Unraveling the chromosome dynamics and DNA metabolism functions of the SMC5/6 complex

The Structural Maintenance of Chromosomes (SMC) protein family harbors cohesin, condensin and the SMC5/6 complex. SMC5/6 plays critical roles in preserving genome stability by regulating DNA repair, replication, and chromatin organization but its mode of action is not well understood. In this work, we investigated SMC5/6 functions in DNA homeostasis and genome organization by using integrative approaches including RNA-seq, Hi-C, and BLISS analyses. We uncovered functional interplay between SMC5/6 and BRCA1 in genome maintenance and common roles in limiting inflammatory response activation. Our results show that loss of SMC5/6 or BRCA1 induces genomic instability characterized by replication stress, fork degradation and double-strand breaks (DSBs), triggering activation of the cGAS/STING pathway and pro-inflammatory signaling. This is linked to increased micronuclei formation, nuclear envelope fragility, and defects in chromatin architecture. Genome-wide Hi-C analysis revealed that SMC5/6 depletion disrupts chromatin compartmentalization, TAD insulation, and long-range chromatin interactions, favoring a shift from repressive (B) to active (A) compartments. Affecting 2% of the genome, these changes precede transcriptional upregulation of inflammatory and cancer-related genes, with significant effects on pathways involved in DNA damage response and immune regulation. Integrating DSB mapping and chromatin organization data, we found that fragile sites such as CpG-rich promoters and early-replicating fragile sites (ERFs) exhibit increased DSB accumulation and gene expression dysregulation upon SMC5/6 depletion. Mechanistically, SMC5/6 safeguards stressed replication forks by preventing excessive fork reversal and degradation, cooperating with BRCA1 to protect their integrity and maintain replicationtranscription homeostasis. Loss of SMC5/6 accelerates fork restart but compromises fidelity, leading to accumulation of fragmented DNA and persistent genome instability. Additionally, changes in chromatin folding induced by SMC5/6 loss impact immune regulation by derepressing inflammatory genes, potentially linking chromatin structural changes to innate immune activation. This study underscores the multifaceted roles of SMC5/6 in maintaining genome integrity through chromatin organization, replication fork protection, and transcriptional regulation. It highlights how SMC5/6 dysfunction contributes to immune dysregulation and cancer progression, providing insights into therapeutic strategies targeting SMC5/6-associated pathways in cancer and immune disorders.

Publisher

University of Galway

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Attribution-NonCommercial-NoDerivatives 4.0 International

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Collections

University of Galway Theses (PhD Theses)