Non-random features of loop-size chromatin fragmentation

Ildikó Szilágyi, Tamás Varga, Lóránt Székvölgyi, Éva Hegedüs, Katalin Goda, Viktória Kaczur, Zsolt Bacsó, Yuji Nakayama, János Pósafi, Sándor Pongor, Gábor Szabó

Research output: Contribution to journalArticle

7 Citations (Scopus)


Upon isolation of DNA from normal eukaryotic cells by standard methods involving extensive proteolytic treatment, a rather homogeneous population of loop-size, double-stranded DNA fragments is regularly obtained. These DNA molecules can be efficiently end-labeled by the DNA polymerase I Klenow fragment, as well as by a 3′- to -5′-exonuclease-free Klenow enzyme, but not by terminal transferase (TdT) unless the ends have been filled up by Klenow, suggesting that dominantly 5′ protruding termini are generated upon fragmentation. The filled-up termini were used for cloning the distal parts of the ∼50 kb fragments. BLAST analysis of the sequence of several clones allowed us to determine the sequence of the non-cloned side of the breakpoints. Comparison of 25, 600 bp-long breakpoint sequences demonstrated prevalence of repetitive elements. Consensus motives characteristic of the breakpoint sequences have been identified. Several sequences exhibit peculiar computed conformational characteristics, with sharp transition or center of symmetry located exactly at the breakpoint. Our data collectively suggest that chromatin fragmentation involves nucleolytic cleavages at fragile/hypersensitive sites delimiting loop-size fragments in a non-random manner. Interestingly, the sequence characteristics of the breakpoints are reminiscent of certain breakpoint cluster regions frequently subject to gene rearrangements.

Original languageEnglish
Pages (from-to)1193-1205
Number of pages13
JournalJournal of cellular biochemistry
Issue number6
Publication statusPublished - Aug 15 2003



  • 50 kb
  • Apoptosis
  • Chromatin
  • Fragility
  • Fragmentation
  • Klenow
  • Terminal transferase

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Szilágyi, I., Varga, T., Székvölgyi, L., Hegedüs, É., Goda, K., Kaczur, V., Bacsó, Z., Nakayama, Y., Pósafi, J., Pongor, S., & Szabó, G. (2003). Non-random features of loop-size chromatin fragmentation. Journal of cellular biochemistry, 89(6), 1193-1205.