LINE L1 retrotransposable element is targeted during the initial stages of apoptotic DNA fragmentation

Abstract

Using a directional cloning strategy, DNA sequence information was obtained corresponding to the site of early radiation-induced apoptotic DNA fragmentation within the human lymphoblastoid cell line TK6. Data were obtained from 88 distinct clones comprising approximately 65 kbp of sequenced material. Analysis of all cloned material showed that sequences in the 10 bp immediately adjacent to the cleavage sites were enriched in short oligoT tracts. The proportion of repetitive DNA within the entire cloned material was found to be within the normal range. However the distribution of Alu and LINE repetitive DNA were biased to positions at or adjacent to the apoptotic cleavage site. In particular, a non-random distribution of five cleavage sites was found clustered within the second ORF of the LINE L1 that partially overlapped with two binding sites for the nuclear matrix-associated protein SATB1. Three other clones, containing alpha satellite elements, were also linked to a DNA matrix binding function. These data indicate that the site of chromatin loop formation at the nuclear matrix may be a specific target for early DNA fragmentation events during apoptosis.

The telomeric region is excluded from nucleosomal fragmentation during apoptosis, but the bulk nuclear chromatin is randomly degraded

“…Therefore, our results point to a random cleavage of the chromatin during apoptosis. This is different from other reports that found preferential sites of apoptotic DNA cleavage, 26,27,28 but there is an equal number of reports supporting our findings.…”

Mapping the initial DNA breaks in apoptotic Jurkat cells using ligation-mediated PCR

“…6,38 However, others have shown that the activation of endogenous and several exogenous nucleases also results in DNA digestion in the proximity of MARs and produces similar sets of high molecular weight 50 and 300 kb fragments as those generated by topoisomerase II inhibitors. 7,36 More direct evidence that MARs are specific targets for early DNA cleavage came recently from the study of Khodarev et al 39 These authors performed a directional cloning of DNA ends corresponding to high molecular weight chromatin fragments produced during radiation-induced apoptosis, and found them to contain ATrich MAR-like sequences.…”

Degradation of chromosomal DNA during apoptosis

“…Subsequently, the application of pulsed-field gel electrophoresis showed that prior to or in the absence of internucleosomal cleavage, chromosomal DNA is cleaved into large fragments of 50-300 kb. 12,13 The sequence of the cleavage sites is A/Trich, as found in the nuclear scaffold region, 14 suggesting that chromatins are cleaved by a nuclease at the nuclear scaffold attachment sites. A different requirement for metal ions (Mg which efficiently undergo apoptotic DNA fragmentation.…”