Genome-wide footprinting: Ready for prime time?

Nature Methods

Volumn 13, Issue 3, 2016, Pages 222-228

  Sung, Myong Hee ^a,b   Baek, Songjoon ^a   Hager, Gordon L ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DNA;

BIOINFORMATICS; CELLS BY BODY ANATOMY; CHROMATIN IMMUNOPRECIPITATION; CRYSTAL STRUCTURE; DNA BINDING; DNA CLEAVAGE; DNA CROSS LINKING; DNA FOOTPRINTING; DNA SEQUENCE; ENHANCER REGION; EPIGENETICS; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; GENE LOCUS; GENETIC ASSOCIATION; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; IN VITRO STUDY; MOLECULAR BIOLOGY; POSITION WEIGHT MATRIX; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; ALGORITHM; CHROMOSOMAL MAPPING; GENETICS; HUMAN; PROCEDURES;

ALGORITHMS; CHROMOSOME MAPPING; DNA; DNA FOOTPRINTING; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS;

EID: 84959449100     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3766     Document Type: Review

References (58)

1. Tullius, T.D. Physical studies of protein-DNA complexes by footprinting. Annu. Rev. Biophys. Biophys. Chem. 18, 213-237 (1989
2. Church, G.M., Ephrussi, A., Gilbert, W., & Tonegawa, S. Cell-Type-specific contacts to immunoglobulin enhancers in nuclei. Nature 313, 798-801 (1985
3. Jackson, P.D., & Felsenfeld, G. A method for mapping intranuclear protein-DNA interactions and its application to a nuclease hypersensitive site. Proc. Natl. Acad. Sci. USA 82, 2296-2300 (1985
4. Hesselberth, J.R., et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283-289 (2009
5. Thurman, R.E., et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012
6. Baek, S., Sung, M.H., & Hager, G.L. Quantitative analysis of genome-wide chromatin remodeling. Methods Mol. Biol. 833, 433-441 (2012
7. Morris, S.A., et al. Overlapping chromatin remodeling systems collaborate genome-wide at dynamic chromatin transitions. Nat. Struct. Mol. Biol. 21, 73-81 (2014
8. John, S., et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264-268 (2011
9. Sung, M.H., Guertin, M.J., Baek, S., & Hager, G.L. DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol. Cell 56, 275-285 (2014
10. He, H.H., et al. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat. Methods 11, 73-78 (2014
11. Pique-Regi, R., et al. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21, 447-455 (2011
12. Neph, S., et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012
13. Mercer, T.R., et al. The human mitochondrial transcriptome. Cell 146, 645-658 (2011
14. Boyle, A.P., et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 21, 456-464 (2011
15. Cuellar-Partida, G., et al. Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics 28, 56-62 (2012
16. Luo, K., & Hartemink, A.J. Using DNase digestion data to accurately identify transcription factor binding sites. Pac. Symp. Biocomput. 2013, 80-91 (2013
17. Gusmao, E.G., Dieterich, C., Zenke, M., & Costa, I.G. Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications. Bioinformatics 30, 3143-3151 (2014
18. Sherwood, R.I., et al. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat. Biotechnol. 32, 171-178 (2014
19. Piper, J., et al. Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data. Nucleic Acids Res. 41, e201 (2013
20. Lazarovici, A., et al. Probing DNA shape and methylation state on a genomic scale with DNase I. Proc. Natl. Acad. Sci. USA 110, 6376-6381 (2013
21. Yardimci, G.G., Frank, C.L., Crawford, G.E., & Ohler, U. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res. 42, 11865-11878 (2014
22. Grøntved, L., et al. Rapid genome-scale mapping of chromatin accessibility in tissue. Epigenetics Chromatin 5, 10 (2012
23. Nakahashi, H., et al. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep. 3, 1678-1689 (2013
24. Poorey, K., et al. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science 342, 369-372 (2013
25. Buenrostro, J.D., et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486-490 (2015
26. Cusanovich, D.A., et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910-914 (2015
27. Voss, T.C., & Hager, G.L. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat. Rev. Genet. 15, 69-81 (2014
