In:
PLOS ONE, Public Library of Science (PLoS), Vol. 16, No. 10 ( 2021-10-21), p. e0258737-
Abstract:
The most basic level of eukaryotic gene regulation is the presence or absence of nucleosomes on DNA regulatory elements. In an effort to elucidate in vivo nucleosome patterns, in vitro studies are frequently used. In vitro , short DNA fragments are more favorable for nucleosome formation, increasing the likelihood of nucleosome occupancy. This may in part result from the fact that nucleosomes prefer to form on the terminal ends of linear DNA. This phenomenon has the potential to bias in vitro reconstituted nucleosomes and skew results. If the ends of DNA fragments are known, the reads falling close to the ends are typically discarded. In this study we confirm the phenomenon of end bias of in vitro nucleosomes. We describe a method in which nearly identical libraries, with different known ends, are used to recover nucleosomes which form towards the terminal ends of fragmented DNA. Finally, we illustrate that although nucleosomes prefer to form on DNA ends, it does not appear to skew results or the interpretation thereof.
Type of Medium:
Online Resource
ISSN:
1932-6203
DOI:
10.1371/journal.pone.0258737
DOI:
10.1371/journal.pone.0258737.g001
DOI:
10.1371/journal.pone.0258737.g002
DOI:
10.1371/journal.pone.0258737.g003
DOI:
10.1371/journal.pone.0258737.g004
DOI:
10.1371/journal.pone.0258737.g005
DOI:
10.1371/journal.pone.0258737.g006
DOI:
10.1371/journal.pone.0258737.g007
DOI:
10.1371/journal.pone.0258737.g008
DOI:
10.1371/journal.pone.0258737.g009
DOI:
10.1371/journal.pone.0258737.g010
DOI:
10.1371/journal.pone.0258737.g011
DOI:
10.1371/journal.pone.0258737.g012
DOI:
10.1371/journal.pone.0258737.t001
DOI:
10.1371/journal.pone.0258737.t002
DOI:
10.1371/journal.pone.0258737.t003
DOI:
10.1371/journal.pone.0258737.s001
DOI:
10.1371/journal.pone.0258737.s002
DOI:
10.1371/journal.pone.0258737.s003
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2021
detail.hit.zdb_id:
2267670-3
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