Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate

A possible solution strategy

Yukihiro Furusawa, Takaho A. Endo, Yuuki Obata, Osamu Ohara, Hiroshi Ohno, Kouji Hase

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Regulatory T cells (Treg) play a central role in the suppression of inflammatory and allergic responses. Colonization of certain gut commensal microbes such as Clostridia class IV and XIVa in the gut can induce development of colonic Treg cells contributing to the maintenance of gut immune homeostasis. Clostridia-derived butyrate promotes the differentiation of naïve T cells into Treg cells through upregulation of Foxp3, the master transcription factor of Treg cells. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that treatment of naïve T cells with butyrate induces Treg-polarizing conditions by enhanced histone H3 acetylation in the promoter and conserved non-coding sequence regions of the Foxp3 locus. In general, global normalization was utilized for ChIP-seq analysis to compare the data obtained from two or more samples. However, global normalization is not appropriate for the evaluation of ChIP-seq data when treatment can affect the total amount of target protein. Here, we introduce a unique normalization method for ChIP-seq analysis in cells treated with butyrate, a pan-HDAC inhibitor that is likely to affect total acetylation levels of histone H3.

Original languageEnglish
Pages (from-to)176-180
Number of pages5
JournalGenomics Data
Volume2
DOIs
Publication statusPublished - 2014

Fingerprint

T-cells
Butyrates
Chromatin Immunoprecipitation
Regulatory T-Lymphocytes
Chromatin
T-Lymphocytes
Acetylation
Clostridium
Histones
Histone Deacetylase Inhibitors
Homeostasis
Transcription Factors
Up-Regulation
Maintenance
Proteins

Keywords

  • Butyrate
  • ChIP-seq
  • HDAC
  • Microarray
  • Normalization
  • Regulatory T cells

ASJC Scopus subject areas

  • Molecular Medicine
  • Biochemistry
  • Biotechnology
  • Genetics

Cite this

Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate : A possible solution strategy. / Furusawa, Yukihiro; Endo, Takaho A.; Obata, Yuuki; Ohara, Osamu; Ohno, Hiroshi; Hase, Kouji.

In: Genomics Data, Vol. 2, 2014, p. 176-180.

Research output: Contribution to journalArticle

Furusawa, Yukihiro ; Endo, Takaho A. ; Obata, Yuuki ; Ohara, Osamu ; Ohno, Hiroshi ; Hase, Kouji. / Pitfalls in global normalization of ChIP-seq data in CD4+ T cells treated with butyrate : A possible solution strategy. In: Genomics Data. 2014 ; Vol. 2. pp. 176-180.
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