Complex interplay between FMRP and DHX9 during DNA replication stress

Arijita Chakraborty, Arijit Dutta, Leonardo G. Dettori, Rosemarie Daoud, Jing Li, Leticia Gonzalez, Xiaoyu Xue, Heidi Hehnly, Patrick Sung, Alaji Bah, Wenyi Feng

Research output: Contribution to journalArticlepeer-review


Mutations in, or deficiency of, fragile X messenger ribonucleoprotein (FMRP) is responsible for the Fragile X syndrome (FXS), the most common cause for inherited intellectual disability. FMRP is a nucleocytoplasmic protein, primarily characterized as a translation repressor with poorly understood nuclear function(s). We recently reported that FXS patient cells lacking FMRP sustain higher level of DNA double-strand breaks (DSBs) than normal cells, specifically at sequences prone to forming R-loops, a phenotype further exacerbated by DNA replication stress. Moreover, expression of FMRP, and not an FMRPI304N mutant known to cause FXS, reduced R-loop-associated DSBs. We subsequently reported that recombinant FMRP directly binds R-loops, primarily through the carboxyl terminal intrinsically disordered region. Here, we show that FMRP directly interacts with an RNA helicase, DHX9. This interaction, which is mediated by the amino terminal structured domain of FMRP, is reduced with FMRPI304N. We also show that FMRP inhibits DHX9 helicase activity on RNA:DNA hybrids and the inhibition is also dependent on the amino terminus. Furthermore, the FMRPI304N mutation causes both FMRP and DHX9 to persist on the chromatin in replication stress. These results suggest an antagonistic relationship between FMRP and DHX9 at the chromatin, where their proper interaction leads to dissociation of both proteins from the fully resolved R-loop. We propose that the absence or the loss of function of FMRP leads to persistent presence of DHX9 or both proteins, respectively, on the unresolved R-loop, ultimately leading to DSBs. Our study sheds new light on our understanding of the genome functions of FMRP.

Original languageEnglish (US)
Article number105572
JournalJournal of Biological Chemistry
Issue number1
StatePublished - Jan 2024


  • DHX9
  • DNA double strand breaks (DSB)
  • DNA replication stress
  • FMR1
  • FMRP
  • Fragile X Syndrome
  • I304N
  • KH2 domain
  • R-loop
  • RNA helicase

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry
  • Cell Biology


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