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| Item Type: | Article |
|---|---|
| Title: | The effect of micrococcal nuclease digestion on nucleosome positioning data |
| Creators Name: | Chung, H.R., Dunkel, I., Heise, F., Linke, C., Krobitsch, S., Ehrenhofer-Murray, A.E., Sperling, S.R. and Vingron, M. |
| Abstract: | Eukaryotic genomes are packed into chromatin, whose basic repeating unit is the nucleosome. Nucleosome positioning is a widely researched area. A common experimental procedure to determine nucleosome positions involves the use of micrococcal nuclease (MNase). Here, we show that the cutting preference of MNase in combination with size selection generates a sequence-dependent bias in the resulting fragments. This strongly affects nucleosome positioning data and especially sequence-dependent models for nucleosome positioning. As a consequence we see a need to re-evaluate whether the DNA sequence is a major determinant of nucleosome positioning in vivo. More generally, our results show that data generated after MNase digestion of chromatin requires a matched control experiment in order to determine nucleosome positions. |
| Keywords: | Algorithms, Automated Pattern Recognition, Chromatin, Codon, Computational Biology, Dimerization, DNA, DNA Sequence Analysis, , Fungal DNA, Fungal Genome, Micrococcal Nuclease, Nucleosomes, Pancreatic Ribonuclease, Protein Databases, Saccharomyces Cerevisiae |
| Source: | PLoS ONE |
| ISSN: | 1932-6203 |
| Publisher: | Public Library of Science |
| Volume: | 5 |
| Number: | 12 |
| Page Range: | e15754 |
| Date: | 29 December 2010 |
| Official Publication: | https://doi.org/10.1371/journal.pone.0015754 |
| PubMed: | View item in PubMed |
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