An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells

Mark G. Carter, Carole A. Stagg, Geppino Falco, Toshiyuki Yoshikawa, Uwem C. Bassey, Kazuhiro Aiba, Lioudmila V. Sharova, Nabeebi Shaik, Minoru S.H. Ko

Research output: Contribution to journalArticlepeer-review

69 Citations (Scopus)


We previously reported that Zscan4 showed heterogeneous expression patterns in mouse embryonic stem (ES) cells. To identify genes that show similar expression patterns, we carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. Most of the genes are involved in transcriptional regulation, and were selected using microarray-based comparisons of gene expression profiles in ES and embryonal carcinoma (EC) cells versus differentiated cell types. Pou5f1 (Oct4, Oct3/4) and Krt8 (EndoA) were used as controls. Hybridization signals were detected on ES cell colonies for 147 genes (60%). The majority (136 genes) of them showed relatively homogeneous expression in ES cell colonies. However, we found that two genes unequivocally showed Zscan4-like spotted expression pattern (spot-in-colony pattern; Whsc2 and Rhox9). We also found that nine genes showed relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). Among these genes, Zfp42/Rex1 showed unequivocally heterogeneous expression in individual ES cells prepared by the CytoSpin. These results show the presence of different types or states of cells within ES cell cultures otherwise thought to be undifferentiated and homogeneous, suggesting a previously unappreciated complexity in ES cell cultures.

Original languageEnglish
Pages (from-to)181-198
Number of pages18
JournalGene Expression Patterns
Issue number3
Publication statusPublished - 2008 Feb
Externally publishedYes


  • Atf4
  • Dppa3
  • E2f2
  • EC cells
  • ES cells
  • EndoA
  • Esrrb
  • Fscn1
  • Heterogeneous gene expression
  • Homogeneous gene expression
  • Krt8
  • Nanog
  • Nelfa
  • Oct3/4
  • Oct4
  • Pa2g4
  • Pgc7
  • Pluripotent stem cells
  • Pou5f1
  • Rest
  • Rex1
  • Rhox9
  • Stella
  • Whsc2
  • Zfp42
  • Zscan4

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Developmental Biology


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