8, 03.05.2016, p. 4259-4268.

Research output: Contribution to journalArticle

Yeom, SY, Son, CH, Kim, BS, Tag, SH, Nam, E, Shin, H, Kim, SH, Gang, H, Lee, HJ, Choi, J, Im, HI, Cho, IJ & Choi, N 2016, 'Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles', Analytical Chemistry, vol. 88, no. 8, pp. 4259-4268. https://doi.org/10.1021/acs.analchem.5b04190
Yeom, Sang Yun ; Son, Choong Hyun ; Kim, Byung Sun ; Tag, Sung Hyun ; Nam, Eunjoo ; Shin, Hyogeun ; Kim, So Hyun ; Gang, Haemin ; Lee, Hyunjoo J. ; Choi, Jungkyu ; Im, Heh In ; Cho, Il Joo ; Choi, Nakwon. / Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles. In: Analytical Chemistry. 2016 ; Vol. 88, No. 8. pp. 4259-4268.
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