Boundary issues between countries can start wars, while boundary issues between people cause personal space problems; but can boundary issues between repetitive loci lead to the development of human disorders? The pathogenesis of the disorders in question, which include fragile X syndrome (FXS), Huntington’s disease, amyotrophic lateral sclerosis, and Friedreich’s ataxia, involves the unstable expansion of repetitive DNA sequences known as short tandem repeats (STRs). A normal healthy human being possesses tens of thousands of short and stable STRs throughout their genome, so why do amplification events only occur at a small subset of disease-associated STRs (daSTRs)?
A possible answer to this conundrum now comes from the 3D Epigenomes and Systems Neurobiology lab of Jennifer E. Phillips-Cremins (University of Pennsylvania, Philadelphia, PA, USA). Fascinatingly, Sun and colleagues establish that daSTRs localize almost exclusively to three-dimensional (3D) chromatin domain boundaries, and this may permit unstable expansion of daSTRs and promote disease progression.
The talented team analyzed previously published high-throughput sequencing chromosome conformation capture (Hi-C) maps generated from human embryonic stem cells and human fetal cortical plate tissue and determined the location of chromatin boundaries by employing a well-established method (based on the directionality index test statistic and a hidden Markov model) and 3DNetMod, a new method recently developed by the authors. Of specific interest to this study is FXS, a disease associated with FMR1 gene silencing due to the expansion of an STR.
Here are the details on how boundary issues can turn short tandem repeats pathogenic:
- While daSTRs display great diversity in relation to sequence, location, and mutation-length threshold, nearly all daSTRs localize near to boundaries between 3D chromatin domains
- these sites may represent hotspots for epigenetic misregulation or topological disruption linked to STR expansion
- The presence of non-disease associated STRs far from chromatin domain boundaries may save them from unwanted expansion
- daSTR-associated chromatin boundaries display elevated CpG island density and heightened occupancy of the CTCF architectural protein
- A combination of ultra-high CpG island density and chromatin boundary localization may “earmark” genomic locations susceptible to STR instability
- Chromosome-conformation-capture-carbon-copy (5C) analysis of cells and tissues derived from an FXS patient (over 900 trinucleotide repeats), his healthy male sibling, and a genetically unrelated FXS male (over 600 trinucleotide repeats) uncovered evidence for severe chromatin boundary disruption associated with the FXS daSTR that results in topological re-organization of the genome surrounding the FMR1 gene
- In the healthy patient, the FMR1 gene associates with a downstream chromatin domain marked by histone modifications characteristic of active enhancers
- In FXS patients, boundary disruption caused by the FXS-associated daSTR expansion leads the FMR1 gene to associate with an upstream chromatin domain devoid of active enhancer marks, thereby leading to pathologic silencing of the FMR1 gene
- Furthermore, FXS patients display a loss of CTCF occupancy at the FMR1 daSTR
- The degree of boundary disruption correlates to both the degree of FMR1 silencing and extent of CTCF occupancy loss at daSTR adjacent sites
Future studies by the authors (in the absence of any unscientific boundary issues!) aim to evaluate the cause and effect relationship between STR instability and chromatin domain boundary disruption in the hope of developing topology-directed therapies.
Discover more on this bordering-on exciting new finding at Cell, August 2018!