Crossref
journal-article
Springer Science and Business Media LLC
Nature Methods (297)
References
63
Referenced
174
-
Solomon, M.J. & Varshavsky, A. Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. USA 82, 6470–6474 (1985).
(
10.1073/pnas.82.19.6470
) / Proc. Natl. Acad. Sci. USA by MJ Solomon (1985) -
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000).
(
10.1126/science.290.5500.2306
) / Science by B Ren (2000) -
Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).
(
10.1126/science.1141319
) / Science by DS Johnson (2007) -
Zentner, G.E. & Henikoff, S. Surveying the epigenomic landscape, one base at a time. Genome Biol. 13, 250 (2012).
(
10.1186/gb4051
) / Genome Biol. by GE Zentner (2012) -
O'Neill, L.P. & Turner, B.M. Immunoprecipitation of native chromatin: NChIP. Methods 31, 76–82 (2003).
(
10.1016/S1046-2023(03)00090-2
) / Methods by LP O'Neill (2003) -
Teytelman, L. et al. Impact of chromatin structures on DNA processing for genomic analyses. PLoS ONE 4, e6700 (2009).
(
10.1371/journal.pone.0006700
) / PLoS ONE by L Teytelman (2009) -
Fan, X. & Struhl, K. Where does mediator bind in vivo? PLoS ONE 4, e5029 (2009).
(
10.1371/journal.pone.0005029
) / PLoS ONE by X Fan (2009) -
Schwartz, Y.B., Kahn, T.G. & Pirrotta, V. Characteristic low density and shear sensitivity of cross-linked chromatin containing polycomb complexes. Mol. Cell Biol. 25, 432–439 (2005).
(
10.1128/MCB.25.1.432-439.2005
) / Mol. Cell Biol. by YB Schwartz (2005) -
Auerbach, R.K. et al. Mapping accessible chromatin regions using Sono-Seq. Proc. Natl. Acad. Sci. USA 106, 14926–14931 (2009).
(
10.1073/pnas.0905443106
) / Proc. Natl. Acad. Sci. USA by RK Auerbach (2009) -
Teytelman, L., Thurtle, D.M., Rine, J. & van Oudenaarden, A. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc. Natl. Acad. Sci. USA 110, 18602–18607 (2013).
(
10.1073/pnas.1316064110
) / Proc. Natl. Acad. Sci. USA by L Teytelman (2013) -
Toth, J. & Biggin, M.D. The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in Drosophila embryos. Nucleic Acids Res. 28, e4 (2000).
(
10.1093/nar/28.2.e4
) / Nucleic Acids Res. by J Toth (2000) -
Jackson, V. Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 17, 125–139 (1999).
(
10.1006/meth.1998.0724
) / Methods by V Jackson (1999) -
Poorey, K. et al. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science 342, 369–372 (2013).
(
10.1126/science.1242369
) / Science by K Poorey (2013) -
Rhee, H.S. & Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408–1419 (2011).
(
10.1016/j.cell.2011.11.013
) / Cell by HS Rhee (2011) -
Gilfillan, G.D. et al. Limitations and possibilities of low cell number ChIP-seq. BMC Genomics 13, 645 (2012).
(
10.1186/1471-2164-13-645
) / BMC Genomics by GD Gilfillan (2012) -
Roca, H. & Franceschi, R.T. Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation. Nucleic Acids Res. 36, 1723–1730 (2008).
(
10.1093/nar/gkn022
) / Nucleic Acids Res. by H Roca (2008) -
Teves, S.S. & Henikoff, S. Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 25, 2387–2397 (2011).
(
10.1101/gad.177675.111
) / Genes Dev. by SS Teves (2011) -
O'Neill, L.P. & Turner, B.M. Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner. EMBO J. 14, 3946–3957 (1995).
(
10.1002/j.1460-2075.1995.tb00066.x
) / EMBO J. by LP O'Neill (1995) -
Zentner, G.E., Tsukiyama, T. & Henikoff, S. ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. PLoS Genet. 9, e1003317 (2013).
(
10.1371/journal.pgen.1003317
) / PLoS Genet. by GE Zentner (2013) -
Henikoff, J.G., Belsky, J.A., Krassovsky, K., MacAlpine, D.M. & Henikoff, S. Epigenome characterization at single base-pair resolution. Proc. Natl. Acad. Sci. USA 108, 18318–18323 (2011).
(
10.1073/pnas.1110731108
) / Proc. Natl. Acad. Sci. USA by JG Henikoff (2011) -
MacIsaac, K.D. et al. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7, 113 (2006).
(
10.1186/1471-2105-7-113
) / BMC Bioinformatics by KD MacIsaac (2006) - Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994). / Proc. Int. Conf. Intell. Syst. Mol. Biol. by TL Bailey (1994)
-
Beinoraviciūte-Kellner, R., Lipps, G. & Krauss, G. In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS Lett. 579, 4535–4540 (2005).
