nach oben

Medical & Biological Engineering & Computing

Erschienen in:

01.08.2007 | Review Article

Unravelling the world of cis-regulatory elements

verfasst von: Zhao Wang, Gong-Hong Wei, De-Pei Liu, Chih-Chuan Liang

Erschienen in: Medical & Biological Engineering & Computing | Ausgabe 8/2007

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Abstract

Genome-wide comparisons indicate that only studying the coding regions will not be enough for explaining the biological complexity of an organism, while the genetic variants and the epigenetic differences of cis-regulatory elements are crucial to elucidate many complicated biological phenomena. Their various regulatory functions also play indispensable roles in forming organismal polymorphism. Recent studies showed that the cis-regulatory elements can regulate gene expression as nuclear organizers, and involve in functional noncoding transcription and produce regulatory noncoding RNA molecules. Novel high-throughput strategies and in silico analysis make a great amount data of cis-regulatory elements available. Particularly, the computational methods could help to combine reductionist studies with network biomedical investigations, and begin the era to understand organismal regulatory events at systems biology level.

Nächster Artikel Assessment of cerebrospinal fluid outflow resistance

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Akutsu T, Miyano S, Kuhara S (2000) Algorithms for inferring qualitative models of biological networks. Pac Symp Biocomput pp.293–304

Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406:378–382

Albert R, Barabasi AL (2002) Statistical mechanics of complex networks. Rev Mod Phys 74:47–97

Alon U, Surette MG, Barkai N, Leibler S (1999) Robustness in bacterial chemotaxis. Nature 397:168–171

Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355

Andrioli LPM, Vasisht V, Theodosopoulou E, Oberstein A, Small S (2002) Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms. Development 129:4931–4940

Aoyagi N, Wassarman DA (2000) Genes encoding Drosophila melanogaster RNA polymerase II general transcription factors: diversity in TFIIA and TFIID components contributes to gene-specific transcriptional regulation. J Cell Biol 150:F45–F50

Arnone MI, Davidson EH (1997) The hardwiring of development organization and function of genomic regulatory systems. Development 124:1851–1864

Avner P, Heard E (2001) X-chromosome inactivation: counting, choice and initiation. Nat Rev Genet 2:59–67

10.

Baltimore D (2001) Our genome unveiled. Nature 409:814–816

11.

Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5:101–113

12.

Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387:913–917

13.

Barrick JE et al (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci USA 101:6421–6426

14.

Barrow JR, Stadler HS, Capecchi MR (2000) Roles of Hoxa1 and Hoxa2 in patterning the early hindbrain of the mouse. Development 127:933–944

15.

Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J (1995) The nuclear matrix: a structural milieu for genomic function. Int Rev Cytol 162A:1–65

16.

Bornhoudt S, Schuster HG (2003) Handbook of graphs and networks: from the genome to the internet. Wiley, Berlin

17.

Bowen NJ, Jordan IK (2002) Transposable elements and the evolution of eukaryotic complexity. Curr Issues Mol Biol 4:65–76

18.

Bulyk ML (2003) Computational prediction of transcription-factor binding site locations. Genome Biol 5:201

19.

Carlson JM, Chakravarty A, Khetani RS, Gross RH (2006) Bounded search for de novo identification of degenerate cis-regulatory elements. BMC Bioinformatics 7:254

20.

Séverine C, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Gene Dev 18:1119–1130

21.

Cheutin T, McNairn AJ, Jenuwein T, Gilbert DM., Singh PB, Misteli T (2003) Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299:721–725

22.

Conte C, Dastugue B, Vaury C (2002) Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes. Mol Cell Biol 22:1767–1777

23.

Cook PR (1999) The organization of replication and transcription. Science 284:1790–1795

24.

Corbino KA (2005) Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 6:R70

25.

Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2:292–301

26.

Desset S, Vaury Ch (2005) Transcriptional interference mediated by retrotransposons within the genome of their host: lessons from alleles of the white gene from Drosophila melanogaster. Cytogenet Genome Res 110:209–214

27.

Dezso Z, Oltvai N, Barabasi AL (2003) Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Genome Res 13:2450–2454

28.

Dorogovtsev SN, Mendes JFF (2003) Evolution of networks:from biological nets to the internet and www. Oxford University Press, OxfordMATH

29.

Fedoriw AM, Stein P, Svoboda P, Schultz RM, Bartolomei MS (2004) Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. Science 303:238–240

30.

