Biology subjects

Subramanian, V. V.

Publications and source records attributed to Subramanian, V. V..

4 recordsLinked to original sources

bioRxiv2026

Dimerization of the S. cerevisiae Spo11 core complex

Spo11 initiates meiotic recombination by introducing programmed DNA double-strand breaks. DNA cleavage occurs via a topoisomerase-like mechanism involving hybrid active sites formed at the dimer interface. However, in contrast to its topoisomerase relative (Topo VI), Spo11 does not form a stable dimer, likely to prevent uncontrolled DNA cleavage. Here, we investigated the dimerization of S. cerevisiae Spo11 in complex with its partners Ski8, Rec102, and Rec104. We show that the Spo11 complex dimerizes transiently on DNA, forming unstable dimeric complexes with duplex and branched DNA substrates. Guided by AlphaFold modeling of a pre-cleavage complex, we identified mutations that reduce dimerization. Surprisingly, DSB formation is resilient to mutagenesis of the Spo11 dimer interface, implying that additional factors promote dimerization in vivo. Finally, we found that Rec102 exerts a key DNA-binding function, essential for catalysis, and show that it also participates in dimerization through trans contacts with Ski8. Our work provides new insights into the mechanism of Spo11 dimerization and the role of its partners in initiating meiotic recombination.

molecular biology↗

bioRxiv2025

Distinct chromatin regulators downmodulate meiotic axis formation and DNA break induction at chromosome ends

In many organisms, meiotic crossover recombination is suppressed near the extreme ends of chromosomes. Here we show that multiple, often chromosome-specific, suppressive mechanisms with differing ranges contribute to the consistently low enrichment of recombination-promoting axis proteins and downregulation of DNA double-strand breaks (DSBs) within 20 kb of telomeres in Saccharomyces cerevisiae. Suppression of axis proteins is associated with cis-encoded signals and correlates with reduced coding density, although whether this sequence feature actively drives suppression remains to be determined. In addition, axis protein suppression requires the histone methyltransferase Dot1 and the Sir silencing complex. We show that Dot1 suppresses Sir complex activity at least in part independently of its canonical target, H3K79, to downmodulate axis protein deposition near chromosome ends. In parallel, the Sir complex, but not Dot1, suppresses the induction of DSBs at a small number of cryptic hotspots by limiting the openness of promoters, the preferred sites of meiotic DSB formation. Much of the reduced DSB induction near chromosome ends persists in dot1 and sir3 mutants, indicating that additional layers of regulation contribute to the robust reduction of meiotic recombination effectors near chromosome ends.

genetics↗

bioRxiv2023

Conserved domains of meiosis-specific CHK2 protein in budding yeast contribute to its kinase activity

Programmed double strand DNA breaks in meiosis can be repaired as inter-homologue crossovers and thereby aid the faithful segregation of homologous chromosomes. Biased repair mechanisms enforce repair with the homologue. Further, DNA breaks left unrepaired lead to checkpoint activation. Meiosis-specific Chk2 kinase in budding yeast mediates the biased repair of meiotic DSBs using homologue partner but also enforces the meiotic checkpoint. Here we investigate Mek1 kinase activity in budding yeast by analyzing novel point mutants derived from an EMS mutagenesis screen. The point mutants in different domains of Mek1 abolish its activity that cannot be rescued by complementation in transheterozygotes. Our findings lend insight on the mechanism of Mek1 function during meiosis.

genetics↗

bioRxiv2017

Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on small chromosomes

Faithful meiotic chromosome inheritance and fertility relies on the stimulation of meiotic crossover recombination by potentially genotoxic DNA double-strand breaks (DSBs). To avoid excessive damage, feedback mechanisms down-regulate DSBs on chromosomes that have successfully initiated crossover repair. In Saccharomyces cerevisiae, this regulation requires the removal of the conserved DSB-promoting protein Hop1/HORMAD during chromosome synapsis. Here, we identify privileged end-adjacent regions (EARs) spanning roughly 100 Kb near all telomeres that escape DSB downregulation. These regions retain Hop1 and continue to break in pachynema despite normal synaptonemal complex deposition. Differential retention of Hop1 requires the disassemblase Pch2/TRIP13, which preferentially removes Hop1 from telomere-distant sequences, and is modulated by the histone deacetylase Sir2 and the nucleoporin Nup2. Importantly, the uniform size of EARs among chromosomes contributes to disproportionately high DSB and repair signals on short chromosomes in pachynema, suggesting that EARs partially underlie the curiously high recombination rate of short chromosomes.

genomics↗