Non-random features of loop-size chromatin fragmentation

摘要: Upon isolation of DNA from normal eukaryotic cells by standard methods involving extensive proteolytic treatment, a rather homogeneous population loop-size, double-stranded fragments is regularly obtained. These molecules can be efficiently end-labeled the polymerase I Klenow fragment, as well 3 0 -t o -5 - exonuclease-free enzyme, but not terminal transferase (TdT) unless ends have been filled up Klenow, suggesting that dominantly 5 protruding termini are generated upon fragmentation. The filled-up were used for cloning distal parts the50 kb fragments. BLAST analysis sequence several clones allowed us to determine non-cloned side breakpoints. Comparison 25, 600 bp-long breakpoint sequences demonstrated prevalence repetitive elements. Consensus motives characteristic identified. Several exhibit peculiar computed conformational characteristics, with sharp transition or center symmetry located exactly at breakpoint. Our data collectively suggest chromatin fragmentation involves nucleolytic cleavages fragile/hypersensitive sites delimiting loop-size in non-random manner. Interestingly, characteristics breakpoints reminiscent certain cluster regions frequently subject