Distinct epigenetic domains separated by a CTCF bound insulator between the tandem genes, BLU and RASSF1A

Jer Wei Chang, Han Shui Hsu, Huey Juin Ni, Ching Ting Chuang, Chi Hui Hsiung, Hui-ming Huang, Yi Ching Wang

Research output: Contribution to journalArticle

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Abstract

Background: Tumor suppressor gene (TSG) RASSF1A and candidate TSG BLU are two tandem head-to-tail genes located at 3p21.3. We hypothesized that there may be a concordance on their gene expression and promoter methylation status. If not, then there may be an insulator located between RASSF1A and BLU genes that provides a barrier activity. Methodology/Principal Findings: We first identified potential transcriptionally important CpG sites using the methylationspecific oligonucleotide array in relation to mRNA expression of RASSF1A and BLU genes in primary lung tumors. We demonstrated that E2F1 bound to the potential transcriptionally important CpG sites in RASSF1A gene of a normal lung cell line expressing RASSF1A transcripts, whereas loss of E2F1 binding to RASSF1A in A549 cancer cell line was the result of DNA methylation. Both RASSF1A and BLU genes had their own potential transcriptionally important CpG regions. However, there was no correlation of methylation status between RASSF1A and BLU. Using gel shift assay and chromatin immunoprecipitation-PCR (ChIP-PCR), we found that CCCTC-binding factor (CTCF) bound to insulator sequences located between these two genes. Bisulfite sequencing and ChIP-PCR revealed distinct methylation and chromatin boundaries separated by the CTCF binding domains in normal cells, whereas such distinct epigenetic domains were not observed in cancer cells. Note that demethylation reagent and histone deacetylase inhibitor treatments led to CTCF binding and recovery of barrier effect for RASSF1A and BLU genes in cancer cells. Conclusions/Significance: Our study dissects the potential transcriptionally important CpG sites for RASSF1A and BLU genes at the sequence level and demonstrates that CTCF binding to the insulator of BLU gene provides a barrier activity within separate epigenetic domains of the juxtaposed BLU and RASSF1A loci in the 3p21.3 gene cluster region.

Original languageEnglish (US)
Article numbere12847
Pages (from-to)1-13
Number of pages13
JournalPLoS One
Volume5
Issue number9
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

Epigenomics
epigenetics
Genes
genes
Methylation
methylation
chromatin
Chromatin Immunoprecipitation
tumor suppressor genes
Tumor Suppressor Genes
Cells
Chromatin
Tumors
cell lines
Neoplasms
Polymerase Chain Reaction
Lung
Histone Deacetylase Inhibitors
bisulfites
Neoplasm Genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Chang, J. W., Hsu, H. S., Ni, H. J., Chuang, C. T., Hsiung, C. H., Huang, H., & Wang, Y. C. (2010). Distinct epigenetic domains separated by a CTCF bound insulator between the tandem genes, BLU and RASSF1A. PLoS One, 5(9), 1-13. [e12847]. https://doi.org/10.1371/journal.pone.0012847

Distinct epigenetic domains separated by a CTCF bound insulator between the tandem genes, BLU and RASSF1A. / Chang, Jer Wei; Hsu, Han Shui; Ni, Huey Juin; Chuang, Ching Ting; Hsiung, Chi Hui; Huang, Hui-ming; Wang, Yi Ching.

In: PLoS One, Vol. 5, No. 9, e12847, 2010, p. 1-13.

Research output: Contribution to journalArticle

Chang, Jer Wei ; Hsu, Han Shui ; Ni, Huey Juin ; Chuang, Ching Ting ; Hsiung, Chi Hui ; Huang, Hui-ming ; Wang, Yi Ching. / Distinct epigenetic domains separated by a CTCF bound insulator between the tandem genes, BLU and RASSF1A. In: PLoS One. 2010 ; Vol. 5, No. 9. pp. 1-13.
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