PUBLICATION
Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
- Authors
- Nakamura, R., Uno, A., Kumagai, M., Morishita, S., Takeda, H.
- ID
- ZDB-PUB-170922-12
- Date
- 2017
- Source
- Epigenetics & chromatin 10: 44 (Journal)
- Registered Authors
- Takeda, Hiroyuki
- Keywords
- DNA methylation, DNA sequence, Nucleosome positioning, Vertebrate
- MeSH Terms
-
- Animals
- Chromatin Assembly and Disassembly
- DNA Methylation*
- Fish Proteins/genetics*
- Fish Proteins/metabolism
- Machine Learning
- Nucleosomes/genetics*
- Nucleosomes/metabolism
- Nucleotide Motifs*
- Oryzias
- Promoter Regions, Genetic
- Sequence Analysis, DNA/methods
- PubMed
- 28931432 Full text @ Epigenetics Chromatin
Citation
Nakamura, R., Uno, A., Kumagai, M., Morishita, S., Takeda, H. (2017) Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts. Epigenetics & chromatin. 10:44.
Abstract
Background Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed.
Results Using DNase I-seq in medaka embryos, we demonstrated that hypomethylated domains (HMDs) specifically possess accessible nucleosome organization with longer linkers, and we reassessed the DNA sequence preference for nucleosome positioning in these specific regions. Remarkably, we found with a supervised machine learning algorithm, k-mer SVM, that nucleosome positioning in HMDs is accurately predictable from DNA sequence alone. Specific short sequences (6-mers) that contribute to the prediction are specifically enriched in HMDs and distribute periodically with approximately 200-bp intervals which prepattern the position of accessible linkers. Surprisingly, the sequence preference of the nucleosome and linker in HMDs is opposite from that reported previously. Furthermore, the periodicity of specific motifs at hypomethylated promoters was conserved in zebrafish.
Conclusion This study reveals strong link between nucleosome positioning and DNA sequence at vertebrate promoters, and we propose hypomethylated DNA-specific regulation of nucleosome positioning.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping