The grammar of transcriptional regulation

Human Genetics

Volumn 133, Issue 6, 2014, Pages 701-711

  Weingarten Gabbay, Shira ^a   Segal, Eran ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

BINDING AFFINITY; BINDING SITE; DNA HELIX; EPIGENETICS; EUKARYOTE; GENE EXPRESSION; NUCLEOSOME; PRIORITY JOURNAL; REGULATORY DNA SEQUENCE; REVIEW; TRANSCRIPTION REGULATION;

EUKARYOTA;

BINDING SITES; DNA; GENE EXPRESSION REGULATION; HUMANS; PROTEIN BINDING; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84901192605     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-013-1413-1     Document Type: Review

References (69)

1. Arnold CD et al (2013) Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339:1074-1077
2. Badis G et al (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720-1723
3. Bakiri L, Matsuo K, Wisniewska M, Wagner EF, Yaniv M (2002) Promoter specificity and biological activity of tethered AP-1 dimers. Mol Cell Biol 22:4952-4964
4. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117:185-198
5. Beisel C, Paro R (2011) Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 12:123-135
6. Berger MF et al (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266-1276
7. Blanco J, Girard F, Kamachi Y, Kondoh H, Gehring WJ (2005) Functional analysis of the chicken delta1-crystallin enhancer activity in Drosophila reveals remarkable evolutionary conservation between chicken and fly. Development 132:1895-1905
8. Burz DS, Rivera-Pomar R, Jackle H, Hanes SD (1998) Cooperative DNA-binding by Bicoid provides a mechanism for threshold-dependent gene activation in the Drosophila embryo. EMBO J 17:5998-6009
9. Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB (2006) Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol 7:16
10. Coleman RA, Pugh BF (1995) Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. J Biol Chem 270:13850-13859
11. Cox RS 3rd, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3:145
12. Crawford GE et al (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16:123-131
13. Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25:1010-1022
14. Dostie J, Dekker J (2007) Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2:988-1002
15. Dunham I et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74
16. Field Y et al (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4:e1000216
17. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C (2004) Clustering of DNA sequences in human promoters. Genome Res 14:1562-1574
18. Gaulton KJ et al (2010) A map of open chromatin in human pancreatic islets. Nat Genet 42:255-259
19. Gencheva M et al (2006) In Vitro and in Vivo nucleosome positioning on the ovine beta-lactoglobulin gene are related. J Mol Biol 361:216-230
20. Gerstein MB et al (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489:91-100
21. Gertz J, Siggia ED, Cohen BA (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457:215-218
22. Giniger E, Ptashne M (1988) Cooperative DNA binding of the yeast transcriptional activator GAL4. Proc Natl Acad Sci USA 85:382-386
23. Gotea V et al (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 20:565-577
24. He X, Hohn T, Futterer J (2000) Transcriptional activation of the rice tungro bacilliform virus gene is critically dependent on an activator element located immediately upstream of the TATA box. J Biol Chem 275:11799-11808
25. Herold M, Bartkuhn M, Renkawitz R (2012) CTCF: insights into insulator function during development. Development 139:1045-1057
26. Hertel KJ, Lynch KW, Maniatis T (1997) Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol 9:350-357
27. Iyer V, Struhl K (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 14:2570-2579
28. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502
29. Jolma A et al (2013) DNA-binding specificities of human transcription factors. Cell 152:327-339
30. Juven-Gershon T, Cheng S, Kadonaga JT (2006) Rational design of a super core promoter that enhances gene expression. Nat Methods 3:917-922
31. Kelly TK et al (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22:2497-2506
32. Kheradpour P et al (2013) Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 23:800-811
33. Khoury AM, Lee HJ, Lillis M, Lu P (1990) Lac repressor-operator interaction: DNA length dependence. Biochim Biophys Acta 1087:55-60
34. Kim JG, Takeda Y, Matthews BW, Anderson WF (1987) Kinetic studies on Cro repressor-operator DNA interaction. J Mol Biol 196:149-158
35. Kinkhabwala A, Guet CC (2008) Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS One 3:e2030
36. Kinney JB, Murugan A, Callan CG Jr, Cox EC (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci USA 107:9158-9163
37. Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA (2012) Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci USA 109:19498-19503
38. Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424:147-151
39. Lidor Nili E et al (2010) p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res 20:1361-1368
40. Ligr M, Siddharthan R, Cross FR, Siggia ED (2006) Gene expression from random libraries of yeast promoters. Genetics 172:2113-2122
41. Melnikov A et al (2012) Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30:271-277
42. Morin R et al (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45:81-94
43. Nguyen DH, D'Haeseleer P (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol 2:2006 0012
44. Papatsenko DA et al (2002) Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. Genome Res 12:470-481
45. Patwardhan RP et al (2009) High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol 27:1173-1175
46. Patwardhan RP et al (2012) Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol 30:265-270
47. Pirrotta V, Gross DS (2005) Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol Cell 18:395-398
48. Ravasi T et al (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140:744-752
49. Raveh-Sadka T et al (2012) Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 44:743-750
50. Reece-Hoyes JS et al (2005) A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol 6:R110
51. Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M (2008) Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet 4:e1000133
52. Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447:425-432
53. Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423:145-150
54. Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191:659-675
55. Schlabach MR, Hu JK, Li M, Elledge SJ (2010) Synthetic design of strong promoters. Proc Natl Acad Sci USA 107:2538-2543
56. Schwartz YB et al (2012) Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res 22:2188-2198
57. Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19:65-71
58. Segal E, Barash Y, Simon I, Friedman N, Koller D (2002) From promoter sequence to expression: a probabilistic framework. In: Proceeding 6th international conference on research in computational molecular biology (RECOMB), Washington, DC
59. Sharon E et al (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol 30:521-530
60. Somma MP, Pisano C, Lavia P (1991) The housekeeping promoter from the mouse CpG island HTF9 contains multiple protein-binding elements that are functionally redundant. Nucleic Acids Res 19:2817-2824
61. Struhl K (1985) Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA 82:8419-8423
62. Takahashi K et al (1986) Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter. Nature 319:121-126
63. Thastrom A, Bingham LM, Widom J (2004) Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J Mol Biol 338:695-709
64. Valouev A et al (2011) Determinants of nucleosome organization in primary human cells. Nature 474:516-520
65. Walhout AJ (2006) Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 16:1445-1454
66. Whitfield TW et al (2012) Functional analysis of transcription factor binding sites in human promoters. Genome Biol 13:R50
67. Wunderlich Z, Mirny LA (2009) Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet 25:434-440
68. Xie X et al (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338-345
69. Yu M et al (1997) GA-binding protein-dependent transcription initiator elements. Effect of helical spacing between polyomavirus enhancer a factor 3(PEA3)/Ets-binding sites on initiator activity. J Biol Chem 272:29060-29067