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Method: Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins
- Haoyi Wang,
- David Mayhew,
- Xuhua Chen,
- Mark Johnston,
- and Robi David Mitra
Genome Res. May 2011 21: 748-755; Published in Advance April 6, 2011, doi:10.1101/gr.114850.110
...events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol 27: 818–829. Liu X, Noll DM, Lieb JD, Clarke ND. 2005. DIP-chip: Rapid and accurate determination of DNA-binding specificity. Genome Res 15: 421–427. Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. 2006. Whole- comparison...
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Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
- Christopher T. Coey and
- David J. Clark
Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
...-third of its consensus sites, we designed an in vitro method to determine preferred binding sites for a DNA-binding protein, called G-SELEX (Fig. 1A). The approach is based on DIP-chip (Liu et al. 2005) and SELEX methods (selective evolution of ligands by exponential enrichment [Darmostuk et al. 2015; Bayat et...
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Methods: Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
- Manman Guo,
- Hui Feng,
- Jun Zhang,
- Wenqin Wang,
- Yi Wang,
- Yuqing Li,
- Chunhui Gao,
- Huanchun Chen,
- Ying Feng,
- and Zheng-Guo He
Genome Res. July 2009 19: 1301-1308; Published in Advance February 18, 2009, doi:10.1101/gr.086595.108
...–2074. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799–804. Liu X, Noll DM, Lieb JD, Clarke ND. 2005. DIP-chip: Rapid and accurate determination of DNA-binding...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...polymerase II (Pol II), as it encounters and is halted by DNA damage. Specific factors exist that mediate this mechanism, which manifests as a more rapid rate of removal of DNA damage from the transcribed strand of active genes. During GG-NER, which operates in all nontranscribing regions of the , repair...
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LETTER: Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
- Xiao Liu,
- Cheol-Koo Lee,
- Joshua A. Granek,
- Neil D. Clarke,
- and Jason D. Lieb
Genome Res. December 2006 16: 1517-1528; Published in Advance October 19, 2006, doi:10.1101/gr.5655606
...from targets unique to ChIP-chip or unique to DIP-chip To this point we have presented evidence that the DNA-binding specificity of Leu3 is equivalent in vivo and in vitro, but that different instances of the Leu3 motif are bound in the two conditions. If that is true, one should be able to derive...
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Research: EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos
- Ghislain Auclair,
- Julie Borgel,
- Lionel A. Sanz,
- Judith Vallet,
- Sylvain Guibert,
- Michael Dumas,
- Patricia Cavelier,
- Michael Girardot,
- Thierry Forné,
- Robert Feil,
- and Michael Weber
Genome Res. February 2016 26: 192-202; Published in Advance November 17, 2015, doi:10.1101/gr.198291.115
.... Alternatively, it is known that EHMT2 is part of larger protein complexes with sequence-specific DNA binding factors that could guide EHMT2 to specific sites. In particular, EHMT2 was identified as a member of the E2F6 complex (Ogawa et al. 2002), which has been linked to the control of DNA methylation in mouse...
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REVIEW: Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
- Albertha J.M. Walhout
Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
...in very good agreement with data obtained using in vivo methods, suggesting that they are effective and rapid methods to identify TF binding specificities, and, perhaps, affinities ( Mukherjee et al. 2004 ; Liu et al. 2005 ). In bacterial one-hybrid assays, a plasmid encoding a TF of interest...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...and experimental approaches in the identification of -scale sets of transcriptional regulatory elements. Given the amount of noncoding sequence that is under selective constraint (∼3.5% of the human ; Waterston et al. 2002 ; Chiaromonte et al. 2003 ), the anticipated number of DNA binding factors (∼1962; Messina...
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