Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells

Yasuto Araki, Zhibin Wang, Chongzhi Zang, William H. Wood, Dustin Schones, Kairong Cui, Tae Young Roh, Brad Lhotsky, Robert P. Wersto, Weiqun Peng, Kevin G. Becker, Keji Zhao, Nan ping Weng

Research output: Contribution to journalArticle

Abstract

Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription is important, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naive and memory CD8+ T cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed four distinct modes (repressive, active, poised, and bivalent), reflecting different functions of these genes in CD8+ T cells. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8+ T cell function.

Original languageEnglish (US)
Pages (from-to)912-925
Number of pages14
JournalImmunity
Volume30
Issue number6
DOIs
StatePublished - Jun 19 2009
Externally publishedYes

Fingerprint

Histones
Methylation
Chromatin
Genome
T-Lymphocytes
Genes
Histone Code
Gene Expression
Aptitude
Transcriptome
Lysine
Lymphocytes
Antigens

Keywords

  • MOLIMMUNO
  • SYSBIO

ASJC Scopus subject areas

  • Immunology and Allergy
  • Infectious Diseases
  • Immunology

Cite this

Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells. / Araki, Yasuto; Wang, Zhibin; Zang, Chongzhi; Wood, William H.; Schones, Dustin; Cui, Kairong; Roh, Tae Young; Lhotsky, Brad; Wersto, Robert P.; Peng, Weiqun; Becker, Kevin G.; Zhao, Keji; Weng, Nan ping.

In: Immunity, Vol. 30, No. 6, 19.06.2009, p. 912-925.

Research output: Contribution to journalArticle

Araki, Y, Wang, Z, Zang, C, Wood, WH, Schones, D, Cui, K, Roh, TY, Lhotsky, B, Wersto, RP, Peng, W, Becker, KG, Zhao, K & Weng, NP 2009, 'Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells', Immunity, vol. 30, no. 6, pp. 912-925. https://doi.org/10.1016/j.immuni.2009.05.006
Araki, Yasuto ; Wang, Zhibin ; Zang, Chongzhi ; Wood, William H. ; Schones, Dustin ; Cui, Kairong ; Roh, Tae Young ; Lhotsky, Brad ; Wersto, Robert P. ; Peng, Weiqun ; Becker, Kevin G. ; Zhao, Keji ; Weng, Nan ping. / Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells. In: Immunity. 2009 ; Vol. 30, No. 6. pp. 912-925.
@article{ad74a110621b47a29323ec7e0c2b7768,
title = "Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells",
abstract = "Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription is important, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naive and memory CD8+ T cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed four distinct modes (repressive, active, poised, and bivalent), reflecting different functions of these genes in CD8+ T cells. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8+ T cell function.",
keywords = "MOLIMMUNO, SYSBIO",
author = "Yasuto Araki and Zhibin Wang and Chongzhi Zang and Wood, {William H.} and Dustin Schones and Kairong Cui and Roh, {Tae Young} and Brad Lhotsky and Wersto, {Robert P.} and Weiqun Peng and Becker, {Kevin G.} and Keji Zhao and Weng, {Nan ping}",
year = "2009",
month = "6",
day = "19",
doi = "10.1016/j.immuni.2009.05.006",
language = "English (US)",
volume = "30",
pages = "912--925",
journal = "Immunity",
issn = "1074-7613",
publisher = "Cell Press",
number = "6",

}

TY - JOUR

T1 - Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells

AU - Araki, Yasuto

AU - Wang, Zhibin

AU - Zang, Chongzhi

AU - Wood, William H.

AU - Schones, Dustin

AU - Cui, Kairong

AU - Roh, Tae Young

AU - Lhotsky, Brad

AU - Wersto, Robert P.

AU - Peng, Weiqun

AU - Becker, Kevin G.

AU - Zhao, Keji

AU - Weng, Nan ping

PY - 2009/6/19

Y1 - 2009/6/19

N2 - Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription is important, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naive and memory CD8+ T cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed four distinct modes (repressive, active, poised, and bivalent), reflecting different functions of these genes in CD8+ T cells. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8+ T cell function.

AB - Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription is important, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naive and memory CD8+ T cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed four distinct modes (repressive, active, poised, and bivalent), reflecting different functions of these genes in CD8+ T cells. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8+ T cell function.

KW - MOLIMMUNO

KW - SYSBIO

UR - http://www.scopus.com/inward/record.url?scp=67349169780&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67349169780&partnerID=8YFLogxK

U2 - 10.1016/j.immuni.2009.05.006

DO - 10.1016/j.immuni.2009.05.006

M3 - Article

C2 - 19523850

AN - SCOPUS:67349169780

VL - 30

SP - 912

EP - 925

JO - Immunity

JF - Immunity

SN - 1074-7613

IS - 6

ER -