Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation

Natarajan V. Bhanu, Simone Sidoli, Benjamin A. Garcia

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

In this study, we trace developmental stages using epigenome changes in human embryonic stem cells (hESCs) treated with drugs modulating either self-renewal or differentiation. Based on microscopy, qPCR and flow cytometry, we classified the treatment outcome as inducing pluripotency (hESC, flurbiprofen and gatifloxacin), mesendoderm (sinomenine), differentiation (cyamarin, digoxin, digitoxin, selegeline and theanine) and lineage-commitment (RA). When we analyzed histone PTMs that imprinted these gene and protein expressions, the above classification was reassorted. Hyperacetylation at H3K4, 9, 14, 18, 56 and 122 as well as H4K5, 8, 12 and 16 emerged as the pluripotency signature of hESCs. Methylations especially of H3 at K9, K20, K27 and K36 characterized differentiation initiation as seen in no-drug control and fluribiprofen. Sinomenine-treated cells clustered close to "differentiation initiators", consistent with flow cytometry where it induced mesendoderm, along with cyamarin and possibly selegnine. Neurectoderm, induced by RA and theanine manifested methylations on H3 shifts to H3.3. By both flow cytometry and histone PTM clustering, it appears that cells treated with gatifloxacin, flurbiprofen, digitoxin and digoxin were not yet lineage-committed or mixed cell types. Taken together, our moderate-throughput histone PTM profiling approach highlighted subtle epigenetic signatures that permitted us to predict divergent lineage progression even in differentiating cells with similar phenotype and gene expression.

Original languageEnglish (US)
Pages (from-to)448-458
Number of pages11
JournalProteomics
Volume16
Issue number3
DOIs
StatePublished - Feb 1 2016
Externally publishedYes

Fingerprint

Histone Code
Pulse time modulation
Flow cytometry
Stem cells
Histones
Digitoxin
Flurbiprofen
Methylation
Digoxin
Flow Cytometry
Gene Expression
Gene expression
Pharmaceutical Preparations
Drug and Narcotic Control
Microscopic examination
Cells
Throughput
Epigenomics
Cluster Analysis
Microscopy

Keywords

  • Differentiation
  • Embryonic stem cells
  • Histones
  • Mass spectrometry
  • Self-renewal
  • Systems biology

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation. / Bhanu, Natarajan V.; Sidoli, Simone; Garcia, Benjamin A.

In: Proteomics, Vol. 16, No. 3, 01.02.2016, p. 448-458.

Research output: Contribution to journalArticle

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