Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Oct 16;104(42):16546-51.
doi: 10.1073/pnas.0702924104. Epub 2007 Oct 8.

Chromosome territory reorganization in a human disease with altered DNA methylation

Maria R Matarazzo  1 , Shelagh Boyle, Maurizio D'Esposito, Wendy A Bickmore
Affiliations

Chromosome territory reorganization in a human disease with altered DNA methylation

Maria R Matarazzo et al. Proc Natl Acad Sci U S A. .

Abstract

Chromosome territory (CT) organization and chromatin condensation have been linked to gene expression. Although individual genes can be transcribed from inside CTs, some regions that have constitutively high expression or are coordinately activated loop out from CTs and decondense. The relationship between epigenetic marks, such as DNA methylation, and higher-order chromatin structures is largely unexplored. DNMT3B mutations in immunodeficiency centromeric instability facial anomalies (ICF) syndrome result in loss of DNA methylation at particular sites, including CpG islands on the inactive X chromosome (Xi). This allows the specific effects of DNA methylation on CTs to be examined. Using fluorescence in situ hybridization, we reveal a differential organization of the human pseudoautosomal region (PAR)2 between the CTs of the X and Y in normal males and the active X (Xa) and the Xi in females. There is also a more condensed chromatin structure on Xi compared with Xa in this region. PAR2 genes are relocalized toward the outside of the Y and Xi CTs in ICF, and on the Xi, we show that this can extend to genes distant from the site of DNA hypomethylation itself. This reorganization is not simply a reflection of the transcriptional activation of the relocalized genes. This report of altered CT organization in a human genetic disease illustrates that DNA hypomethylation at restricted sites in the genome can lead to more extensive changes in nuclear organization away from the original site of epigenetic change.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Genomic map of PAR2 of the human sex chromosomes. Map of the PAR2 on Xq and Yq showing, from the centromere to the telomere (tel), the positions of the genes (open boxes), and the cosmid probes (gray lines) used in FISH experiments. The hatched box indicates the heterochromatin of Yq12.
Fig. 2.
Fig. 2.
Nuclear organization of PAR2 in male and female cells. (a) DNA FISH, using Y (top row) or X (bottom row) chromosome paints (green) together with cosmid probes (red) for SPRY3, SYBL1, and IL9R on methanol/acetic acid (MA)-fixed nuclei of normal male LCLs. Nuclei were counterstained with DAPI (blue). (Scale bar, 5 μm.) (b) Mean [±95% confidence interval (CI)] position for each allele of the three PAR2 genes relative to the edge of the X and Y CT in MA-fixed cells. Because the territory of the X chromosome is larger than that of the Y (reflecting their different DNA contents), the position of each cosmid probe signal was normalized relative to the radius of a circle of area equal to that of the corresponding CT. The significance of the differences in position between X- and Y-linked alleles is indicated. *, P ≤ 0.01; **, P ≤ 0.005. (n ≥ 70.) (c) Four-color DNA FISH, using chromosome paints for 10q (red) and the X (green), together with an SYBL1-specific probe (yellow, arrow) on nuclei of the female fibroblast cell line GM07693 that carries a balanced translocation, 46,X,t(X;10). The normal chromosome is Xi. The karyogram of the normal and derivative chromosomes X and 10 is shown at Left. (Scale bar, 5 μm.) (d) Mean (±95% CI) position (in micrometers) for each allele of the three PAR2 genes relative to the edge of the Xa and Xi CT in MA-fixed GM07693 cells. The significance of the differences in position between alleles is indicated. ***, P ≤ 0.000. (n ≥ 65.) (e) (Left) RNA FISH with XIST probe. (Right) DNA FISH, using SYBL1 and X chromosome paint. Shown are pictures of the same nucleus on two different planes of focus in the z axis to visualize the 3D position of SYBL1 probe (Scale bar, 5 μm.). (f) Mean (±95% CI) position (in micrometers) for each allele of the three PAR2 genes relative to the edge of the Xa and Xi CT in paraformaldehyde-fixed WI38 cells. ***, P ≤ 0.000. (n ≥ 50.)
Fig. 3.
Fig. 3.
Interphase chromatin condensation of PAR2. (a) FISH with probes for SPRY3 and SYBL1 in nuclei from male (Left) or female GM07693 (Right) cells. The X- and Y-linked alleles in male cells were distinguished by cohybridization with a Y chromosome paint. The Xa and Xi alleles in GM07693 cells were distinguished by hybridization with a chromosome 10 BAC (RP11 596L14). (b) Distribution of squared interphase distances (in square micrometers) measured between SPRY3 and SYBL1, SYBL1 and IL9R, and SPRY3 and IL9R probes on X and Y in male cells (Left) and Xa and Xi in female cells (Right). (n ≥ 57.) (c) Mean (±95% CI) squared interphase distances (in square micrometers) measured between SPRY3 and SYBL1 and SYBL1 and IL9R probes on X and Y in male cells (Left) and Xa and Xi in female cells. (n ≥ 57.)
Fig. 4.
Fig. 4.
PAR2 interphase organization in control and ICF male cells. (a) 2D FISH with probe for SYBL1 (red) and Y chromosome paint (green) in control (Left) and ICF (Right) male LCLs. (b) Mean (±95% CI) position (in micrometers) for each allele of the three PAR2 genes relative to the edge of the X and Y CT (Left) and Xa and Xi (Right) in ICF male LCLs and female fibroblasts. The significance of differences in position between alleles is indicated. *, P ≤ 0.01; **, P ≤ 0.005. (n ≥ 65.) (c) Mean (±95% CI) position (in micrometers) for SYBL1-Y, SPRY3-Y, and IL9R-Y alleles relative to the edge of the Y territory in WT and ICF cells. ***, P ≤ 0.000. (n ≥ 70.) (d) Distribution of squared interphase distances (in square micrometers) measured between SPRY3 and SYBL1, SYBL1 and IL9R, and SPRY3 and IL9R probes on Y chromosomes in WT and ICF cells. (n ≥ 50.) (e) Mean (±95% CI) of the position (in micrometers) for SYBL1-Xi, SPRY3-Xi, IL9R-Xi, and IDS-Xi alleles relative to the edge of the Xi territory in WT (WI38 for SYBL1, SPRY3, and IL9R and GM01871 for IDS) and ICF fibroblasts. ***, P ≤ 0.000. (n ≥ 50.)
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Heard E, Bickmore W. Curr Opin Cell Biol. 2007;19(3):311–316. - PubMed
    1. Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA. J Cell Biol. 2002;157:579–589. - PMC - PubMed
    1. Mahy NL, Perry PE, Bickmore WA. J Cell Biol. 2002;159:753–763. - PMC - PubMed
    1. Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ. J Cell Biol. 2006;172:177–187. - PMC - PubMed
    1. Chambeyron S, Bickmore WA. Genes Dev. 2004;18:1119–1130. - PMC - PubMed

Publication types