(
10.1016/j.febslet.2005.07.009
) / FEBS Lett. by R Beinoraviciūte-Kellner (2005) -
Hartley, P.D. & Madhani, H.D. Mechanisms that specify promoter nucleosome location and identity. Cell 137, 445–458 (2009).
(
10.1016/j.cell.2009.02.043
) / Cell by PD Hartley (2009) -
Ju, Q.D., Morrow, B.E. & Warner, J.R. REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb. Mol. Cell Biol. 10, 5226–5234 (1990).
(
10.1128/MCB.10.10.5226
) / Mol. Cell Biol. by QD Ju (1990) -
Cho, G., Kim, J., Rho, H.M. & Jung, G. Structure-function analysis of the DNA binding domain of Saccharomyces cerevisiae ABF1. Nucleic Acids Res. 23, 2980–2987 (1995).
(
10.1093/nar/23.15.2980
) / Nucleic Acids Res. by G Cho (1995) -
Hesselberth, J.R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283–289 (2009).
(
10.1038/nmeth.1313
) / Nat. Methods by JR Hesselberth (2009) -
Galas, D.J. & Schmitz, A. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157–3170 (1978).
(
10.1093/nar/5.9.3157
) / Nucleic Acids Res. by DJ Galas (1978) -
Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90 (2012).
(
10.1038/nature11212
) / Nature by S Neph (2012) -
Stormo, G.D. DNA binding sites: representation and discovery. Bioinformatics 16, 16–23 (2000).
(
10.1093/bioinformatics/16.1.16
) / Bioinformatics by GD Stormo (2000) -
Blanchette, M. & Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739–748 (2002).
(
10.1101/gr.6902
) / Genome Res. by M Blanchette (2002) -
Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).
(
10.1101/gr.3715005
) / Genome Res. by A Siepel (2005) -
Ganapathi, M. et al. Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res. 39, 2032–2044 (2011).
(
10.1093/nar/gkq1161
) / Nucleic Acids Res. by M Ganapathi (2011) -
Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004).
(
10.1038/nature02800
) / Nature by CT Harbison (2004) -
Henikoff, S., Henikoff, J.G., Sakai, A., Loeb, G.B. & Ahmad, K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 19, 460–469 (2009).
(
10.1101/gr.087619.108
) / Genome Res. by S Henikoff (2009) -
Schwendemann, A. & Lehmann, M. Pipsqueak and GAGA factor act in concert as partners at homeotic and many other loci. Proc. Natl. Acad. Sci. USA 99, 12883–12888 (2002).
(
10.1073/pnas.202341499
) / Proc. Natl. Acad. Sci. USA by A Schwendemann (2002) - The modENCODE Consortium et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787–1797 (2010).
-
Moorman, C. et al. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 103, 12027–12032 (2006).
(
10.1073/pnas.0605003103
) / Proc. Natl. Acad. Sci. USA by C Moorman (2006) -
Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y. & Greenleaf, W.J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10.1038/nmeth.2688 (2013).
(
10.1038/nmeth.2688
) -
Lohman, T.M. & Mascotti, D.P. Thermodynamics of ligand-nucleic acid interactions. Methods Enzymol. 212, 400–424 (1992).
(
10.1016/0076-6879(92)12026-M
) / Methods Enzymol. by TM Lohman (1992) -
Hager, G.L., McNally, J.G. & Misteli, T. Transcription dynamics. Mol. Cell 35, 741–753 (2009).
(
10.1016/j.molcel.2009.09.005
) / Mol. Cell by GL Hager (2009) -
Wilkins, R.C. & Lis, J.T. GAGA factor binding to DNA via a single trinucleotide sequence element. Nucleic Acids Res. 26, 2672–2678 (1998).
(
10.1093/nar/26.11.2672
) / Nucleic Acids Res. by RC Wilkins (1998) -
Soeller, W.C., Oh, C.E. & Kornberg, T.B. Isolation of cDNAs encoding the Drosophila GAGA transcription factor. Mol. Cell Biol. 13, 7961–7970 (1993).
(
10.1128/MCB.13.12.7961
) / Mol. Cell Biol. by WC Soeller (1993) -
Zhao, X., Muller, E.G. & Rothstein, R. A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Mol. Cell 2, 329–340 (1998).
(
10.1016/S1097-2765(00)80277-4
) / Mol. Cell by X Zhao (1998) -
Gelbart, M.E., Rechsteiner, T., Richmond, T.J. & Tsukiyama, T. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Mol. Cell Biol. 21, 2098–2106 (2001).
(
10.1128/MCB.21.6.2098-2106.2001
) / Mol. Cell Biol. by ME Gelbart (2001) -
Furuyama, S. & Biggins, S. Centromere identity is specified by a single centromeric nucleosome in budding yeast. Proc. Natl. Acad. Sci. USA 104, 14706–14711 (2007).
