Chromosome territory reorganization in a human disease with altered DNA methylation

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. X inactivation ͉ Y chromosomeT o fully understand the orchestration of gene expression, it is necessary to understand how chromatin is spatially organized within the cell nucleus. In particular, the position of a gene with respect to its chromosome territory (CT) and the chromatin condensation of its genomic region have been linked to gene activation and repression (1). Although individual genes can be transcribed from inside of CTs (2), some regions that have constitutively high gene expression (3,4) or are subject to coordinate gene activation during development (5, 6) or differentiation (7) or in response to physiological stimuli (8) locate at the edge or outside of their CT. This level of nuclear reorganization is often accompanied by a visible level of chromatin decondensation (5, 6, 9). The precise function, if any, of repositioning toward the outside of CTs remains unclear (1), but it may allow for genes to access a nuclear environment enriched in the components of the transcription (10) and/or mRNAprocessing machinery (4,11,12) and so enhance the efficiency of transcription.The interplay between this level of higher-order chromatin organization and epigenetic mechanisms that act at primary levels of chromatin structure, such as DNA methylation, is a little-explored area. In plants, changes in the architecture of CTs can be induced by treatment with inhibitors of DNA methylation (13). However, the genome-wide demethylation that follows 5-azacytidine treatment or genetic deficiency in DNA methyltransferase...

Flow Cytometric and Laser Scanning Microscopic Approaches in Epigenetics Research

“…However, global hypomethylation is subject to a high degree of variability, unaccounted for by our current level of understanding (10,11). In addition to neoplastic transformation, problems of epigenetic regulation, including CpG methylation disorders are also involved in a wide range of pathological phenomena (12,13). In most eukaryotes, methylation of DNA occurs at the cytosine residues of cytosine-phospho-guanine (CpG) dinucleotides.…”

Involvement of microRNA-451 in resistance of the MCF-7 breast cancer cells to chemotherapeutic drug doxorubicin

“…In contrast, conclusive data show that increased resistance of cancer cells to chemotherapeutic agents is associated with epigenetic alterations that include changes in DNA methylation and histone modifications (4,5,7). The karyotypic hypothesis (8) is closely related to the epigenetic one in view of the wellknown fact that epigenetic changes are a necessary prerequisite to karyotypic changes (9). In this regard, karyotypic changes may be considered as a consequence of the epigenetic alterations progression and may serve as indirect evidence of the importance of epigenetic dysregulation in the acquisition of cancer drug resistance.…”

Gene Positioning

“…Repositioning of genes, small chromatin regions, or CTs is also seen in other diseases, such as facioscapulohumeral muscular dystrophy (FSHD) (Masny et al 2004), immunodeficiency centromeric instability facial anomalities (ICF) (Matarazzo et al 2007), epilepsy (Borden and Manuelidis 1988), or in male factor infertility (Finch et al 2008). ICF syndrome is caused by mutations in DNA methyltransferase 3B (DNMT3B) and is associated with DNA hypomethylation at specific genomic sites, such as the SYBL1 gene promoter which becomes derepressed.…”

“…Interestingly, in ICF male and female patients, the SYBL1 inactive allele, located on the Y and inactive X chromosome, respectively, relocates outside of its respective CT, recapitulating the position of the active alleles (Fig. 2C) (Matarazzo et al 2007). In females, but not in males, both inactive SYBL1 and its silent neighbor SPRY3 loop out from the CT, suggesting that the reorganization extends beyond the derepressed, hypomethylated gene (Matarazzo et al 2007).…”

“…2C) (Matarazzo et al 2007). In females, but not in males, both inactive SYBL1 and its silent neighbor SPRY3 loop out from the CT, suggesting that the reorganization extends beyond the derepressed, hypomethylated gene (Matarazzo et al 2007).…”