Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions

PLoS Computational Biology

Volumn 9, Issue 12, 2013, Pages

  Chen, Chieh Chun ^a   Xiao, Shu ^b   Xie, Dan ^a   Cao, Xiaoyi ^b   Song, Chun Xiao ^c   Wang, Ting ^d   He, Chuan ^c   Zhong, Sheng ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; BINDING ENERGY; DNA; STATISTICAL MECHANICS; STEM CELLS; TRANSCRIPTION; TRANSCRIPTION FACTORS;

BINDING-SITES; DNA-BINDING; EPIGENOMES; EPIGENOMICS; EXPLOSIVE GROWTH; GENE-REGULATION; GENOMICS; MICE EMBRYONIC STEM CELLS; TRANSCRIPTION FACTOR BINDING; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES;

5-METHYLCYTOSINE; ANIMALS; CYTOSINE; DNA; EMBRYONIC STEM CELLS; EPIGENOMICS; GENOME; HISTONES; MICE; MODELS, BIOLOGICAL; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 84892757801     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003367     Document Type: Article

References (65)

1. Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, et al. (2008) FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132: 958-970.
2. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
3. Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
4. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
5. Tanay A, (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 16: 962-972.
6. Beer MA, Tavazoie S, (2004) Predicting gene expression from sequence. Cell 117: 185-198.
7. Foat BC, Morozov AV, Bussemaker HJ, (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 22: e141-149.
8. Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ, (2006) A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data-a case study using E2F1. Genome Res 16: 1585-1595.
9. Smith AD, Sumazin P, Zhang MQ, (2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A 102: 1560-1565.
10. Datta D, Zhao H, (2008) Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics 24: 545-552.
11. Zhou Q, Liu JS, (2008) Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res 36: 4137-4148.
12. He HH, Meyer CA, Shin H, Bailey ST, Wei G, et al. (2010) Nucleosome dynamics define transcriptional enhancers. Nat Genet 42: 343-347.
13. Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, et al. (2012) Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics 28: 56-62.
14. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
15. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
16. Arvey A, Agius P, Noble WS, Leslie C, (2012) Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Research 22: 1723-1734.
17. Boyle AP, Song L, Lee B-K, London D, Keefe D, et al. (2011) High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Research 21: 456-464.
18. Ernst J, Plasterer HL, Simon I, Bar-Joseph Z, (2010) Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res 20: 526-536.
19. Segal E, Widom J, (2009) From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet 10: 443-456.
20. Shea MA, Ackers GK, (1985) The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 181: 211-230.
21. Buchler NE, Gerland U, Hwa T, (2003) On schemes of combinatorial transcription logic. Proceedings of the National Academy of Sciences of the United States of America 100: 5136-5141.
22. Gertz J, Siggia ED, Cohen BA, (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457: 215-218.
23. Raveh-Sadka T, Levo M, Segal E, (2009) Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19: 1480-1496.
24. Mirny LA, (2010) Nucleosome-mediated cooperativity between transcription factors. Proc Natl Acad Sci U S A 107: 22534-22539.
25. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U, (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451: 535-540.
26. Janssens H, Hou S, Jaeger J, Kim AR, Myasnikova E, et al. (2006) Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38: 1159-1165.
27. Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, et al. (2010) Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Mol Syst Biol 6: 341.
28. He X, Chen CC, Hong F, Fang F, Sinha S, et al. (2009) A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PLoS One 4: e8155.
29. Biggin MD, Animal transcription networks as highly connected, quantitative continua. Dev Cell 21: 611-626.
30. Karlic R, Chung HR, Lasserre J, Vlahovicek K, Vingron M, (2010) Histone modification levels are predictive for gene expression. Proceedings of the National Academy of Sciences of the United States of America 107: 2926-2931.
31. Yu P, Xiao S, Xin X, Song CX, Huang W, et al. (2012) Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation. Genome Res 23 (2):: 352-64.
32. Marks H, Chow JC, Denissov S, Francoijs KJ, Brockdorff N, et al. (2009) High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res 19: 1361-1373.
33. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
34. Chen X, Xu H, Yuan P, Fang F, Huss M, et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106-1117.
35. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253-257.
36. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29: 68-72.
37. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
38. Hardy S, Jacques PE, Gevry N, Forest A, Fortin ME, et al. (2009) The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition. PLoS Genet 5: e1000687.
39. Talbert PB, Henikoff S, (2010) Histone variants-ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11: 264-275.
40. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proceedings of the National Academy of Sciences of the United States of America 107: 21931-21936.
41. Stormo GD, (1990) Consensus patterns in DNA. Methods Enzymol 183: 211-221.
42. Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, et al. (2010) Comparative epigenomic analysis of murine and human adipogenesis. Cell 143: 156-169.
43. Xiao S, Xie D, Cao X, Yu P, Xing X, et al. (2012) Comparative epigenomic annotation of regulatory DNA. Cell 149: 1381-1392.
44. Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, et al. (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36: D102-106.
45. Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ, (2008) E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res 18: 1763-1777.
46. Wei GH, Badis G, Berger MF, Kivioja T, Palin K, et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J 29: 2147-2160.
47. Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, et al. (2003) The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113: 631-642.
48. Raj A, van Oudenaarden A, (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216-226.
49. Palsson BO (2011) Systems Biology: Simulation of Dynamic Network States: Caambridge Univ. Press.
50. Elowitz MB, Levine AJ, Siggia ED, Swain PS, (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
51. Raser JM, O'Shea EK, (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
52. Alon U (2007) An introduction to systems biology: design principles of biological circuits. Boca Raton, FL: Chapman & Hall/CRC. xvi, 301 p., 304 p. of plates p.
53. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
54. Evans MJ, Kaufman MH, (1981) Establishment in culture of pluripotential cells from mouse embryos. Nature 292: 154-156.
55. Nichols J, Zevnik B, Anastassiadis K, Niwa H, Klewe-Nebenius D, et al. (1998) Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95: 379-391.
56. Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, et al. (2011) Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet 43: 1091-1097.
57. Zhang Z, Jones A, Sun CW, Li C, Chang CW, et al. (2011) PRC2 complexes with JARID2, MTF2, and esPRC2p48 in ES cells to modulate ES cell pluripotency and somatic cell reprogramming. Stem Cells 29: 229-240.
58. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, et al. The dynamic architecture of Hox gene clusters. Science 334: 222-225.
59. Zhang C, Xuan Z, Otto S, Hover JR, McCorkle SR, et al. (2006) A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res 34: 2238-2246.
60. He X, Duque TS, Sinha S, (2011) Evolutionary Origins of Transcription Factor Binding Site Clusters. Mol Biol Evol 29 (3):: 1059-70.
61. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, et al. (2010) Variation in transcription factor binding among humans. Science 328: 232-235.
62. Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, et al. (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42: 631-634.
63. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
64. Press WH FB, Teukolsky SA, Vetterling WT (1992) Numerical Recipes in C: The Art of Scientific Computing Cambridge University Press.
65. Shaffer JP, (1995) Multiple hypothesis testing. Annual Review of Psychology 46: 24.