Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioningстатья
Статья опубликована в высокорейтинговом журнале
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Дата последнего поиска статьи во внешних источниках: 17 августа 2020 г.
Аннотация:Nucleosomes are the most abundant protein–DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The de- tails of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory sig- nals. Hydroxyl-radical footprinting (HRF) of protein– DNA complexes is a chemical technique that probes nucleosome organization in solution with a high pre- cision unattainable by other methods. In this work we propose an integrative modeling method for con- structing high-resolution atomistic models of nucle- osomes based on HRF experiments. Our method pre- cisely identifies DNA positioning on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints. We performed high- resolution HRF for Saccharomyces cerevisiae cen- tromeric nucleosome of unknown structure and char- acterized it using our integrative modeling approach. Our model provides the basis for further understand- ing the cooperative engagement and interplay be- tween Cse4p protein and the A-tracts important for centromere function.