Yeast High Mobility Group Protein HMO2, a subunit of the chromatin remodeling complex INO80, binds preferentially to DNA ends

Abstract

High Mobility Group Proteins (HMG) are non‐histone chromosomal proteins which are common in eukaryotes. They bind to DNA in a non sequence specific manner. HMO2 from Saccharomyces cerevisiae is an HMGB protein that is a component of the DNA‐damage‐dependent chromatin remodeling complex INO80, which is involved in double strand break repair. The gene encoding HMO2 was amplified from yeast genomic DNA. It was expressed in E. coli Rosetta Blue cells and purified using nickel affinity chromatography. DNA binding assays indicate that HMO2 binds to supercoiled DNA with higher affinity than linear DNA and that it can restrain DNA supercoils. Like other HMGB proteins it has a preference for distorted DNA such as four‐way junctions (4WJs) and DNA with loops and abasic sites. Analysis of DNA constructs of increasing length suggests that HMO2 may bind distorted DNA as a dimer. DNA end‐joining and exonuclease protection assays show that it binds preferentially to the DNA ends, both blunt and cohesive ends, and that the sequence of the single‐stranded overhangs plays in DNA end‐binding. Since HMO2 has been reported to recruit the INO80 complex to the region of a double strand break, and since it effectively protects DNA ends against exonucleolytic cleavage, it is possible that it contributes to DNA repair beyond its role in INO80 recruitment.