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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
...a linker with a TEV cleavage site. Because H3 and H2B bind exclusively in the context of the histone octamer, myc cleavage only occurs after nucleosome formation on DNA. Accordingly, at any given genomic locus, HA levels report on nucleosome (H3) occupancy, and myc levels report on the associated H3...
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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
...splicing efficiency and shape intron evolution in Paramecium has not been studied so far.Here, we investigated a possible role of nucleosome positioning in the recognition of introns in P. tetraurelia. We mapped the nucleosome occupancy in the somatic MAC through paired-end (PE) MNase-seq. We compared...
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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
...is higher than at TSSs.The high levels of supercoiling at high-occupancy rex sites could result from condensin translocation, as shown previously for Saccharomyces cerevisiae condensin, which moves processively along DNA over long (≥10 kb) distances (Terakawa et al. 2017). Supercoiling of chromatin fibers...
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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
..., such as transcription (Piña et al. 1990; Lam et al. 2008). In light of this, it is crucial to understand how nucleosomes are organized across the . Genome-wide nucleosome maps in major model organisms have revealed strikingly similar nucleosome patterns near gene starts, where a nucleosome-depleted region upstream...
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Research: Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation
- Hongfang Qiu,
- Răzvan V. Chereji,
- Cuihua Hu,
- Hope A. Cole,
- Yashpal Rawal,
- David J. Clark,
- and Alan G. Hinnebusch
Genome Res. February 2016 26: 211-225; Published in Advance November 24, 2015, doi:10.1101/gr.196337.115
...sorted maps depicting average Rpb3 occupancies in theCDSof uninduced versus induced cells show thatmost genes exhibiting appreciable SM induction of Qiu et al. 214 Genome Research www..org Rpb3 are clustered near the top and thus display strong eviction of promoter nucleosomes (Fig. 2D, ii, iii, left...
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Research: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin
- J. Peter Svensson,
- Manu Shukla,
- Victoria Menendez-Benito,
- Ulrika Norman-Axelsson,
- Pauline Audergon,
- Indranil Sinha,
- Jason C. Tanny,
- Robin C. Allshire,
- and Karl Ekwall
Genome Res. June 2015 25: 872-883; Published in Advance March 16, 2015, doi:10.1101/gr.188870.114
....ekwall@ki.se Abstract Nucleosome composition actively contributes to chromatin structure and accessibility. Cells have developed mechanisms to remove or recycle histones, generating a landscape of differentially aged nucleosomes. This study aimed to create a high-resolution, genome-wide map of nucleosome turnover...
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Research: Canonical nucleosome organization at promoters forms during genome activation
- Yong Zhang,
- Nadine L. Vastenhouw,
- Jianxing Feng,
- Kai Fu,
- Chenfei Wang,
- Ying Ge,
- Andrea Pauli,
- Paul van Hummelen,
- Alexander F. Schier,
- and X. Shirley Liu
Genome Res. February 2014 24: 260-266; Published in Advance November 27, 2013, doi:10.1101/gr.157750.113
...to identify determinants of nucleosome positioning: A unifying model for establishing the -wide pattern. Mol Cell 48: 5–15. Jiang C, Pugh BF. 2009a. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae . Genome Biol 10: R109. Jiang C, Pugh BF. 2009b. Nucleosome...
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Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
...et al. 2005). An initial clue regarding the -wide organization of histone modifications was achieved by employing ChIP-seq to map H3K4me3, H3K27ac, and H2A.Z in interphase and mitotic cells. The -wide maps of H3K4me3 and H2A.Z revealed that the general genomic localization of these marks is conserved...
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Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
- Christopher T. Coey and
- David J. Clark
Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
...are not completely blocked by chromatin.To test whether AP-1 motifs are differentially located relative to nucleosomes, we divided the motifs into RY, RR/YY, and YR types and sorted each set by Gcn4 occupancy in vivo or in vitro (Supplemental Fig. S6A). Heat maps showing nucleosome occupancy in induced cells (Cole...
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Research: A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon
- Joshua A. Baller,
- Jiquan Gao,
- Radostina Stamenova,
- M. Joan Curcio,
- and Daniel F. Voytas
Genome Res. April 2012 22: 704-713; Published in Advance January 4, 2012, doi:10.1101/gr.129585.111
...A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon Joshua A. Baller 1 , 2 , 5 , Jiquan Gao 1 , 5 , Radostina Stamenova 3 , M. Joan Curcio 3 , 4 and Daniel F. Voytas 1 , 6...

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