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Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer.

Rafique S, Thomas JS, Sproul D, Bickmore WA - Genome Biol. (2015)

Bottom Line: This occurs not only at individual genes, but also over larger chromosomal domains.For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus.In MCF7 cells, we show that this depends on the presence of estrogen.

View Article: PubMed Central - PubMed

Affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. sehrishrafique@hotmail.com.

ABSTRACT

Background: Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers.

Results: We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen.

Conclusions: Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.

No MeSH data available.


Related in: MedlinePlus

Refinement and analysis of the 16p11.2 RER region in breast cancer cell lines. aBlack bars indicate genes along 16p11.2, oriented from centromere (top) to telomere (bottom), which have significant TCSs at varying window (2n + 1) size with n from 1 to 10. Gene expression data are from tumor cell lines [20]. Gene names are listed to the right, as are the position of fluorescence in situ hybridization (FISH) probes that were used to examine the four RER subregions. b Box plots show the distribution of normalized FISH interprobe distances (d2/r2) [31, 32] measured across the four subregions of the 16p11.2 RER region in MCF7 and MDAMB231 breast cancer cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). c Unsupervised cluster analysis of gene expression z scores for subregion 2 in 48 breast cancer cell lines (red ER−, blue ER+) [20]. Cell line names are indicated along the bottom of the heat map. Red/green z scores equate to increased/decreased gene expression, respectively. Genes are ordered by their position on the chromosome and listed to the right. The yellow boxes indicate cell lines examined by FISH. d Example FISH images using probe pairs (red and green) that delineate subregion 2 (as in (a)) in ER+ cell lines MCF7 and LY2 (upper panels), and ER− cell lines MDAMB231 and MDAMB468 (lower panels). DNA is stained with DAPI (blue). Scale bar = 5 μm. The boxplots to the right show the distribution of normalized FISH interprobe distances (d2/r2) across subregion 2 in the four cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1)
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Fig5: Refinement and analysis of the 16p11.2 RER region in breast cancer cell lines. aBlack bars indicate genes along 16p11.2, oriented from centromere (top) to telomere (bottom), which have significant TCSs at varying window (2n + 1) size with n from 1 to 10. Gene expression data are from tumor cell lines [20]. Gene names are listed to the right, as are the position of fluorescence in situ hybridization (FISH) probes that were used to examine the four RER subregions. b Box plots show the distribution of normalized FISH interprobe distances (d2/r2) [31, 32] measured across the four subregions of the 16p11.2 RER region in MCF7 and MDAMB231 breast cancer cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). c Unsupervised cluster analysis of gene expression z scores for subregion 2 in 48 breast cancer cell lines (red ER−, blue ER+) [20]. Cell line names are indicated along the bottom of the heat map. Red/green z scores equate to increased/decreased gene expression, respectively. Genes are ordered by their position on the chromosome and listed to the right. The yellow boxes indicate cell lines examined by FISH. d Example FISH images using probe pairs (red and green) that delineate subregion 2 (as in (a)) in ER+ cell lines MCF7 and LY2 (upper panels), and ER− cell lines MDAMB231 and MDAMB468 (lower panels). DNA is stained with DAPI (blue). Scale bar = 5 μm. The boxplots to the right show the distribution of normalized FISH interprobe distances (d2/r2) across subregion 2 in the four cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1)

Mentions: To determine whether 16p11.2 is one contiguous block of RER, or several different subregions, we analyzed TCSs generated by varying the number of neighboring genes (n) used in the sliding window analysis (from 10 — the value used for the original analysis – down to 1). As n decreased to 8 and below, genes with remaining high TCSs were resolved into distinct two RER subregions (2 and 3) that are located more proximal on 16p11.2 than the LRES region defined by Hsu et al. [21] (subregion 1 in Fig. 5a).Fig. 5


Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer.

Rafique S, Thomas JS, Sproul D, Bickmore WA - Genome Biol. (2015)

Refinement and analysis of the 16p11.2 RER region in breast cancer cell lines. aBlack bars indicate genes along 16p11.2, oriented from centromere (top) to telomere (bottom), which have significant TCSs at varying window (2n + 1) size with n from 1 to 10. Gene expression data are from tumor cell lines [20]. Gene names are listed to the right, as are the position of fluorescence in situ hybridization (FISH) probes that were used to examine the four RER subregions. b Box plots show the distribution of normalized FISH interprobe distances (d2/r2) [31, 32] measured across the four subregions of the 16p11.2 RER region in MCF7 and MDAMB231 breast cancer cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). c Unsupervised cluster analysis of gene expression z scores for subregion 2 in 48 breast cancer cell lines (red ER−, blue ER+) [20]. Cell line names are indicated along the bottom of the heat map. Red/green z scores equate to increased/decreased gene expression, respectively. Genes are ordered by their position on the chromosome and listed to the right. The yellow boxes indicate cell lines examined by FISH. d Example FISH images using probe pairs (red and green) that delineate subregion 2 (as in (a)) in ER+ cell lines MCF7 and LY2 (upper panels), and ER− cell lines MDAMB231 and MDAMB468 (lower panels). DNA is stained with DAPI (blue). Scale bar = 5 μm. The boxplots to the right show the distribution of normalized FISH interprobe distances (d2/r2) across subregion 2 in the four cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1)
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Fig5: Refinement and analysis of the 16p11.2 RER region in breast cancer cell lines. aBlack bars indicate genes along 16p11.2, oriented from centromere (top) to telomere (bottom), which have significant TCSs at varying window (2n + 1) size with n from 1 to 10. Gene expression data are from tumor cell lines [20]. Gene names are listed to the right, as are the position of fluorescence in situ hybridization (FISH) probes that were used to examine the four RER subregions. b Box plots show the distribution of normalized FISH interprobe distances (d2/r2) [31, 32] measured across the four subregions of the 16p11.2 RER region in MCF7 and MDAMB231 breast cancer cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). c Unsupervised cluster analysis of gene expression z scores for subregion 2 in 48 breast cancer cell lines (red ER−, blue ER+) [20]. Cell line names are indicated along the bottom of the heat map. Red/green z scores equate to increased/decreased gene expression, respectively. Genes are ordered by their position on the chromosome and listed to the right. The yellow boxes indicate cell lines examined by FISH. d Example FISH images using probe pairs (red and green) that delineate subregion 2 (as in (a)) in ER+ cell lines MCF7 and LY2 (upper panels), and ER− cell lines MDAMB231 and MDAMB468 (lower panels). DNA is stained with DAPI (blue). Scale bar = 5 μm. The boxplots to the right show the distribution of normalized FISH interprobe distances (d2/r2) across subregion 2 in the four cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1)
Mentions: To determine whether 16p11.2 is one contiguous block of RER, or several different subregions, we analyzed TCSs generated by varying the number of neighboring genes (n) used in the sliding window analysis (from 10 — the value used for the original analysis – down to 1). As n decreased to 8 and below, genes with remaining high TCSs were resolved into distinct two RER subregions (2 and 3) that are located more proximal on 16p11.2 than the LRES region defined by Hsu et al. [21] (subregion 1 in Fig. 5a).Fig. 5

Bottom Line: This occurs not only at individual genes, but also over larger chromosomal domains.For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus.In MCF7 cells, we show that this depends on the presence of estrogen.

View Article: PubMed Central - PubMed

Affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. sehrishrafique@hotmail.com.

ABSTRACT

Background: Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers.

Results: We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen.

Conclusions: Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.

No MeSH data available.


Related in: MedlinePlus