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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes—the nucleosome repeat length (NRL)—is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites...
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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
...sequences coming from a different organism. When introduced in the cell, this sequence will be interpreted by the cellular machinery, and the resulting activity can be unpredictable. To date, there is no way to know whether the nucleosomes will assemble and position themselves on the DNA as expected...
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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
...over the transcription units compared with the flanking regions, showing regular arrays of nucleosomes over transcription units (Fig. 1C,D; Supplemental Fig. S1C,D). As expected, we were able to identify NFRs upstream of the TSSs of Paramecium genes, followed by an array of well-positioned nucleosomes...
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Method: Mapping nucleosome positions using DNase-seq
- Jianling Zhong,
- Kaixuan Luo,
- Peter S. Winter,
- Gregory E. Crawford,
- Edwin S. Iversen,
- and Alexander J. Hartemink
Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115
...substantial information about nucleosome translational positioning and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. To accomplish this, we first describe and characterize the distinctive DNase I cleavage profile on nucleosome-associated DNA. The features...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
...bound regions to orthogonal genomic annotations, or identifying TR–target interactions with cross-species evidence.ResultsFor the current study, we focused on an initial set of eight TRs to establish methodology and to calibrate expectations: ASCL1, HES1, MECP2, MEF2C, NEUROD1, PAX6, RUNX1, and TCF4...
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...mechanisms act on chromatin to change nucleosome positioning along the DNA and to modify histone residues for controlling the recruitment of regulatory factors or histone–DNA affinity (Bannister and Kouzarides 2011; Owen-Hughes and Gkikopoulos 2012). Acetylation of histones on their N terminus, for example...
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Method: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
- Brendan F. Miller,
- Dhananjay Bambah-Mukku,
- Catherine Dulac,
- Xiaowei Zhuang,
- and Jean Fan
Genome Res. October 2021 31: 1843-1855; Published in Advance May 25, 2021, doi:10.1101/gr.271288.120
...resolved spots or beads, resulting in RNA sequencing measurements with uniformly gridded 2D positional information. To validate MERINGUE, we expected that identified spatially heterogeneous genes in the MOB should mark transcriptionally distinct and spatially organized cell layers or combinations of cell...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...-resectioning that extends up to ∼8 kb away from the break. We also examined the temporal dynamics of NHEJ-mediated repair in a G1-arrested population. Concomitant with DSB repair by NHEJ, we observed the redeposition and precise repositioning of nucleosomes at their originally occupied positions. This re...
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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
...DNA packaging unit in eukaryotes, is fundamental for understanding regulation because nucleosomes modulate DNA access by their positioning along the . A cell-population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across...
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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
...(Kaplan et al. 2009). The predicted nucleosome occupancy is scored by a probability for each nucleotide position to be located in the nucleosome center (or dyad). We selected the maximal [nucmax] score (for the most likely predicted dyad position) within the mean length of ChIP-seq peak (320 bp) for each...

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