28. Sung, M.H., & McNally, J.G. Live cell imaging and systems biology. Wiley Interdiscip. Rev. Syst. Biol. Med. 3, 167-182 (2011
29. Hager, G.L., McNally, J.G., & Misteli, T. Transcription dynamics. Mol. Cell 35, 741-753 (2009
30. Voss, T.C., et al. Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. Cell 146, 544-554 (2011
31. Morisaki, T., Muller, W.G., Golob, N., Mazza, D., & McNally, J.G. Single-molecule analysis of transcription factor binding at transcription sites in live cells. Nat. Commun. 5, 4456 (2014
32. van Royen, M.E., et al. Androgen receptor complexes probe DNA for recognition sequences by short random interactions. J. Cell Sci. 127, 1406-1416 (2014
33. Groeneweg, F.L., et al. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP. PLoS ONE 9, e90532 (2014
34. Gebhardt, J.C., et al. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods 10, 421-426 (2013
35. Crocker, J., et al. Low affinity binding site clusters confer Hox specificity and regulatory robustness. Cell 160, 191-203 (2015
36. Chen, J., et al. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell 156, 1274-1285 (2014
37. Sharp, Z.D., et al. Estrogen-receptor-Alpha exchange and chromatin dynamics are ligand-And domain-dependent. J. Cell Sci. 119, 4101-4116 (2006
38. Bosisio, D., et al. A hyper-dynamic equilibrium between promoter-bound and nucleoplasmic dimers controls NF-kB-dependent gene activity. EMBO J. 25, 798-810 (2006
39. McNally, J.G., Mueller, W.G., Walker, D., Wolford, R.G., & Hager, G.L. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science 287, 1262-1265 (2000
40. Stergachis, A.B., et al. Conservation of trans-Acting circuitry during mammalian regulatory evolution. Nature 515, 365-370 (2014
41. Neph, S., et al. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274-1286 (2012
42. Badis, G., et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723 (2009
43. Jolma, A., et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013
44. Weirauch, M.T., et al. Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 31, 126-134 (2013
45. 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, 1213-1218 (2013
46. Gerstein, M.B., et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012
47. Bailey, T.L., et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009
48. Grant, C.E., Bailey, T.L., & Noble, W.S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011
49. Biddie, S.C., et al. Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. Mol. Cell 43, 145-155 (2011
50. Lickwar, C.R., Mueller, F., Hanlon, S.E., McNally, J.G., & Lieb, J.D. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484, 251-255 (2012
51. Malnou, C.E., et al. Heterodimerization with different Jun proteins controls c-Fos intranuclear dynamics and distribution. J. Biol. Chem. 285, 6552-6562 (2010
52. Mayr, B.M., Guzman, E., & Montminy, M. Glutamine rich and basic region/leucine zipper (bZIP) domains stabilize cAMP-response element-binding protein (CREB) binding to chromatin. J. Biol. Chem. 280, 15103-15110 (2005
53. Guertin, M.J., Zhang, X., Coonrod, S.A., & Hager, G.L. Transient ER binding and p300 redistribution support a squelching mechanism for E2-repressed genes. Mol. Endocrinol. 28, 1522-1533 (2014
54. Grøntved, L., et al. Transcriptional activation by the thyroid hormone receptor through ligand dependent receptor recruitment and chromatin remodeling. Nat. Commun. 6, 7048 (2015
55. Marcelli, M., et al. Quantifying effects of ligands on androgen receptor nuclear translocation, intranuclear dynamics, and solubility. J. Cell. Biochem. 98, 770-788 (2006
56. Yu, J., et al. An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell 17, 443-454 (2010
57. Tirard, M., Almeida, O.F., Hutzler, P., Melchior, F., & Michaelidis, T.M. Sumoylation and proteasomal activity determine the transactivation properties of the mineralocorticoid receptor. Mol. Cell. Endocrinol. 268, 20-29 (2007
58. Le Billan, F., et al. Cistrome of the aldosterone-Activated mineralocorticoid receptor in human renal cells. FASEB J. 29, 3977-3989 (2015