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Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23: 341–351. doi:10.1101/gr.142067.112 ↵Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W, Li X, et al. 2013b. H3.3 actively marks enhancers and primes gene transcription via opening higher...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...) -wide absolute occupancy measurement in chromatin by differential cytosine methylation at position C-5 in CpG or GpC motifs and called it occupancy measurement via DNA methylation and high-throughput sequencing (ODM-seq) (Fig. 1A, right). Comparing DNA methylation of in vitro reconstituted nucleosomes...
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Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...digestion. Digestion by a nuclease, such as micrococcal nuclease (MNase), provides a complementary perspective to understanding chromatin occupancy by probing accessibility at base-pair precision. Recent -wide mapping studies have used nucleosome-sized MNase-seq fragments to characterize the dynamics...
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Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
..., Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. 2013. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23: 341–351. doi:10.1101/gr.142067.112 ↵Chen W, Liu Y, Zhu S, Green CD, Wei G, Han JDJ. 2014. Improved nucleosome-positioning algorithm iNPS for accurate...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
.... The position of nucleosomes on DNA and the organization of nucleosomes into higher-order chromatin structures also plays major roles in gene regulation (Kouzarides 2007; Li et al. 2007). For example, nucleosomes can occlude sequence-specific transcription factors and the transcriptional machinery from...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...GE. 2008. High-resolution mapping and characterization of open chromatin across the . Cell 132: 311–322. ↵Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. 2013. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23: 341–351. ↵Chen J, Li E, Zhang...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...parameters that define it: first, the nucleosome position itself; second, its occupancy; and finally, its fuzziness, with the latter term meaning the degree of freedom that a nucleosome has to take up its unitary position within in a population of cells. This degree of freedom is high when a fuzzy nucleosome...
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Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
- Sara González,
- Alicia García,
- Enrique Vázquez,
- Rebeca Serrano,
- Mar Sánchez,
- Luis Quintales,
- and Francisco Antequera
Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
...in green. The y-axis indicates occupancy normalized to the average. Vertical dashed lines indicate the position of the ura4 ORF. Nucleosomes are numbered as in A. (D) Nucleosome occupancymap of the 1_6, 1_3, and Shuffled strains (blue) and DANPOS analysis. Left yaxis indicates the log2-fold difference...
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Research: DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
- Leslie Y. Beh,
- Manuel M. Müller,
- Tom W. Muir,
- Noam Kaplan,
- and Laura F. Landweber
Genome Res. November 2015 25: 1727-1738; Published in Advance September 1, 2015, doi:10.1101/gr.188516.114
...the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena is intrinsically unfavorable for nucleosome formation, we propose...
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Method: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
- Alicia N. Schep,
- Jason D. Buenrostro,
- Sarah K. Denny,
- Katja Schwartz,
- Gavin Sherlock,
- and William J. Greenleaf
Genome Res. November 2015 25: 1757-1770; Published in Advance August 27, 2015, doi:10.1101/gr.192294.115
...of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis...
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