(
10.1073/pnas.0706985104
) / Proc. Natl. Acad. Sci. USA by S Furuyama (2007) -
Melnikova, L. et al. Interaction between the GAGA factor and Mod(mdg4) proteins promotes insulator bypass in Drosophila. Proc. Natl. Acad. Sci. USA 101, 14806–14811 (2004).
(
10.1073/pnas.0403959101
) / Proc. Natl. Acad. Sci. USA by L Melnikova (2004) -
Horowitz, H. & Berg, C.A. The Drosophila pipsqueak gene encodes a nuclear BTB-domain-containing protein required early in oogenesis. Development 122, 1859–1871 (1996).
(
10.1242/dev.122.6.1859
) / Development by H Horowitz (1996) -
Weber, C.M., Henikoff, J.G. & Henikoff, S. H2A.Z nucleosomes enriched over active genes are homotypic. Nat. Struct. Mol. Biol. 17, 1500–1507 (2010).
(
10.1038/nsmb.1926
) / Nat. Struct. Mol. Biol. by CM Weber (2010) -
Stamatoyannopoulos, J.A. What does our genome encode? Genome Res. 22, 1602–1611 (2012).
(
10.1101/gr.146506.112
) / Genome Res. by JA Stamatoyannopoulos (2012) -
Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
(
10.1093/bioinformatics/btq033
) / Bioinformatics by AR Quinlan (2010) -
Machanick, P. & Bailey, T.L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696–1697 (2011).
(
10.1093/bioinformatics/btr189
) / Bioinformatics by P Machanick (2011) -
Zhu, L.J. et al. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 39, D111–D117 (2011).
(
10.1093/nar/gkq858
) / Nucleic Acids Res. by LJ Zhu (2011) -
Spivak, A.T. & Stormo, G.D. ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res. 40, D162–D168 (2012).
(
10.1093/nar/gkr1180
) / Nucleic Acids Res. by AT Spivak (2012) -
Bryne, J.C. et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 36, D102–D106 (2008).
(
10.1093/nar/gkm955
) / Nucleic Acids Res. by JC Bryne (2008) -
Morrow, B.E., Ju, Q. & Warner, J.R. A bipartite DNA-binding domain in yeast Reb1p. Mol. Cell Biol. 13, 1173–1182 (1993).
(
10.1128/MCB.13.2.1173
) / Mol. Cell Biol. by BE Morrow (1993) -
Lang, W.H. & Reeder, R.H. The REB1 site is an essential component of a terminator for RNA polymerase I in Saccharomyces cerevisiae. Mol. Cell Biol. 13, 649–658 (1993).
(
10.1128/MCB.13.1.649
) / Mol. Cell Biol. by WH Lang (1993) -
Kharchenko, P.V. et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471, 480–485 (2011).
(
10.1038/nature09725
) / Nature by PV Kharchenko (2011) -
Meyer, L.R. et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, D64–D69 (2013).
(
10.1093/nar/gks1048
) / Nucleic Acids Res. by LR Meyer (2013) -
Cherry, J.M. et al. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40, D700–D705 (2012).
(
10.1093/nar/gkr1029
) / Nucleic Acids Res. by JM Cherry (2012) -
Sherman, F. Getting started with yeast. Methods Enzymol. 350, 3–41 (2002).
(
10.1016/S0076-6879(02)50954-X
) / Methods Enzymol. by F Sherman (2002) -
Landt, S.G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012).
(
10.1101/gr.136184.111
) / Genome Res. by SG Landt (2012) -
Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
(
10.1038/nmeth.2089
) / Nat. Methods by CA Schneider (2012)
Dates
Type | When |
---|---|
Created | 11 years, 8 months ago (Dec. 15, 2013, 3:47 p.m.) |
Deposited | 2 years, 3 months ago (May 18, 2023, 7:13 p.m.) |
Indexed | 4 days, 11 hours ago (Aug. 30, 2025, 12:29 p.m.) |
Issued | 11 years, 8 months ago (Dec. 15, 2013) |
Published | 11 years, 8 months ago (Dec. 15, 2013) |
Published Online | 11 years, 8 months ago (Dec. 15, 2013) |
Published Print | 11 years, 7 months ago (Feb. 1, 2014) |
@article{Kasinathan_2013, title={High-resolution mapping of transcription factor binding sites on native chromatin}, volume={11}, ISSN={1548-7105}, url={http://dx.doi.org/10.1038/nmeth.2766}, DOI={10.1038/nmeth.2766}, number={2}, journal={Nature Methods}, publisher={Springer Science and Business Media LLC}, author={Kasinathan, Sivakanthan and Orsi, Guillermo A and Zentner, Gabriel E and Ahmad, Kami and Henikoff, Steven}, year={2013}, month=dec, pages={203–209} }