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Research: Relationship between histone modifications and transcription factor binding is protein family specific
- Beibei Xin and
- Remo Rohs
Genome Res. March 2018 28: 321-333; Published in Advance January 11, 2018, doi:10.1101/gr.220079.116
...fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...
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Method: ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
- Tyler J. Hansen and
- Emily Hodges
Genome Res. August 2022 32: 1529-1541; Published in Advance July 20, 2022, doi:10.1101/gr.276766.122
..., active regions contain EP300 at their center with histone 3 lysine 27 acetylation (H3K27ac) more broadly distributed across the center; histone 3 lysine 4 mono-methylation (H3K4me1) is also present at distal regions, whereas histone 3 lysine 4 tri-methylation (H3K4me3) is at proximal regions. In addition...
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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
...methylation is more complex as it depends on the position and state of methylation (mono-, di-, or trimethylation) (Martin and Zhang 2005). Studies using different model organisms have linked the methylation of histone H3 at both lysines 4 and 36 to transcriptionally active regions (Barski et al. 2007...
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Research: A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development
- Claus Schertel,
- Monica Albarca,
- Claudia Rockel-Bauer,
- Nicholas W. Kelley,
- Johannes Bischof,
- Korneel Hens,
- Erik van Nimwegen,
- Konrad Basler,
- and Bart Deplancke
Genome Res. April 2015 25: 514-523; Published in Advance January 7, 2015, doi:10.1101/gr.181305.114
...on an Illumina HiSeq 2500 machine at the Lausanne Genomics Technologies Facility (GTF), obtaining more than 200 million 100-bp reads per sequenced lane. The following antibodies (Abcam) were used in this study: ab6002, anti-Histone H3 (tri methyl K27); ab28940, anti-Histone H3 (mono+di+tri methyl K79); ab8895...
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Research: Coordinated histone modifications are associated with gene expression variation within and between species
- Misook Ha,
- Danny W-K. Ng,
- Wen-Hsiung Li,
- and Z. Jeffrey Chen
Genome Res. April 2011 21: 590-598; Published in Advance February 4, 2011, doi:10.1101/gr.116467.110
...nucleosomes were evenly distributed across the , whereas H3K9ac and H3K4me3 were predominantly enriched in genic regions (Supplemental Fig. S1), consistent with the report that H3K4 mono-, di-, and tri-methylation are highly enriched in gene-rich euchromatin (Zhang et al. 2009). The overall distribution of H3...
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Letter: Nucleosomes are well positioned in exons and carry characteristic histone modifications
- Robin Andersson,
- Stefan Enroth,
- Alvaro Rada-Iglesias,
- Claes Wadelius,
- and Jan Komorowski
Genome Res. October 2009 19: 1732-1741; Published in Advance August 17, 2009, doi:10.1101/gr.092353.109
..., the exon-expression level is highly dependent on the H3K79me1 exonic signal (Fig. 5D). Second, the Tudor domain of TP53BP1 is known to interact with mono- and di-methylated forms of H3K79 (Huyen et al. 2004). Interestingly, TP53BP1 has been shown to interact with U2 snRNA, along with several other proteins...
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Method: Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
- Arttu Jolma,
- Teemu Kivioja,
- Jarkko Toivonen,
- Lu Cheng,
- Gonghong Wei,
- Martin Enge,
- Mikko Taipale,
- Juan M. Vaquerizas,
- Jian Yan,
- Mikko J. Sillanpää,
- Martin Bonke,
- Kimmo Palin,
- Shaheynoor Talukder,
- Timothy R. Hughes,
- Nicholas M. Luscombe,
- Esko Ukkonen,
- and Jussi Taipale
Genome Res. June 2010 20: 861-873; Published in Advance April 8, 2010, doi:10.1101/gr.100552.109
...Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities Arttu Jolma 1 , 2 , Teemu Kivioja 1 , 3 , Jarkko Toivonen 3 , Lu Cheng 3 , Gonghong Wei 1 , Martin Enge 2 , Mikko...
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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
...We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell...
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Resource: Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
- Ozren Bogdanović,
- Ana Fernandez-Miñán,
- Juan J. Tena,
- Elisa de la Calle-Mustienes,
- Carmen Hidalgo,
- Ila van Kruysbergen,
- Simon J. van Heeringen,
- Gert Jan C. Veenstra,
- and José Luis Gómez-Skarmeta
Genome Res. October 2012 22: 2043-2053; Published in Advance May 16, 2012, doi:10.1101/gr.134833.111
...of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac). Nevertheless, little is known about the dynamics and the potential roles of these marks during vertebrate embryogenesis. Here, we provide genomic maps of H3K4me1/me3 and H3K...
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Research: Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations
- Daniel M. Ibrahim,
- Peter Hansen,
- Christian Rödelsperger,
- Asita C. Stiege,
- Sandra C. Doelken,
- Denise Horn,
- Marten Jäger,
- Catrin Janetzki,
- Peter Krawitz,
- Gundula Leschik,
- Florian Wagner,
- Till Scheuer,
- Mareen Schmidt-von Kegler,
- Petra Seemann,
- Bernd Timmermann,
- Peter N. Robinson,
- Stefan Mundlos,
- and Jochen Hecht
Genome Res. December 2013 23: 2091-2102; Published in Advance August 30, 2013, doi:10.1101/gr.157610.113
...to be investigated on a genome-wide scale, enabling new approaches for the investigation of gene regulation. Here, we present the application of ChIP-seq to explore the effect of missense mutations in TFs on their genome-wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we...

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