The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis

Jihye Han, Sin Gi Park, Jae Bum Bae, Jung Kyoon Choi, Jae Myun Lyu, Sung Hee Park, Hei Sung Kim, Young-Joon Kim, Sangsoo Kim, Tae Yoon Kim

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Psoriasis and atopic dermatitis (AD) are skin diseases that are characterized by polarized CD4+ T cell responses. During the polarization of naïve CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. In this study, we profiled the genome-wide DNA methylation status of naïve CD4+ T cells in patients with psoriasis or AD and healthy controls using a ChIP-seq method. Only psoriasis patient T cells, not those of AD patients, showed distinct hypomethylation (>4-fold) compared to healthy control T cells in twenty-six regions of the genome ranging in size from 10 to 70. kb. These regions were mostly pericentromeric on 10 different chromosomes and incidentally coincided with various strong epigenomic signals, such as histone modifications and transcription factor binding sites, that had been observed in the ENCODE project implying the potential epigenetic regulation in psoriasis development. The gene-centric analysis indicated that the promoter regions of 121 genes on the X chromosome had dramatically elevated methylation levels in psoriasis patient T-cells compared to those from healthy controls (>4-fold). Moreover, immune-related genes on the X chromosome had higher hypermethylation than other genes (P= 0.046). No such patterns were observed with AD patient T cells. These findings imply that methylation changes in naïve CD4+ T cells may affect CD4+ T cell polarization, especially in the pathogenesis of psoriasis.

Original languageEnglish
Pages (from-to)157-163
Number of pages7
JournalBiochemical and Biophysical Research Communications
Volume422
Issue number1
DOIs
Publication statusPublished - 2012 May 25

Fingerprint

T-cells
DNA Methylation
Atopic Dermatitis
Psoriasis
Genes
Genome
T-Lymphocytes
Chromosomes
X-Linked Genes
Methylation
Epigenomics
Histone Code
Polarization
Chromosomes, Human, Pair 10
Transcription
Skin Diseases
Genetic Promoter Regions
Histones
Skin
Transcription Factors

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Han, Jihye ; Park, Sin Gi ; Bae, Jae Bum ; Choi, Jung Kyoon ; Lyu, Jae Myun ; Park, Sung Hee ; Kim, Hei Sung ; Kim, Young-Joon ; Kim, Sangsoo ; Kim, Tae Yoon. / The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis. In: Biochemical and Biophysical Research Communications. 2012 ; Vol. 422, No. 1. pp. 157-163.
@article{2a9a8a730bd44ff8ab5ed124062edef0,
title = "The characteristics of genome-wide DNA methylation in na{\"i}ve CD4+ T cells of patients with psoriasis or atopic dermatitis",
abstract = "Psoriasis and atopic dermatitis (AD) are skin diseases that are characterized by polarized CD4+ T cell responses. During the polarization of na{\"i}ve CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. In this study, we profiled the genome-wide DNA methylation status of na{\"i}ve CD4+ T cells in patients with psoriasis or AD and healthy controls using a ChIP-seq method. Only psoriasis patient T cells, not those of AD patients, showed distinct hypomethylation (>4-fold) compared to healthy control T cells in twenty-six regions of the genome ranging in size from 10 to 70. kb. These regions were mostly pericentromeric on 10 different chromosomes and incidentally coincided with various strong epigenomic signals, such as histone modifications and transcription factor binding sites, that had been observed in the ENCODE project implying the potential epigenetic regulation in psoriasis development. The gene-centric analysis indicated that the promoter regions of 121 genes on the X chromosome had dramatically elevated methylation levels in psoriasis patient T-cells compared to those from healthy controls (>4-fold). Moreover, immune-related genes on the X chromosome had higher hypermethylation than other genes (P= 0.046). No such patterns were observed with AD patient T cells. These findings imply that methylation changes in na{\"i}ve CD4+ T cells may affect CD4+ T cell polarization, especially in the pathogenesis of psoriasis.",
author = "Jihye Han and Park, {Sin Gi} and Bae, {Jae Bum} and Choi, {Jung Kyoon} and Lyu, {Jae Myun} and Park, {Sung Hee} and Kim, {Hei Sung} and Young-Joon Kim and Sangsoo Kim and Kim, {Tae Yoon}",
year = "2012",
month = "5",
day = "25",
doi = "10.1016/j.bbrc.2012.04.128",
language = "English",
volume = "422",
pages = "157--163",
journal = "Biochemical and Biophysical Research Communications",
issn = "0006-291X",
publisher = "Academic Press Inc.",
number = "1",

