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The early apoptotic DNA fragmentation targets a small number of specific open chromatin regions

Miriam Di Filippo1, Giorgio Bernardi

  • 1Laboratory of Molecular Evolution, Stazione Zoologica Anton Dohrn, Naples, Italy.

Plos One
|April 7, 2009
PubMed

Insights

Early apoptotic DNA fragmentation targets specific open chromatin regions. This novel approach reveals preferred accessibility landscapes in interphase nuclei, offering new insights into DNA degradation.

Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • Apoptosis involves DNA fragmentation, a process not fully understood at the chromatin level.
  • Identifying specific DNA cleavage sites during early apoptosis is crucial for understanding genome regulation.

Purpose of the Study:

  • To investigate the specific genomic locations targeted during early apoptotic DNA fragmentation.
  • To characterize the chromatin accessibility landscape during apoptosis using a novel method.

Main Methods:

  • Induction of apoptosis in chicken liver by ex vivo incubation.
  • Cloning and sequencing of low molecular-weight DNA fragments generated during apoptosis.
  • Comparison of apoptotic DNA fragmentation sites with micrococcal nuclease (MNase) digestion patterns.

Main Results:

  • Apoptotic DNA fragmentation predominantly occurs at specific open chromatin regions, particularly within and around genes.
  • A limited number of chromosomal sites are repeatedly targeted during apoptosis.
  • MNase digestion shows a broader preference for gene regions but lacks the specificity observed in apoptosis-induced fragmentation.

Conclusions:

  • Early apoptotic DNA fragmentation is a targeted process, not random degradation.
  • The study identifies a "preferred accessibility landscape" in interphase chromatin that is vulnerable during apoptosis.
  • This new approach provides a mild and non-intrusive method for mapping chromatin accessibility.

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