The g-rich repeats in FMR1 and C9orf72 loci are hotspots for local unpairing of DNA

Manar Abu Diab, Hagar Mor-Shaked, Eliora Cohen, Yaara Cohen-Hadad, Oren Ram, Silvina Epsztejn-Litman, Rachel Eiges*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


Pathological mutations involving noncoding microsatellite repeats are typically located near promoters in CpG islands and are coupled with extensive repeat instability when sufficiently long. What causes these regions to be prone to repeat instability is not fully understood. There is a general consensus that instability results from the induction of unusual structures in the DNA by the repeats as a consequence of mispairing between complementary strands. In addition, there is some evidence that repeat instability is mediated by RNA transcription through the formation of three-stranded nucleic structures composed of persistent DNA:RNA hybrids, concomitant with single-strand DNA displacements (R-loops). Using human embryonic stem cells with wild-type and repeat expanded alleles in the FMR1 (CGGs) and C9orf72 (GGGGCCs) genes, we show that these loci constitute preferential sites (hotspots) for DNA unpairing. When R-loops are formed, DNA unpairing is more extensive, and is coupled with the interruptions of double-strand structures by the nontranscribing (G-rich) DNA strand. These interruptions are likely to reflect unusual structures in the DNA that drive repeat instability when the G-rich repeats considerably expand. Further, we demonstrate that when the CGGs in FMR1 are hyper-methylated and transcriptionally inactive, local DNA unpairing is abolished. Our study thus takes one more step toward the identification of dynamic, unconventional DNA structures across the G-rich repeats at FMR1 and C9orf72 disease-associated loci.

Original languageAmerican English
Pages (from-to)1239-1252
Number of pages14
Issue number4
StatePublished - Dec 2018

Bibliographical note

Funding Information:
We thank the families who donated the FXS and C9/ALS embryos for hESC line derivation. We would also like to thank Amir Eden for fruitful discussions and David Zeevi for critically reading the manuscript, Motti Peretz for assistance with the graphic design, Anna Typsin for the illustrations, and Clinton E. Leysath for the S9.6 monoclonal antibody. We thank the Genomic Applications Laboratory, The Core Research Facility, Faculty of Medicine – Ein Kerem, The Hebrew University of Jerusalem, Israel for the next-generation sequencing. This research was supported by the Israel Science Foundation (grant 1480/15 to R.E.) and the Legacy Heritage Biomedical Program of the Israel Science Foundation (grant 1260/16 to R.E.). We declare no conflicts of interest.

Publisher Copyright:
© 2018 by the Genetics Society of America.


  • C9orf72
  • FMR1
  • R-loops
  • Single-strand DNA displacements
  • Unstable repeat expansions


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