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The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions
We report here that early apoptotic DNA fragmentation, as obtained by using an entirely new approach, is the result of an attack at a small number of specific open chromatin regions of interphase nuclei. This was demonstrated as follows: (i) chicken liver was excised and kept in sterile tubes for 1...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661134/ https://www.ncbi.nlm.nih.gov/pubmed/19347039 http://dx.doi.org/10.1371/journal.pone.0005010 |
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author | Di Filippo, Miriam Bernardi, Giorgio |
author_facet | Di Filippo, Miriam Bernardi, Giorgio |
author_sort | Di Filippo, Miriam |
collection | PubMed |
description | We report here that early apoptotic DNA fragmentation, as obtained by using an entirely new approach, is the result of an attack at a small number of specific open chromatin regions of interphase nuclei. This was demonstrated as follows: (i) chicken liver was excised and kept in sterile tubes for 1 to 3 hours at 37°C; (ii) this induced apoptosis (possibly because of oxygen deprivation), as shown by the electrophoretic nucleosomal ladder produced by DNA preparations; (iii) low molecular-weight DNA fragments (∼200 bp) were cloned, sequenced, and shown to derive predominantly from genes and surrounding 100 kb regions; (iv) a few hundred cuts were produced, very often involving the same chromosomal sites; (v) at comparable DNA degradation levels, micrococcal nuclease (MNase) also showed a general preference for genes and surrounding regions, but MNase cuts were located at sites that were quite distinct from, and less specific than, those cut by apoptosis. In conclusion, the approach presented here, which is the mildest and least intrusive approach, identifies a preferred accessibility landscape in interphase chromatin. |
format | Text |
id | pubmed-2661134 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-26611342009-04-06 The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions Di Filippo, Miriam Bernardi, Giorgio PLoS One Research Article We report here that early apoptotic DNA fragmentation, as obtained by using an entirely new approach, is the result of an attack at a small number of specific open chromatin regions of interphase nuclei. This was demonstrated as follows: (i) chicken liver was excised and kept in sterile tubes for 1 to 3 hours at 37°C; (ii) this induced apoptosis (possibly because of oxygen deprivation), as shown by the electrophoretic nucleosomal ladder produced by DNA preparations; (iii) low molecular-weight DNA fragments (∼200 bp) were cloned, sequenced, and shown to derive predominantly from genes and surrounding 100 kb regions; (iv) a few hundred cuts were produced, very often involving the same chromosomal sites; (v) at comparable DNA degradation levels, micrococcal nuclease (MNase) also showed a general preference for genes and surrounding regions, but MNase cuts were located at sites that were quite distinct from, and less specific than, those cut by apoptosis. In conclusion, the approach presented here, which is the mildest and least intrusive approach, identifies a preferred accessibility landscape in interphase chromatin. Public Library of Science 2009-04-06 /pmc/articles/PMC2661134/ /pubmed/19347039 http://dx.doi.org/10.1371/journal.pone.0005010 Text en Di Filippo et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Di Filippo, Miriam Bernardi, Giorgio The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions |
title | The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions |
title_full | The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions |
title_fullStr | The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions |
title_full_unstemmed | The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions |
title_short | The Early Apoptotic DNA Fragmentation Targets a Small Number of Specific Open Chromatin Regions |
title_sort | early apoptotic dna fragmentation targets a small number of specific open chromatin regions |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661134/ https://www.ncbi.nlm.nih.gov/pubmed/19347039 http://dx.doi.org/10.1371/journal.pone.0005010 |
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