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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...to access gene promoters. Many key genes were accessible at the two-cell stage or earlier. For example, Arntl is associated with the rhythmic opening of chromatin at promoters and regulates DNA accessibility for other TFs (Menet et al. 2014); Nfya forms a histone-like structure binding to DNA and promotes...
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Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
- Julie Dubois-Chevalier,
- Vanessa Dubois,
- Hélène Dehondt,
- Parisa Mazrooei,
- Claire Mazuy,
- Aurélien A. Sérandour,
- Céline Gheeraert,
- Penderia Guillaume,
- Eric Baugé,
- Bruno Derudas,
- Nathalie Hennuyer,
- Réjane Paumelle,
- Guillemette Marot,
- Jason S. Carroll,
- Mathieu Lupien,
- Bart Staels,
- Philippe Lefebvre,
- and Jérôme Eeckhoute
Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
...-specific functions. The transcriptional regulatory logic defined in this study is summarized. The size of the TR and TRM above the chromatin and of the boxes below the chromatin correlates with the occurrence of binding and DNA motif at the distinct classes of CRM, respectively. Refer to Discussion for details...
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Research: Genome-wide depletion of replication initiation events in highly transcribed regions
- Melvenia M. Martin,
- Michael Ryan,
- RyangGuk Kim,
- Anna L. Zakas,
- Haiqing Fu,
- Chii Mei Lin,
- William C. Reinhold,
- Sean R. Davis,
- Sven Bilke,
- Hongfang Liu,
- James H. Doroshow,
- Mark A. Reimers,
- Manuel S. Valenzuela,
- Yves Pommier,
- Paul S. Meltzer,
- and Mirit I. Aladjem
Genome Res. November 2011 21: 1822-1832; Published in Advance August 3, 2011, doi:10.1101/gr.124644.111
...investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. In yeast, DNA replication initiates within nucleosome-free regions, but studies in mammalian cells have not revealed a similar relationship. Here, we have used genome-wide massively...
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Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
- Antonio L.C. Gomes,
- Thomas Abeel,
- Matthew Peterson,
- Elham Azizi,
- Anna Lyubetskaya,
- Luís Carvalho,
- and James Galagan
Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
...: antluiz@bu.edu , jgalag@bu.edu Abstract The comprehension of protein and DNA binding in vivo is essential to understand gene regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a global map of the regulatory binding network. Most ChIP-seq analysis tools focus...
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Methods: A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
- Victor X. Jin,
- Alina Rabinovich,
- Sharon L. Squazzo,
- Roland Green,
- and Peggy J. Farnham
Genome Res. December 2006 16: 1585-1595; Published in Advance October 19, 2006, doi:10.1101/gr.5520206
...of a specific factor to DNA. However, there are several different mechanisms by which a factor can be recruited to the DNA and be identified in a ChIP–chip assay ( Kato et al. 2004 ). Three types of interactions between a transcription factor and its binding site on DNA include: (1) direct binding...
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Methods: Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions
- Mahesh Yaragatti,
- Claudio Basilico,
- and Lisa Dailey
Genome Res. June 2008 18: 930-938; Published in Advance April 25, 2008, doi:10.1101/gr.073460.107
.... , Davidson, E.H. ( 2005 ) Logic functions of the genomic cis -regulatory code . Proc. Natl. Acad. Sci. 102 : 4954 – 4959 . ↵ Johnson, D.S. , Mortazavi, A. , Myers, R.M. , Wold, B. ( 2007 ) Genome-wide mapping of in vivo protein-DNA interactions . Science 316 : 1497 – 1502 . ↵ Khambata-Ford, S. , Liu, Y...
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Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
- Ian C. McDowell,
- Alejandro Barrera,
- Anthony M. D'Ippolito,
- Christopher M. Vockley,
- Linda K. Hong,
- Sarah M. Leichter,
- Luke C. Bartelt,
- William H. Majoros,
- Lingyun Song,
- Alexias Safi,
- D. Dewran Koçak,
- Charles A. Gersbach,
- Alexander J. Hartemink,
- Gregory E. Crawford,
- Barbara E. Engelhardt,
- and Timothy E. Reddy
Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
...(GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibility predetermine GR binding and activity. However, there are vast excesses of both features relative to the number of GR binding sites. Thus, these features alone are unlikely to account for the specificity...
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Resource: Impact of regulatory variation across human iPSCs and differentiated cells
- Nicholas E. Banovich,
- Yang I. Li,
- Anil Raj,
- Michelle C. Ward,
- Peyton Greenside,
- Diego Calderon,
- Po Yuan Tung,
- Jonathan E. Burnett,
- Marsha Myrthil,
- Samantha M. Thomas,
- Courtney K. Burrows,
- Irene Gallego Romero,
- Bryan J. Pavlovic,
- Anshul Kundaje,
- Jonathan K. Pritchard,
- and Yoav Gilad
Genome Res. January 2018 28: 122-131; Published in Advance December 5, 2017, doi:10.1101/gr.224436.117
...in chromatin marks and our ATAC-seq peaks, we used stratified LDscore regression (Supplemental Materials; Finucane et al. 2015).Neural network models for chromatin accessibilityTo predict the chromatin activity of a genomic locus across three cell types (iPSC, LCL, and iPSC-CM) from the DNA sequence, we used...
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Research: Damage-responsive elements in Drosophila regeneration
- Elena Vizcaya-Molina,
- Cecilia C. Klein,
- Florenci Serras,
- Rakesh K. Mishra,
- Roderic Guigó,
- and Montserrat Corominas
Genome Res. December 2018 28: 1852-1866; Published in Advance November 20, 2018, doi:10.1101/gr.233098.117
...by coordinated actions of genomic regions that control the activity of multiple sequence-specific DNA binding proteins. Using -wide approaches to interrogate chromatin function, we here identify the elements that regulate tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after...
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Research: CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
- Joseph C. Corbo,
- Karen A. Lawrence,
- Marcus Karlstetter,
- Connie A. Myers,
- Musa Abdelaziz,
- William Dirkes,
- Karin Weigelt,
- Martin Seifert,
- Vladimir Benes,
- Lars G. Fritsche,
- Bernhard H.F. Weber,
- and Thomas Langmann
Genome Res. November 2010 20: 1512-1525; Published in Advance August 6, 2010, doi:10.1101/gr.109405.110
...curves in Fig. 2E). Since primary DNA sequence can influence nucleosome placement (Tillo and Hughes 2009), we hypothesized that theGC-rich peakwithin CBRs might represent a nucleosome positioning signal. We therefore determined the predicted nucleosome occupancy over all replicated CBRs using...

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