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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
...observe the TF occupancy landscape, let alone quantify how it changes across conditions. We developed TF occupancy profiler (TOP), a Bayesian hierarchical regression framework, to profile -wide quantitative occupancy of numerous TFs using data from a single chromatin accessibility experiment (DNase...
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Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...with cobinding of these lineage specifiers. Altogether, these results support the claim that MEDEA analysis of chromatin accessibility data can highlight lineage specifier motifs.MEDEA analysis across 610 ENCODE DNase-seq data sets reveals known and novel regulatory interactions underlying lineage specification...
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Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
- Federico Comoglio,
- Hyun Jung Park,
- Stefan Schoenfelder,
- Iros Barozzi,
- Daniel Bode,
- Peter Fraser,
- and Anthony R. Green
Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
...have made it possible to map these repertoires -wide and across a wide range of cell types and organisms (The ENCODE Project Consortium 2012; Shlyueva et al. 2014). Putative enhancers can be defined as DNase I hypersensitive sites (DHSs) marked by monomethylated lysine 4 on histone H3 (H3K4me1...
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Research: Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response
- Petros Kolovos,
- Theodore Georgomanolis,
- Anna Koeferle,
- Joshua D. Larkin,
- Lilija Brant,
- Miloš Nikolicć,
- Eduardo G. Gusmao,
- Anne Zirkel,
- Tobias A. Knoch,
- Wilfred F. van Ijcken,
- Peter R. Cook,
- Ivan G. Costa,
- Frank G. Grosveld,
- and Argyris Papantonis
Genome Res. November 2016 26: 1478-1489; Published in Advance September 15, 2016, doi:10.1101/gr.210005.116
..., white arrow) showed decreasing H3K27ac levels upon stimulation, compared to an increase at peaks that carry motifs (Fig. 2A, black arrow). A sensitive analysis ofmotifs located specifically within DNase I-hypersensitive (DHS) footprints (Gusmao et al. 2016) showed that peaks encoding the canonical motif...
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Research: Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- Weisheng Wu,
- Yong Cheng,
- Cheryl A. Keller,
- Jason Ernst,
- Swathi Ashok Kumar,
- Tejaswini Mishra,
- Christapher Morrissey,
- Christine M. Dorman,
- Kuan-Bei Chen,
- Daniela Drautz,
- Belinda Giardine,
- Yoichiro Shibata,
- Lingyun Song,
- Max Pimkin,
- Gregory E. Crawford,
- Terrence S. Furey,
- Manolis Kellis,
- Webb Miller,
- James Taylor,
- Stephan C. Schuster,
- Yu Zhang,
- Francesca Chiaromonte,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. October 2011 21: 1659-1671; Published in Advance July 27, 2011, doi:10.1101/gr.125088.111
...by the actions of transcription factors that bind to specific DNA sequences in cis-regulatory modules (CRMs), such as promoters and enhancers. Chromatin containing active CRMs is in an open or accessible configuration, leading to DNase hypersensitivity (Gross and Garrard 1988). Active modules are associated...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...type, as well as understanding how the specificity of such a network is encoded in the DNA sequence of genomic enhancers. Profiling accessible chromatin via DNase I hypersensitive sequencing (DNase-seq) or via the assay for transposase-accessible chromatin using sequencing (ATAC-seq) represents...
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Resource: A genome-wide interactome of DNA-associated proteins in the human liver
- Ryne C. Ramaker,
- Daniel Savic,
- Andrew A. Hardigan,
- Kimberly Newberry,
- Gregory M. Cooper,
- Richard M. Myers,
- and Sara J. Cooper
Genome Res. November 2017 27: 1950-1960; Published in Advance October 11, 2017, doi:10.1101/gr.222083.117
...understanding of transcriptional control within a physiological context. Recently, reference epis, consisting of histone modification, DNase hypersensitivity, and DNA methylation measurements, have been compiled for more than 100 primary tissues by the Roadmap Epigenomics Consortium et al. (2015...
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Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
- Wendy A. Kellner,
- Joshua S.K. Bell,
- and Paula M. Vertino
Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
...1600 Genome Research 25:1600–1609 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/15; www..org www..org relationships among chromatin looping interactions, enhancer activity, and Pol II pausing dynamics are incompletely understood. In this study,we investigate the relationship between...
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Research: Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
- Yujia Sun,
- Chung-Yi Nien,
- Kai Chen,
- Hsiao-Yun Liu,
- Jeff Johnston,
- Julia Zeitlinger,
- and Christine Rushlow
Genome Res. November 2015 25: 1703-1714; Published in Advance September 2, 2015, doi:10.1101/gr.192542.115
...motifs are present nearby (Satija and Bradley 2012). Furthermore, deleting Zld motifs in select Twist (Twi), Dl and Bcd enhancers in transgenic reporter assays resulted in decreased TF binding (Yáñez-Cuna et al. 2012; Foo et al. 2014; Xu et al. 2014), and in the case of the sog enhancer, decreased DNase...
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Research: Enhancer transcripts mark active estrogen receptor binding sites
- Nasun Hah,
- Shino Murakami,
- Anusha Nagari,
- Charles G. Danko,
- and W. Lee Kraus
Genome Res. August 2013 23: 1210-1223; Published in Advance May 1, 2013, doi:10.1101/gr.152306.112
...to their mechanisms of action and aid in their identification. In this regard, histone modifications (e.g., H3 lysine 4monomethyl, H3K4me1; H3 lysine 27 acetyl, H3K27ac), histone variants (e.g., H2A.Z), coactivators (e.g., EP300, CREBBP, Mediator), and an open chromatin architecture (e.g., DNase I hypersensitivity...

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