The grammar of transcriptional regulation

详细信息    查看全文

• 作者：Shira Weingarten-Gabbay (1)
  Eran Segal (1)
  
• 刊名：Human Genetics
• 出版年：2014
• 出版时间：June 2014
• 年：2014
• 卷：133
• 期：6
• 页码：701-711
• 全文大小：
• 参考文献：1. Arnold CD et al (2013) Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339:1074鈥?077 CrossRef
  2. Badis G et al (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720鈥?723 CrossRef
  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鈥?964 CrossRef
  4. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117:185鈥?98 CrossRef
  5. Beisel C, Paro R (2011) Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 12:123鈥?35 CrossRef
  6. Berger MF et al (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266鈥?276 CrossRef
  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鈥?905 CrossRef
  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鈥?009 CrossRef
  9. Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB (2006) Flexible promoter architecture requirements for coactivator recruitment. BMC Mol Biol 7:16 CrossRef
  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鈥?3859 CrossRef
  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鈥?31 CrossRef
  13. Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25:1010鈥?022 CrossRef
  14. Dostie J, Dekker J (2007) Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2:988鈥?002 CrossRef
  15. Dunham I et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57鈥?4 CrossRef
  16. Field Y et al (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4:e1000216 CrossRef
  17. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C (2004) Clustering of DNA sequences in human promoters. Genome Res 14:1562鈥?574 CrossRef
  18. Gaulton KJ et al (2010) A map of open chromatin in human pancreatic islets. Nat Genet 42:255鈥?59 CrossRef
  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鈥?30 CrossRef
  20. Gerstein MB et al (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489:91鈥?00 CrossRef
  21. Gertz J, Siggia ED, Cohen BA (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457:215鈥?18 CrossRef
  22. Giniger E, Ptashne M (1988) Cooperative DNA binding of the yeast transcriptional activator GAL4. Proc Natl Acad Sci USA 85:382鈥?86 CrossRef
  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鈥?77 CrossRef
  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鈥?1808 CrossRef
  25. Herold M, Bartkuhn M, Renkawitz R (2012) CTCF: insights into insulator function during development. Development 139:1045鈥?057 CrossRef
  26. Hertel KJ, Lynch KW, Maniatis T (1997) Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol 9:350鈥?57 CrossRef
  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鈥?579
  28. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497鈥?502 CrossRef
  29. Jolma A et al (2013) DNA-binding specificities of human transcription factors. Cell 152:327鈥?39 CrossRef
  30. Juven-Gershon T, Cheng S, Kadonaga JT (2006) Rational design of a super core promoter that enhances gene expression. Nat Methods 3:917鈥?22 CrossRef
  31. Kelly TK et al (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22:2497鈥?506 CrossRef
  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鈥?11 CrossRef
  33. Khoury AM, Lee HJ, Lillis M, Lu P (1990) Lac repressor-operator interaction: DNA length dependence. Biochim Biophys Acta 1087:55鈥?0 CrossRef
  34. Kim JG, Takeda Y, Matthews BW, Anderson WF (1987) Kinetic studies on Cro repressor-operator DNA interaction. J Mol Biol 196:149鈥?58 CrossRef
  35. Kinkhabwala A, Guet CC (2008) Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS One 3:e2030 CrossRef
  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鈥?163 CrossRef
  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鈥?9503 CrossRef
  38. Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424:147鈥?51 CrossRef
  39. Lidor Nili E et al (2010) p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res 20:1361鈥?368 CrossRef
  40. Ligr M, Siddharthan R, Cross FR, Siggia ED (2006) Gene expression from random libraries of yeast promoters. Genetics 172:2113鈥?122 CrossRef
  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鈥?77 CrossRef
  42. Morin R et al (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45:81鈥?4 CrossRef
  43. Nguyen DH, D鈥橦aeseleer P (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol 2:2006 0012 CrossRef
  44. Papatsenko DA et al (2002) Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. Genome Res 12:470鈥?81 CrossRef
  45. Patwardhan RP et al (2009) High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol 27:1173鈥?175 CrossRef
  46. Patwardhan RP et al (2012) Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol 30:265鈥?70 CrossRef
  47. Pirrotta V, Gross DS (2005) Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol Cell 18:395鈥?98 CrossRef
  48. Ravasi T et al (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140:744鈥?52 CrossRef
  49. Raveh-Sadka T et al (2012) Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 44:743鈥?50 CrossRef
  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 CrossRef
  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 CrossRef
  52. Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447:425鈥?32 CrossRef
  53. Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423:145鈥?50 CrossRef
  54. Satchwell SC, Drew HR, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191:659鈥?75 CrossRef
  55. Schlabach MR, Hu JK, Li M, Elledge SJ (2010) Synthetic design of strong promoters. Proc Natl Acad Sci USA 107:2538鈥?543 CrossRef
  56. Schwartz YB et al (2012) Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res 22:2188鈥?198 CrossRef
  57. Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19:65鈥?1 CrossRef
  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鈥?30 CrossRef
  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鈥?824 CrossRef
  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鈥?423 CrossRef
  62. Takahashi K et al (1986) Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter. Nature 319:121鈥?26 CrossRef
  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鈥?09 CrossRef
  64. Valouev A et al (2011) Determinants of nucleosome organization in primary human cells. Nature 474:516鈥?20 CrossRef
  65. Walhout AJ (2006) Unraveling transcription regulatory networks by protein-DNA and protein鈥損rotein interaction mapping. Genome Res 16:1445鈥?454 CrossRef
  66. Whitfield TW et al (2012) Functional analysis of transcription factor binding sites in human promoters. Genome Biol 13:R50 CrossRef
  67. Wunderlich Z, Mirny LA (2009) Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet 25:434鈥?40 CrossRef
  68. Xie X et al (2005) Systematic discovery of regulatory motifs in human promoters and 3鈥?UTRs by comparison of several mammals. Nature 434:338鈥?45 CrossRef
  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鈥?9067 CrossRef
  
• 作者单位：Shira Weingarten-Gabbay (1)
  Eran Segal (1)
  
  1. Department of Computer Science, Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
  
• ISSN：1432-1203

文摘

Eukaryotes employ combinatorial strategies to generate a variety of expression patterns from a relatively small set of regulatory DNA elements. As in any other language, deciphering the mapping between DNA and expression requires an understanding of the set of rules that govern basic principles in transcriptional regulation, the functional elements involved, and the ways in which they combine to orchestrate a transcriptional output. Here, we review the current understanding of various grammatical rules, including the effect on expression of the number of transcription factor binding sites, their location, orientation, affinity and activity; co-association with different factors; and intrinsic nucleosome organization. We review different methods that are used to study the grammar of transcription regulation, highlight gaps in current understanding, and discuss how recent technological advances may be utilized to bridge them.