Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers

Abstract

DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to ∼100 tandem 3.3-kb units at subtelomeric 4q and 10q. D4Z4 displayed hypomethylation in some cancers and hypermethylation in others relative to normal tissues. Surprisingly, in cancers with extensive D4Z4 methylation there was a barrier to hypermethylation spreading to the beginning of this disease-associated array (facioscapulohumeral muscular dystrophy, FSHD) despite sequence conservation in repeat units throughout the array. We infer a different chromatin structure at the proximal end of the array than at interior repeats, consistent with results from chromatin DNaseI sensitivity assays indicating a boundary element near the beginning of the array. The relative chromatin DNaseI sensitivity in FSHD and control myoblasts and lymphoblasts was as follows: a non-genic D4Z4-adjacent sequence (p13E-11, array-proximal)> untranscribed gene standards > D4Z4 arrays> constitutive heterochromatin (satellite 2; P < 10−4 for all comparisons). Cancers displaying D4Z4 hypermethylation also exhibited a hypermethylation-resistant subregion within the 3.3-kb D4Z4 repeat units. This subregion contains runs of G that form G-quadruplexes in vitro. Unusual DNA structures might contribute to topological constraints that link short 4q D4Z4 arrays to FSHD and make long ones phenotypically neutral.

SORBS2transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy

“…The number of D4Z4 repeats might influence the ability of repressor or enhancer binding sequences within the repeats to loop and form contacts with other genes in the 4q region and thereby influence transcription (Pirozhkova et al 2008;Tsumagari et al 2008;Bodega et al 2009;Ottaviani et al 2009). This implies that looping is disturbed upon D4Z4 array contraction in FSHD1A.…”

D4Z4as a prototype of CTCF and lamins-dependent insulator in human cells

“…[42][43][44][45] This proximal anchoring may provide a relatively high mobility of the 4q end, which has a large diffusion volume, change by the length of D4Z4 array (Fig. 3).…”

DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix

“…19,39,40 In this chromosomal region, altered levels of DNA methylation have also been associated with other genetic diseases such as the Rett's syndrome and the ICF syndrome, 25 as well as in several types of cancer. [28][29][30] Here, we have first studied the NM association of a 368-bp-long DNA segment containing four different SSLPs. Taken together, these SSLPs account for the majority of the genotypes identified within the FR-MAR.…”

“…It is known that the methylation level of the D4Z4 array varies between normal cells, FSHD myoblasts and cervical carcinoma cells. 19,[29][30][31][32] However, the methylation status of the FR-MAR sequence was not studied earlier. The total DNA was isolated from several muscular and cervical cell lines and treated as described in Materials and methods section.…”

“…Other genetic and epigenetic abnormalities affecting the subtelomeric region of chromosome 4q have also been observed in various pathologies including the Rett and ICF syndromes, 25 as well as in several types of cancer. [26][27][28][29][30][31][32] Here, we have tested whether mechanisms controlling the association of the FR-MAR to the NM could be similar in different cell types. We have used primary myoblasts from FSHD patients and cervical carcinoma cell lines where the D4Z4 repeat array can be either strongly methylated or demethylated.…”