Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant

Chromosomal abnormalities associated with hypomethylation of classical sate llite regions are characteristic for the ICF immunodeficiency syndrome. We, as well as others, have found that these effects derive from mutations in the DNMT3B DNA methyltransferase gene. Here we examine further the molecula r phenotype of ICF cells and report several examples of extensive hypomethy lation that are associated with advanced replication time, nuclease hyperse nsitivity and a variable escape from silencing for genes on the inactive X and Y chromosomes. Our analysis suggests that all genes on the inactive X c hromosome may be extremely hypomethylated at their 5' CpG islands, Our stud ies of G6PD in one ICF female and SYBL1 in another ICF female provide the f irst examples of abnormal escape from X chromosome inactivation in untransf ormed human fibroblasts, XIST RNA localization is normal in these cells, ar guing against an independent silencing role for this RNA in somatic cells. SYBL1 silencing is also disrupted on the Y chromosome in ICF male cells. In creased chromatin sensitivity to nuclease was found at all hypomethylated p romoters examined, including those of silenced genes, The persistence of in activation in these latter cases appears to depend critically on delayed re plication of DNA because escape from silencing was only seen when replicati on was advanced to an active X-like pattern.