Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis

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...

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Autores principales:	David A. Bates, Charles E. Bates, Andrew S. Earl, Colin Skousen, Ashley N. Fetbrandt, Jordon Ritchie, Paul M. Bodily, Steven M. Johnson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c86a3649f67341a7baec3e8da3f8a2c1
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spelling	oai:doaj.org-article:c86a3649f67341a7baec3e8da3f8a2c12021-11-04T06:07:15ZProximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis1932-6203https://doaj.org/article/c86a3649f67341a7baec3e8da3f8a2c12021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8530345/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.David A. BatesCharles E. BatesAndrew S. EarlColin SkousenAshley N. FetbrandtJordon RitchiePaul M. BodilySteven M. JohnsonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q David A. Bates Charles E. Bates Andrew S. Earl Colin Skousen Ashley N. Fetbrandt Jordon Ritchie Paul M. Bodily Steven M. Johnson Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
description	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.
format	article
author	David A. Bates Charles E. Bates Andrew S. Earl Colin Skousen Ashley N. Fetbrandt Jordon Ritchie Paul M. Bodily Steven M. Johnson
author_facet	David A. Bates Charles E. Bates Andrew S. Earl Colin Skousen Ashley N. Fetbrandt Jordon Ritchie Paul M. Bodily Steven M. Johnson
author_sort	David A. Bates
title	Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
title_short	Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
title_full	Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
title_fullStr	Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
title_full_unstemmed	Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
title_sort	proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/c86a3649f67341a7baec3e8da3f8a2c1
work_keys_str_mv	AT davidabates proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT charlesebates proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT andrewsearl proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT colinskousen proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT ashleynfetbrandt proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT jordonritchie proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT paulmbodily proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis AT stevenmjohnson proximalendbiasfrominvitroreconstitutednucleosomesandtheresultondownstreamdataanalysis
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Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis

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