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 Ko

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

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
Volume8
Issue number3
DOIs
Publication statusPublished - 2008 Feb
Externally publishedYes

Fingerprint

In Situ Hybridization
Embryonic Stem Cells
Genes
Cell Culture Techniques
Embryonal Carcinoma Stem Cells
Mouse Embryonic Stem Cells
Transcriptome

Keywords

  • Atf4
  • Dppa3
  • E2f2
  • EC cells
  • EndoA
  • ES cells
  • 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

  • Genetics
  • Molecular Biology
  • Cellular and Molecular Neuroscience
  • Developmental Neuroscience

Cite this

An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. / Carter, Mark G.; Stagg, Carole A.; Falco, Geppino; Yoshikawa, Toshiyuki; Bassey, Uwem C.; Aiba, Kazuhiro; Sharova, Lioudmila V.; Shaik, Nabeebi; Ko, Minoru.

In: Gene Expression Patterns, Vol. 8, No. 3, 02.2008, p. 181-198.

Research output: Contribution to journalArticle

Carter, MG, Stagg, CA, Falco, G, Yoshikawa, T, Bassey, UC, Aiba, K, Sharova, LV, Shaik, N & Ko, M 2008, 'An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells', Gene Expression Patterns, vol. 8, no. 3, pp. 181-198. https://doi.org/10.1016/j.gep.2007.10.009
Carter, Mark G. ; Stagg, Carole A. ; Falco, Geppino ; Yoshikawa, Toshiyuki ; Bassey, Uwem C. ; Aiba, Kazuhiro ; Sharova, Lioudmila V. ; Shaik, Nabeebi ; Ko, Minoru. / An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. In: Gene Expression Patterns. 2008 ; Vol. 8, No. 3. pp. 181-198.
@article{eea3695629c945b5acb265bdb09ceb5f,
title = "An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells",
abstract = "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.",
keywords = "Atf4, Dppa3, E2f2, EC cells, EndoA, ES cells, 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",
author = "Carter, {Mark G.} and Stagg, {Carole A.} and Geppino Falco and Toshiyuki Yoshikawa and Bassey, {Uwem C.} and Kazuhiro Aiba and Sharova, {Lioudmila V.} and Nabeebi Shaik and Minoru Ko",
year = "2008",
month = "2",
doi = "10.1016/j.gep.2007.10.009",
language = "English",
volume = "8",
pages = "181--198",
journal = "Gene Expression Patterns",
issn = "1567-133X",
publisher = "Elsevier",
number = "3",

}

TY - JOUR

T1 - An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells

AU - Carter, Mark G.

AU - Stagg, Carole A.

AU - Falco, Geppino

AU - Yoshikawa, Toshiyuki

AU - Bassey, Uwem C.

AU - Aiba, Kazuhiro

AU - Sharova, Lioudmila V.

AU - Shaik, Nabeebi

AU - Ko, Minoru

PY - 2008/2

Y1 - 2008/2

N2 - 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.

AB - 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.

KW - Atf4

KW - Dppa3

KW - E2f2

KW - EC cells

KW - EndoA

KW - ES cells

KW - Esrrb

KW - Fscn1

KW - Heterogeneous gene expression

KW - Homogeneous gene expression

KW - Krt8

KW - Nanog

KW - Nelfa

KW - Oct3/4

KW - Oct4

KW - Pa2g4

KW - Pgc7

KW - Pluripotent stem cells

KW - Pou5f1

KW - Rest

KW - Rex1

KW - Rhox9

KW - Stella

KW - Whsc2

KW - Zfp42

KW - Zscan4

UR - http://www.scopus.com/inward/record.url?scp=38049041930&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38049041930&partnerID=8YFLogxK

U2 - 10.1016/j.gep.2007.10.009

DO - 10.1016/j.gep.2007.10.009

M3 - Article

C2 - 18178135

AN - SCOPUS:38049041930

VL - 8

SP - 181

EP - 198

JO - Gene Expression Patterns

JF - Gene Expression Patterns

SN - 1567-133X

IS - 3

ER -