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1
Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions.
Biophys J. 2017 Feb 7;112(3):505-511. doi: 10.1016/j.bpj.2016.12.041. Epub 2017 Jan 25.
2
Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches.
J Biomol Struct Dyn. 2010 Jun;27(6):747-64. doi: 10.1080/07391102.2010.10508583.
3
A genomic code for nucleosome positioning.
Nature. 2006 Aug 17;442(7104):772-8. doi: 10.1038/nature04979. Epub 2006 Jul 19.
4
Prediction of nucleosome occupancy in Saccharomyces cerevisiae using position-correlation scoring function.
Genomics. 2011 Nov;98(5):359-66. doi: 10.1016/j.ygeno.2011.07.008. Epub 2011 Aug 2.
5
A high-resolution atlas of nucleosome occupancy in yeast.
Nat Genet. 2007 Oct;39(10):1235-44. doi: 10.1038/ng2117. Epub 2007 Sep 16.
6
Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals.
Mol Biosyst. 2009 Dec;5(12):1703-12. doi: 10.1039/b905132e. Epub 2009 May 29.
7
Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution.
Biochem Soc Trans. 2012 Apr;40(2):377-82. doi: 10.1042/BST20110730.
8
The molecular evolution of nucleosome positioning through sequence-dependent deformation of the DNA polymer.
J Biomol Struct Dyn. 2010 Jun;27(6):765-80. doi: 10.1080/07391102.2010.10508584.
10
A comparative evaluation on prediction methods of nucleosome positioning.
Brief Bioinform. 2014 Nov;15(6):1014-27. doi: 10.1093/bib/bbt062. Epub 2013 Sep 10.

引用本文的文献

1
The importance of DNA sequence for nucleosome positioning in transcriptional regulation.
Life Sci Alliance. 2024 Jun 3;7(8). doi: 10.26508/lsa.202302380. Print 2024 Aug.
2
Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.
J Chem Phys. 2023 Nov 28;159(20). doi: 10.1063/5.0165136.
3
The role of transcript regions and amino acid choice in nucleosome positioning.
NAR Genom Bioinform. 2023 Sep 11;5(3):lqad080. doi: 10.1093/nargab/lqad080. eCollection 2023 Sep.
4
Multiplexing mechanical and translational cues on genes.
Biophys J. 2022 Nov 15;121(22):4311-4324. doi: 10.1016/j.bpj.2022.10.011. Epub 2022 Oct 13.
5
Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.
Int J Mol Sci. 2022 Apr 28;23(9):4869. doi: 10.3390/ijms23094869.
6
The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.
Int J Mol Sci. 2021 Jul 30;22(15):8233. doi: 10.3390/ijms22158233.
7
Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution.
Genes (Basel). 2021 Jun 1;12(6):851. doi: 10.3390/genes12060851.
8
Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells.
Nat Commun. 2021 May 5;12(1):2524. doi: 10.1038/s41467-021-22688-x.
9
On the role of transcription in positioning nucleosomes.
PLoS Comput Biol. 2021 Jan 8;17(1):e1008556. doi: 10.1371/journal.pcbi.1008556. eCollection 2021 Jan.
10
Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters.
Nat Commun. 2020 Feb 26;11(1):1075. doi: 10.1038/s41467-020-14950-5.

本文引用的文献

1
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach.
PLoS One. 2016 Jun 7;11(6):e0156905. doi: 10.1371/journal.pone.0156905. eCollection 2016.
2
Why Do Nucleosomes Unwrap Asymmetrically?
J Phys Chem B. 2016 Jul 7;120(26):5855-63. doi: 10.1021/acs.jpcb.6b00391. Epub 2016 Mar 24.
3
Ensembl Genomes 2016: more genomes, more complexity.
Nucleic Acids Res. 2016 Jan 4;44(D1):D574-80. doi: 10.1093/nar/gkv1209. Epub 2015 Nov 17.
4
Chromatin-remodeling and the initiation of transcription.
Q Rev Biophys. 2015 Nov;48(4):465-70. doi: 10.1017/S0033583515000116.
5
Nucleosome positioning: resources and tools online.
Brief Bioinform. 2016 Sep;17(5):745-57. doi: 10.1093/bib/bbv086. Epub 2015 Sep 26.
6
Determinants of nucleosome positioning and their influence on plant gene expression.
Genome Res. 2015 Aug;25(8):1182-95. doi: 10.1101/gr.188680.114. Epub 2015 Jun 10.
7
The effects of chromatin organization on variation in mutation rates in the genome.
Nat Rev Genet. 2015 Apr;16(4):213-23. doi: 10.1038/nrg3890. Epub 2015 Mar 3.
9
Canonical nucleosome organization at promoters forms during genome activation.
Genome Res. 2014 Feb;24(2):260-6. doi: 10.1101/gr.157750.113. Epub 2013 Nov 27.
10
A comparative evaluation on prediction methods of nucleosome positioning.
Brief Bioinform. 2014 Nov;15(6):1014-27. doi: 10.1093/bib/bbt062. Epub 2013 Sep 10.

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