}

The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis. / Han, Jihye; Park, Sin Gi; Bae, Jae Bum; Choi, Jung Kyoon; Lyu, Jae Myun; Park, Sung Hee; Kim, Hei Sung; Kim, Young-Joon; Kim, Sangsoo; Kim, Tae Yoon.

In: Biochemical and Biophysical Research Communications, Vol. 422, No. 1, 25.05.2012, p. 157-163.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis

AU - Han, Jihye

AU - Park, Sin Gi

AU - Bae, Jae Bum

AU - Choi, Jung Kyoon

AU - Lyu, Jae Myun

AU - Park, Sung Hee

AU - Kim, Hei Sung

AU - Kim, Young-Joon

AU - Kim, Sangsoo

AU - Kim, Tae Yoon

PY - 2012/5/25

Y1 - 2012/5/25

N2 - Psoriasis and atopic dermatitis (AD) are skin diseases that are characterized by polarized CD4+ T cell responses. During the polarization of naïve CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. In this study, we profiled the genome-wide DNA methylation status of naïve CD4+ T cells in patients with psoriasis or AD and healthy controls using a ChIP-seq method. Only psoriasis patient T cells, not those of AD patients, showed distinct hypomethylation (>4-fold) compared to healthy control T cells in twenty-six regions of the genome ranging in size from 10 to 70. kb. These regions were mostly pericentromeric on 10 different chromosomes and incidentally coincided with various strong epigenomic signals, such as histone modifications and transcription factor binding sites, that had been observed in the ENCODE project implying the potential epigenetic regulation in psoriasis development. The gene-centric analysis indicated that the promoter regions of 121 genes on the X chromosome had dramatically elevated methylation levels in psoriasis patient T-cells compared to those from healthy controls (>4-fold). Moreover, immune-related genes on the X chromosome had higher hypermethylation than other genes (P= 0.046). No such patterns were observed with AD patient T cells. These findings imply that methylation changes in naïve CD4+ T cells may affect CD4+ T cell polarization, especially in the pathogenesis of psoriasis.

AB - Psoriasis and atopic dermatitis (AD) are skin diseases that are characterized by polarized CD4+ T cell responses. During the polarization of naïve CD4+ T cells, DNA methylation plays an important role in the regulation of gene transcription. In this study, we profiled the genome-wide DNA methylation status of naïve CD4+ T cells in patients with psoriasis or AD and healthy controls using a ChIP-seq method. Only psoriasis patient T cells, not those of AD patients, showed distinct hypomethylation (>4-fold) compared to healthy control T cells in twenty-six regions of the genome ranging in size from 10 to 70. kb. These regions were mostly pericentromeric on 10 different chromosomes and incidentally coincided with various strong epigenomic signals, such as histone modifications and transcription factor binding sites, that had been observed in the ENCODE project implying the potential epigenetic regulation in psoriasis development. The gene-centric analysis indicated that the promoter regions of 121 genes on the X chromosome had dramatically elevated methylation levels in psoriasis patient T-cells compared to those from healthy controls (>4-fold). Moreover, immune-related genes on the X chromosome had higher hypermethylation than other genes (P= 0.046). No such patterns were observed with AD patient T cells. These findings imply that methylation changes in naïve CD4+ T cells may affect CD4+ T cell polarization, especially in the pathogenesis of psoriasis.

UR - http://www.scopus.com/inward/record.url?scp=84861454178&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84861454178&partnerID=8YFLogxK

U2 - 10.1016/j.bbrc.2012.04.128

DO - 10.1016/j.bbrc.2012.04.128

M3 - Article

VL - 422

SP - 157

EP - 163

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

SN - 0006-291X

IS - 1

ER -