Biology subjects

Likhodeeva, M.

Publications and source records attributed to Likhodeeva, M..

2 recordsLinked to original sources

bioRxiv2026

Sequence-dependent binding modes of INO80 control +1 nucleosome positioning

Cellular self-organisation counteracts entropy at the expenditure of energy. In case of the first level of nuclear DNA organisation, this relates to regular nucleosome arrays and interspaced nucleosome-depleted regions (NDRs), for example at promoters or replication origins1-5. The organisation of nucleosomes as building blocks of chromatin is orchestrated by the collective activities of ATP-dependent chromatin remodellers6-9. Yet, how remodellers achieve positional specificity, in particular regarding the promoter-proximal +1 nucleosomes, remains unclear. Here, we show that the S. cerevisiae chromatin remodeller INO80 unexpectedly distinguishes DNA sequence asymmetry within the +1 nucleosome of the SWH1 gene through distinct inhibited and active nucleosome-binding modes. In structural and biochemical analyses of INO80 on nucleosomes with the endogenous sequence, we identified an inhibited binding mode where the entire INO80 remodelling unit flipped on the +1 nucleosome. INO80 adopted this remodelling-incompetent binding mode when facing the promoter, but a remodelling-competent mode when facing the gene body. This directional read-out of intra-nucleosomal DNA sequence asymmetry, together with extranucleosomal NDR sequence features, prevented nucleosome sliding into the NDR while permitting array formation over the gene. Our work shows how DNA features contribute to ATP-dependent self-organisation of promoter chromatin by INO80.

biochemistry↗

bioRxiv2025

Chromatin Protection by the Chromosomal Passenger Complex

The chromosomal passenger complex (CPC; Borealin-Survivin-INCENP-Aurora B kinase) ensures accurate chromosome segregation by orchestrating sister chromatid cohesion, error-correction of kinetochore-microtubule attachments and spindle assembly checkpoint. Correct spatiotemporal regulation of CPC localization is critical for its function. Phosphorylations of Histone H3 Thr3 and Histone H2A Thr120 and modification-independent nucleosome interactions involving Survivin and Borealin contribute to CPC centromere enrichment. However, mechanistic basis for how various nucleosome binding elements collectively contribute to CPC centromere enrichment and whether CPC has any non-catalytic role at centromere remain open questions. Combining a high-resolution cryoEM structure of CPC-bound H3Thr3ph nucleosome with atomic force microscopy and biochemical and cellular assays, we demonstrate that CPC employs multipartite interactions involving both static and dynamic interactions, which facilitate its engagement at nucleosome acidic patch and DNA entry-exit site. Perturbing the CPC-nucleosome interaction compromises protection against MNase digestion in vitro, as well as the dynamic centromere association of CPC and centromeric chromatin stability in cells. Our work provides a mechanistic basis for the previously unexplained non-catalytic role of CPC in maintaining centromeric chromatin critical for kinetochore function.

biochemistry↗