ABSTRACT
Cooks syndrome (CS) is an ultrarare limb malformation due to in tandem microduplications involving KCNJ2 and extending to the 5' regulatory element of SOX9. To date, six CS families were resolved at the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the SOX9-KCNJ2/Sox9-Kcnj2 locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the KCNJ2 locus. On chromosome 17, the breakpoint mapped between KCNJ16 and KCNJ2, and combined with a ~ 5 kb deletion in the 5' of KCNJ2. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated KCNJ2 from a putative enhancer. Gene expression analysis demonstrated downregulation of KCNJ2 in both patient's blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5' of KCNJ2 may mimic the developmental consequences of in tandem duplications affecting the SOX9-KCNJ2/Sox9-Kcnj2 locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.
Subject(s)
Fingers/abnormalities , Foot Deformities, Congenital/genetics , Gene Rearrangement , Hand Deformities, Congenital/genetics , Potassium Channels, Inwardly Rectifying/genetics , Regulatory Sequences, Nucleic Acid , Adolescent , Adult , Chromosome Breakpoints , Chromosomes, Human, Pair 1/genetics , Chromosomes, Human, Pair 17/genetics , Facies , Female , Humans , In Situ Hybridization, Fluorescence , Male , Potassium Channels, Inwardly Rectifying/chemistry , Sequence Deletion , Translocation, Genetic , Young AdultABSTRACT
It is not clear how spontaneous DNA double-strand breaks (DSBs) form and are processed in normal cells, and whether they predispose to cancer-associated translocations. We show that DSBs in normal mammary cells form upon release of paused RNA polymerase II (Pol II) at promoters, 5' splice sites and active enhancers, and are processed by end-joining in the absence of a canonical DNA-damage response. Logistic and causal-association models showed that Pol II pausing at long genes is the main predictor and determinant of DSBs. Damaged introns with paused Pol II-pS5, TOP2B and XRCC4 are enriched in translocation breakpoints, and map at topologically associating domain boundary-flanking regions showing high interaction frequencies with distal loci. Thus, in unperturbed growth conditions, release of paused Pol II at specific loci and chromatin territories favors DSB formation, leading to chromosomal translocations.
Subject(s)
DNA Breaks, Double-Stranded , Genetic Loci , Neoplasms/genetics , Neoplasms/metabolism , RNA Polymerase II/metabolism , Animals , Cell Line, Tumor , Cells, Cultured , DNA Repair , Enhancer Elements, Genetic , Etoposide/pharmacology , Flow Cytometry , Fluorescent Antibody Technique , Gene Expression Regulation, Neoplastic/drug effects , Genomics/methods , Introns , Neoplasms/pathology , Promoter Regions, Genetic , RNA Splice Sites , Topoisomerase Inhibitors/pharmacology , Transcription Initiation SiteABSTRACT
We summarize the picture emerging from recently proposed models of polymer physics describing the general features of chromatin large scale spatial architecture, as revealed by microscopy and Hi-C experiments.
