The CGG triplet repeat binding protein 1 counteracts DNA secondary structure formation to prevent transcription-replication stress

ABSTRACT: Short tracts of trinucleotide repeats with less than 10 repeats are found frequently throughout the genome without any apparent negative impact on DNA replication fork progression or transcription elongation. CGG binding protein 1 (CGGBP1) binds to CGG triplet repeats and has been implicated in multiple cellular processes such as transcription, replication and DNA damage. Here, we show that CGGBP1 binds to human gene promoter sites with short CGG repeat tracts prone to G-quadruplex and R-loop secondary structure formation. Depletion of CGGBP1 in human cells leads to substantial transcriptomic changes which coincides with increased replication fork stalling and transcription-replication conflicts. Consistently, an episomal model locus as well as endogenous candidate genes containing short tracts of CGG repeats show R-loop accumulation and increased RNAPII chromatin occupancy in CGGBP1-depleted cells. Mass spectrometry identifies the DEAD-box helicase DDX41 as a specific interaction partner of CGGBP1, thereby providing mechanistic insight how CGGBP1 can counteract the formation of secondary DNA structures at CGG repeats. Together, our work shows that short trinucleotide repeats are a source of genome-destabilizing secondary structures and cells rely on specific DNA-binding factors to maintain proper transcription and replication progression at short trinucleotide repeats.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Ann-Christine König  

LAB HEAD: Stephan Hamperl

PROVIDER: PXD045654 | Pride | 2025-10-20

REPOSITORIES: Pride