Biology subjects

Semlow, D. R.

Publications and source records attributed to Semlow, D. R..

3 recordsLinked to original sources

bioRxiv2026

HMCES DNA-protein cross-links promote template slippage during DNA replication

During replication, nucleolytic processing of apurinic/apyrimidinic (AP) sites in single-stranded (ss)DNA is attenuated by the evolutionarily conserved 5-hydroxymethylcytosine binding, embryonic-specific (HMCES) protein. HMCES forms a covalent thiazolidine linkage with the ring-opened aldehyde form of a ssDNA AP site to stabilize the AP site and suppress the formation of DNA double-strand breaks. The resulting HMCES DNA-protein cross-link (DPC) can then be digested by the SPRTN protease and bypassed through mutagenic translesion synthesis (TLS). Here, we use Xenopus egg extracts and molecular dynamics simulations to investigate how HMCES-DPC formation influences the mutagenicity of AP site bypass. We show that SPRTN processes the HMCES-DPC to a five amino acid peptide adduct prior to TLS. Surprisingly, the mutagenicity of HMCES-DPC bypass is insensitive to the extent of DPC proteolysis and depends only on cross-link formation, which traps the AP site in a more dynamic ring-opened configuration. We further show that the spectrum of mutations produced during bypass of HMCES-adducts strongly depends on the template strand nucleotide immediately 5 of the AP site. Our data support a model in which HMCES-DPC formation increases the conformational flexibility of the DNA template, allowing template slippage and use of the 5 template nucleotide to direct insertion opposite the adducted AP site.

biochemistry↗

bioRxiv2025

ATM promotes reversed fork processing during DNA interstrand cross-link repair

During replication-coupled DNA interstrand cross-link (ICL) repair, fork reversal is thought to enable the Fanconi anemia (FA) pathway to resolve the ICL through nucleolytic incisions. Subsequent fork restoration then allows nascent DNA strand extension past the lesion. Although these fork remodeling events are crucial for ICL repair, their regulation remains poorly understood. Here, we use cell-free Xenopus egg extracts to investigate fork dynamics during ICL repair by the FA pathway. We find that the ataxia telangiectasia-mutated (ATM) kinase is activated concomitantly with fork reversal and promotes resection of the reversed fork intermediate. This resection depends on the coordinated activities of the EXO1 and DNA2 nucleases. Our data indicate that EXO1 initiates 5 to 3 resection of nascent lagging strands in the regressed arm, while DNA2 performs 5 to 3 resection of recessed lagging strands. We further show that the inhibition of protein phosphatase 2A (PP2A) during ICL repair results in ATM hyperactivation, reversed fork over-resection, and formation of aberrant end-joining products, indicating that PP2A counteracts ATM signaling to constrain reversed fork resection. Taken together, this work implicates reversed forks as substrates for ATM activation and reveals a phospho-regulatory circuit that governs reversed fork processing during ICL repair.

molecular biology↗

bioRxiv2021

The HMCES DNA-protein cross-link functions as a constitutive DNA repair intermediate

The HMCES protein forms a covalent DNA-protein cross-link (DPC) with abasic (AP) sites in ssDNA, and the resulting HMCES-DPC is thought to suppress double-strand break formation in S phase. However, the dynamics of HMCES cross-linking and whether any DNA repair pathways normally include an HMCES-DPC intermediate remain unknown. Here, we show that an HMCES-DPC forms efficiently on the AP site generated during replication-coupled DNA interstrand cross-link (ICL) repair. We use this system to show that HMCES cross-links form on DNA after the replicative CMG helicase has passed over the AP site, and that HMCES is subsequently removed by the SPRTN protease. The HMCES-DPC suppresses DSB formation, slows translesion synthesis (TLS) past the AP site, and introduces a bias for insertion of deoxyguanosine opposite the AP site. These data show that HMCES-DPCs can form as constitutive intermediates in replication-coupled repair, and they suggest a general model of how HMCES protects AP sites during DNA replication.

molecular biology↗