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Method: Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers
- Aleksander Jankowski,
- Ewa Szczurek,
- Ralf Jauch,
- Jerzy Tiuryn,
- and Shyam Prabhakar
Genome Res. August 2013 23: 1307-1318; Published in Advance April 3, 2013, doi:10.1101/gr.154922.113
...TF dimers that bind rigidly spacedmotif complexes. The inflexibility of these motif complexes implies that dimerization on DNA frequently imposes strict constraints on the relative spatial conformation of the participating TFs. As in the case of OCT4 and SOX2, a small number of additional motif...
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Article: Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
- Timothy E. Reddy,
- Florencia Pauli,
- Rebekka O. Sprouse,
- Norma F. Neff,
- Kimberly M. Newberry,
- Michael J. Garabedian,
- and Richard M. Myers
Genome Res. December 2009 19: 2163-2171; Published in Advance October 2, 2009, doi:10.1101/gr.097022.109
...factor involved in regulating circadian rhythms. Overall, the genome-wide determination and analysis of GR:DNA binding and transcriptional response to hormone reveals new insights into the complexities of gene regulatory activities managed by GR. Footnotes ↵ 4 Corresponding author. E...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...the PET sequencing strategy, in which short and paired tags are extracted from the ends of long DNA fragments for ultra-high-throughput sequencing. The PET sequences can be accurately mapped to the reference , thus demarcating the genomic boundaries of PET-represented DNA fragments and revealing...
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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
...but not in transfected NIH3T3 mouse fibroblasts, which do not express SOX2, POU5F1, or NANOG ( Fig. 4B ). Furthermore, while most of the SOX2-IP’d DNAs aligned with genomic regions enriched for H3K4me3, the distal elements tended to do so only in ES cells, but not in NP cells or MEFs ( Fig. 4C ; Supplemental Fig. 3...
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Research: Combinatorial binding of transcription factors in the pluripotency control regions of the genome
- Luciana Ferraris,
- Allan P. Stewart,
- Jinsuk Kang,
- Alec M. DeSimone,
- Matthew Gemberling,
- Dean Tantin,
- and William G. Fairbrother
Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110
..., USA The pluripotency control regions (PluCRs) are defined as genomic regions that are bound by POU5F1, SOX2, and NANOG in vivo. We utilized a high-throughput binding assay to record more than 270,000 different DNA/protein binding measurements along incrementally tiled windows of DNA within these Plu...
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Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- Andre J. Faure,
- Dominic Schmidt,
- Stephen Watt,
- Petra C. Schwalie,
- Michael D. Wilson,
- Huiling Xu,
- Robert G. Ramsay,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
...and ChIP signal. Evidence from these statistical analyses in wild-type cells, and comparisons to maps of TF binding in Rad21 -cohesin haploinsufficient mouse liver, suggests that cohesin helps to stabilize large protein–DNA complexes. Finally, we observe that the presence of mirrored CTCF binding events...
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Research: Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
- Hong-Bing Yu,
- Rory Johnson,
- Galih Kunarso,
- and Lawrence W. Stanton
Genome Res. August 2011 21: 1284-1293; Published in Advance June 1, 2011, doi:10.1101/gr.114488.110
...sought to reconstruct the genomic repressor network that controls gene transcription in ESC. ChIP DNAs prepared from REST and five of its cofactors were subjected to high-throughput sequencing. For each experiment 11.2–15.8 million sequence reads were uniquely mapped to the mouse . In order to find...
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LETTER: Suz12 binds to silenced regions of the genome in a cell-type-specific manner
- Sharon L. Squazzo,
- Henriette O’Geen,
- Vitalina M. Komashko,
- Sheryl R. Krig,
- Victor X. Jin,
- Sung-wook Jang,
- Raphael Margueron,
- Danny Reinberg,
- Roland Green,
- and Peggy J. Farnham
Genome Res. July 2006 16: 890-900; Published in Advance June 2, 2006, doi:10.1101/gr.5306606
...not be as easily visualized. OCT4 and SUZ12 have a common set of target genes in embryonic cells None of the components of the PRC2/3/4 are site-specific DNA-binding proteins, and therefore it is not clear how specific regions of the mammalian are targeted for interaction with the PRCs. The DNA-binding factor AEBP...
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Resource: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- Lingyun Song,
- Zhancheng Zhang,
- Linda L. Grasfeder,
- Alan P. Boyle,
- Paul G. Giresi,
- Bum-Kyu Lee,
- Nathan C. Sheffield,
- Stefan Gräf,
- Mikael Huss,
- Damian Keefe,
- Zheng Liu,
- Darin London,
- Ryan M. McDaniell,
- Yoichiro Shibata,
- Kimberly A. Showers,
- Jeremy M. Simon,
- Teresa Vales,
- Tianyuan Wang,
- Deborah Winter,
- Zhuzhu Zhang,
- Neil D. Clarke,
- Ewan Birney,
- Vishwanath R. Iyer,
- Gregory E. Crawford,
- Jason D. Lieb,
- and Terrence S. Furey
Genome Res. October 2011 21: 1757-1767; Published in Advance July 12, 2011, doi:10.1101/gr.121541.111
...in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites and contained DNA motifs recognized...
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Method: Models of human core transcriptional regulatory circuitries
- Violaine Saint-André,
- Alexander J. Federation,
- Charles Y. Lin,
- Brian J. Abraham,
- Jessica Reddy,
- Tong Ihn Lee,
- James E. Bradner,
- and Richard A. Young
Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115
...of DNA-binding motifs that are actually bound by the TFs from ChIP-seq data for POU5F1, SOX2, and NANOG in H1 hESCs, in either SE constituents or sets of random genomic sequences of the same size. (E) Venn diagram showing the average numbers, across 84 samples, of: 1. TFs having motifs that are expressed...

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