Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
| Autor: | Andrew S. Earl, Steven M. Johnson, David A. Bates, Colin Skousen, Ashley N. Fetbrandt, Jordon Ritchie, Charles E. Bates, Paul Bodily |
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| Rok vydání: | 2021 |
| Předmět: |
Transcription
Genetic Science Genomics In Vitro Techniques chemistry.chemical_compound Animals Nucleosome Genomic library Caenorhabditis elegans Caenorhabditis elegans Proteins Genome Multidisciplinary biology Chemistry DNA Nucleosomes Chromatin Histone Terminal (electronics) DNA methylation biology.protein Biophysics Medicine Research Article |
| Zdroj: | PLoS ONE, Vol 16, Iss 10 (2021) PLoS ONE PLoS ONE, Vol 16, Iss 10, p e0258737 (2021) |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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