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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
...be automatically determined from the fragment size distribution by a DPMM.SEM probabilistic modelSEM is based on a hierarchical GMM that describes the likelihood of observing a set of MNase-seq fragments from a set of nucleosomes. Each nucleosome contributes a distribution of reads surrounding its genomic position...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...with high splicing efficiency. Our data reveal a complex link between GC content, nucleosome positioning, and intron evolution in Paramecium.In eukaryotes, genomic DNA is compacted by histones into chromatin. The basic unit of chromatin is the nucleosome, which comprises a histone octamer made of the four...
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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
...bodies. We then use the model as an in silico model of the yeast machinery to predict the effect of every single mutation along the . In doing so, we assign to every nucleotide a score representing its importance regarding the nucleosome positioning process. This genomic track is accessible at Git...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...-strandedness, which is most pronounced at transcript end sites, is dependent on high AT content and symmetrically positioned nucleosomes. We propose that sharp transitions in sequence composition at functional genomic elements constitute a common regulatory code and that DNA structure and propagation of torsional...
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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
...by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased...
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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
..., Spain Corresponding author: cpg@usal.es ↵ 3 These authors contributed equally to this work. Abstract In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding...
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Research: The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand
- Rahima Ziane,
- Alain Camasses,
- and Marta Radman-Livaja
Genome Res. February 2022 32: 337-356; Published in Advance January 18, 2022, doi:10.1101/gr.275387.121
.... It is unclear how chromatin structure survives disruptions caused by genomic replication or whether chromatin features are instructive of the transcription state of the underlying gene. We developed a method to monitor budding yeast replication, transcription, and chromatin maturation dynamics on each daughter...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...captured by sequence-based nucleosome positioning programs are reflected in PT values, we started from the control sequences. We randomly selected 5000–6000 genomic sequences from human and yeast s as 320-bp control sequences and found [nucmax] predicted nucleosome scores (dyad) within each region...
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Research: Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium
- James L. Platt,
- Nicholas A. Kent,
- Alan R. Kimmel,
- and Adrian J. Harwood
Genome Res. April 2017 27: 591-600; Published in Advance March 22, 2017, doi:10.1101/gr.216309.116
...development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use -wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between...
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Research: Determinants of nucleosome positioning and their influence on plant gene expression
- Ming-Jung Liu,
- Alexander E. Seddon,
- Zing Tsung-Yeh Tsai,
- Ian T. Major,
- Monique Floer,
- Gregg A. Howe,
- and Shin-Han Shiu
Genome Res. August 2015 25: 1182-1195; Published in Advance June 10, 2015, doi:10.1101/gr.188680.114
...-disfavoring sequence poly(dA/dT) around TF binding sites (TFBSs) significantly affects transcription in yeast (Raveh-Sadka et al. 2012), showing the importance of chromatin structure as a determinant of gene expression.In plants, -wide nucleosome positions have been determined for Arabidopsis thaliana (Chodavarapu et...

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