City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
Clin Epigenetics. 2013 Sep 30;5(1):17. doi: 10.1186/1868-7083-5-17.
A remarkable correspondence exists between the cytogenetic locations of the known fragile sites and frequently reported sites of hypermethylation. The best-known features of fragile sites are sequence motifs that are prone to the spontaneous formation of a non-B DNA structure. These facts, coupled with the known enzymological specificities of DNA methyltransferase 1 (DNMT1), the ATP-dependent and actin-dependent helicases, and the ten-eleven translocation (TET) dioxygenases, suggest that these enzymes are involved in an epigenetic cycle that maintains the unmethylated state at these sites by resolving non-B structure, preventing both the sequestration of DNA methyltransferases (DNMTs) and hypermethylation in normal cells.
The innate tendency of DNA sequences present at fragile sites to form non-B DNA structures results in de novo methylation of DNA at these sites that is held in check in normal cells by the action of ATP-dependent and actin-dependent helicases coupled with the action of TET dioxygenases. This constitutes a previously unrecognized epigenetic repair cycle in which spontaneously forming non-B DNA structures formed at fragile sites are methylated by DNMTs as they are removed by the action of ATP-dependent and actin-dependent helicases, with the resulting nascent methylation rendered non-transmissible by TET dioxygenases.
A strong prediction of the hypothesis is that knockdown of ATP-dependent and actin-dependent helicases will result in enhanced bisulfite sensitivity and hypermethylation at non-B structures in multiple fragile sites coupled with global hypomethylation.
A key implication of the hypothesis is that helicases, like the lymphoid-specific helicase and alpha thalassemia/mental retardation syndrome X-linked helicase, passively promote accurate maintenance of DNA methylation by preventing the sequestration of DNMTs at sites of unrepaired non-B DNA structure. When helicase action is blocked due to mutation or downregulation of the respective genes, DNMTs stall at unrepaired non-B structures in fragile sites after methylating them and are unable to methylate other sites in the genome, resulting in hypermethylation at non-B DNA-forming sites, along with hypomethylation elsewhere.
已知的脆性位点的细胞遗传学位置与频繁报道的超甲基化位点之间存在显著的对应关系。脆性位点的最显著特征是易于自发形成非 B 型 DNA 结构的序列基序。这些事实，再加上 DNA 甲基转移酶 1（DNMT1）、ATP 依赖性和肌动蛋白依赖性解旋酶以及十号十一号转位（TET）双加氧酶的已知酶学特异性，表明这些酶参与了一种表观遗传循环，通过解决非 B 结构来维持这些位点的未甲基化状态，防止 DNA 甲基转移酶（DNMTs）的隔离和正常细胞中的过度甲基化。
存在于脆性位点的 DNA 序列自发形成非 B 型 DNA 结构的固有趋势导致这些位点的 DNA 新甲基化，而在正常细胞中，ATP 依赖性和肌动蛋白依赖性解旋酶与 TET 双加氧酶的作用结合在一起，阻止了这种新甲基化的发生。这构成了一个以前未被识别的表观遗传修复循环，其中在脆性位点自发形成的非 B 型 DNA 结构被 DNMT 甲基化，而 ATP 依赖性和肌动蛋白依赖性解旋酶的作用将其去除，由此产生的新生甲基化被 TET 双加氧酶使其不可传递。
该假说的一个强有力预测是，ATP 依赖性和肌动蛋白依赖性解旋酶的敲低将导致多个脆性位点中非 B 结构的亚硫酸氢盐敏感性增强和过度甲基化，同时伴有全局低甲基化。
该假说的一个关键意义是，解旋酶，如淋巴特异性解旋酶和α-地中海贫血/智力迟钝综合征 X 连锁解旋酶，通过防止 DNMT 在未修复的非 B 型 DNA 结构位点上的隔离，被动促进 DNA 甲基化的准确维持。当由于突变或各自基因的下调而阻断解旋酶的作用时，DNMT 在脆性位点的未修复的非 B 结构处停滞，在甲基化它们之后无法甲基化基因组中的其他位点，导致非 B 型 DNA 形成位点的过度甲基化，同时其他位点的低甲基化。
