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Research: Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
- Elise A. Mahé,
- Thierry Madigou,
- Aurélien A. Sérandour,
- Maud Bizot,
- Stéphane Avner,
- Frédéric Chalmel,
- Gaëlle Palierne,
- Raphaël Métivier,
- and Gilles Salbert
Genome Res. June 2017 27: 947-958; Published in Advance April 10, 2017, doi:10.1101/gr.211466.116
...-DhMRs or undergoing activation for up-DhMRs (Sérandour et al. 2012). In order to obtain a more complete view of these dynamic processes at the full sets of up- and down-DhMRs, we first analyzed the temporal variations of H3K4me1 and H3K27ac histone modifications -wide by ChIP-seq, together with those of 5hmC and 5m...
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Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
- Yamile Marquez,
- Markus Höpfler,
- Zahra Ayatollahi,
- Andrea Barta,
- and Maria Kalyna
Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
...DNA methylation, histone modifications, and positioning of nucleosomes over introns and exons and at exon/intron boundaries contribute significantly to the recognition of the core splicing signals and can change splice site selection, resulting in AS events (Braunschweig et al. 2013; Reddy et al. 2013...
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Research: Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- Nicole C. Riddle,
- Aki Minoda,
- Peter V. Kharchenko,
- Artyom A. Alekseyenko,
- Yuri B. Schwartz,
- Michael Y. Tolstorukov,
- Andrey A. Gorchakov,
- Jacob D. Jaffe,
- Cameron Kennedy,
- Daniela Linder-Basso,
- Sally E. Peach,
- Gregory Shanower,
- Haiyan Zheng,
- Mitzi I. Kuroda,
- Vincenzo Pirrotta,
- Peter J. Park,
- Sarah C.R. Elgin,
- and Gary H. Karpen
Genome Res. February 2011 21: 147-163; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110
...remain poorly characterized. At the core of chromatin are the histone proteins, which assemble DNA into nucleosomes, providing the basis for higher order chromatin packaging. A variety of post-translational histone modifications are used in combination to define alternative chromatin states (Jenuwein...
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Method: Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
- Su Wang,
- Chongzhi Zang,
- Tengfei Xiao,
- Jingyu Fan,
- Shenglin Mei,
- Qian Qin,
- Qiu Wu,
- Xujuan Li,
- Kexin Xu,
- Housheng Hansen He,
- Myles Brown,
- Clifford A. Meyer,
- and X. Shirley Liu
Genome Res. October 2016 26: 1417-1429; Published in Advance July 27, 2016, doi:10.1101/gr.201574.115
...cell types. Second, chromatin exists in several “states” (Barski et al. 2007; Heintzman et al. 2007; Ernst and Kellis 2010; Ernst et al. 2011; Hoffman et al. 2013) with a spectrum of functional properties that may be identified using ChIP-seq of histone modifications. In particular, transcription...
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Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- Yong Cheng,
- Weisheng Wu,
- Swathi Ashok Kumar,
- Duonan Yu,
- Wulan Deng,
- Tamara Tripic,
- David C. King,
- Kuan-Bei Chen,
- Ying Zhang,
- Daniela Drautz,
- Belinda Giardine,
- Stephan C. Schuster,
- Webb Miller,
- Francesca Chiaromonte,
- Yu Zhang,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
...that participates in erythroid differentiation, at least in part by complexing with GATA1 (Shivdasani et al. 1995); this latter feature is associated with positive regulation of target genes (Tripic et al. 2009). Furthermore, given the important role of histone modifications in gene regulation and the established...
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ARTICLE: The landscape of histone modifications across 1% of the human genome in five human cell lines
- Christoph M. Koch,
- Robert M. Andrews,
- Paul Flicek,
- Shane C. Dillon,
- Ulaş Karaöz,
- Gayle K. Clelland,
- Sarah Wilcox,
- David M. Beare,
- Joanna C. Fowler,
- Phillippe Couttet,
- Keith D. James,
- Gregory C. Lefebvre,
- Alexander W. Bruce,
- Oliver M. Dovey,
- Peter D. Ellis,
- Pawandeep Dhami,
- Cordelia F. Langford,
- Zhiping Weng,
- Ewan Birney,
- Nigel P. Carter,
- David Vetrie,
- and Ian Dunham
Genome Res. June 2007 17: 691-707; doi:10.1101/gr.5704207
...with the transcriptional start sites (TSSs) of genes, while H3K4me1 and H4ac have more widespread distributions. TSSs reveal characteristic patterns of both types of modification present and the position relative to TSSs. These patterns differ between active and inactive genes and in particular the state of H3K4me3 and H3...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., a particular gene of interest (GOI) remains a persistent experimental and conceptual challenge. This gene-centric question is complicated by the multilayered regulatory environment in which each gene resides, comprising 3D chromatin structure, enhancer–promoter looping, DNA accessibility, histone modifications...
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LETTER: Two Breakpoint Clusters at Fragile Site FRA3B Form Phased Nucleosomes
- David J. Mulvihill and
- Yuh-Hwa Wang
Genome Res. July 2004 14: 1350-1357; doi:10.1101/gr.2304404
...nucleosome positioning elements. These results suggest that other factors appear to cooperate with the DNA sequence of these regions to impart nucleosome phasing. This study provides the first information on the chromatin structure of breakpoint regions in a common fragile site. The observation of phased...
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Research: Genome-wide phosphoacetylation of histone H3 at Drosophila enhancers and promoters
- Wendy A. Kellner,
- Edward Ramos,
- Kevin Van Bortle,
- Naomi Takenaka,
- and Victor G. Corces
Genome Res. June 2012 22: 1081-1088; Published in Advance April 16, 2012, doi:10.1101/gr.136929.111
...by modENCODE are shown in Supplemental Figure S4. Both H3K9acS10ph and H3K27acS28ph have very similar profiles as H3K4me3, suggesting these histone modifications occur on the same nucleosomes, the peak of which is located at the first nucleosome downstream from the TSS (Fig. 6A). These results suggest...
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Research: Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin
- Sophie Chantalat,
- Arnaud Depaux,
- Patrick Héry,
- Sophie Barral,
- Jean-Yves Thuret,
- Stefan Dimitrov,
- and Matthieu Gérard
Genome Res. September 2011 21: 1426-1437; Published in Advance July 29, 2011, doi:10.1101/gr.118091.110
...is available for this article.] Modulation of the biochemical properties of nucleosomes through histone covalent modifications plays a crucial role in the regulation of transcription in mammals (Kouzarides 2007; Ruthenburg et al. 2007). These modifications can alter the structure of chromatin and stimulate...

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