Feng DX, Liu DP, Huang Y, Wu L, Li TC, Wu M, Tang XB, Liang CC (2001) The expression of human alpha-like globin genes in transgenic mice mediated by bacterial artificial chromosome. Proc Natl Acad Sci USA 98:15073–15077

31.

Ferguson-Smith AC (2000) Genetic imprinting: silencing elements have their say. Curr Biol 10:R872–R875

32.

Frith MC, Hansen U, Weng Z (2001) Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17:878–889

33.

Gaudet J, Mango SE (2002) Regulation of organogenesis by the Caenorhabditis elegans, FoxA protein PHA-41. Science 295:821–825

34.

Gerasimova TI, Byrd K, Corces VG (2000) A chromatin insulator determines the nuclear localization of DNA. Mol Cell 6:1025–1035

35.

Gibbs WW (2003) The unseen genome: gems among the junk. Sci Am 289:26–33

36.

Gottgens B et al (2000) Analysis of vertebrate SCL loci identifies conserved enhancers. Nat Biotechnol 18:181–186

37.

Graveley BR (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet 17:100–107

38.

Greenfield A (2000) Applications of DNA microarrays to the transcriptional analysis of mammalian genomes. Mamm Genome 11:609–613

39.

Gribnau J, Diderich K, Pruzina S, Calzolari R, Fraser P (2000) Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol Cell 5:377–386

40.

Guo L, Hu-Li J, Paul WE (2005) Probabilistic regulation in TH2 cells accounts for monoallelic expression of IL-4 and IL-13. Immunity 23:89–99

41.

Haddad F, Bodell PW, Qin AX, Giger JM, Baldwin KM (2003) Role of antisense RNA in coordinating cardiac myosin heavy chain gene switching. J Biol Chem 278:37132–37138

42.

Hardison R, Krane D, Vandenbergh D, Cheng JF, Mansberger J, Taddie J, Schwartz S, Huang XQ, Miller W (1991) Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G + C-rich region of mammalian genomes. J Mol Biol 222:233–249

43.

Hardison RC (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16:369–372

44.

Harismendy O, Gendrel CG, Soularue P, Gidrol X, Sentenac A, Werner M, Lefebvre O (2003) Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J 22:4738–4747

45.

He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5:522–531

46.

Heng HH, Goetze S, Ye CJ, Liu G, Stevens JB, Bremer SW, Wykes SM, Bode J, Krawetz SA (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J Cell Sci 117:999–1008

47.

Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, Brown EL (2000) Genomic analysis of gene expression in C. elegans. Science 290:809–812

48.

Holter NS, Maritan A, Cieplak M, Fedoroff NV, Banavar JR (2001) Dynamic modeling of gene expression data. Proc Natl Acad Sci USA 98:1693–1698

49.

Hood L, Rowen L, Koop BF (1995) Human and mouse T-cell receptor loci: genomics, evolution, diversity, and serendipity. Ann NY Acad Sci 758:390–412

50.

Meredith LH, Davidson EH (2004) cis-Regulatory control circuits in development. Dev Biol 271: 109–118

51.

Hudson TJ (2003) Wanted: regulatory SNPs. Nat Genet 33:439–440

52.

Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296:1205–1214

53.

Iarovaia OV, Akopov SB, Nikolaev LG, Sverdlov ED, Razin SV (2005) Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix. Nucleic Acids Res 33:4157–4163

54.

Iglesias AR, Kindlund E, Tammi M, Wadelius C (2004) Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding. Gene 341:149–165

55.

Ishii K, Arib G, Lin C, Van Houwe G, Laemmli UK (2002) Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 109:551–562

56.

Jeannie TL (2005) Regulation of X-chromosome counting by Tsix and Xite sequences. Science 309:768–771

57.

Knight JC, Keating BJ, Kwiatkowski DP (2004) Allele-specific repression of lymphotoxin-alpha by activated B cell factor-1. Nat Genet 36:394–399

58.

Knight JC, Keating BJ, Rockett KA, Kwiatkowski DP (2003) In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat Genet 33:469–475

59.

Koop BF, Hood L (1994) Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nat Genet 7:48–53

60.

Kosak ST, Groudine M (2004) Form follows function: the genomic organization of cellular differentiation. Gene Dev 18:1371–1384

61.

Kuhn EJ, Geyer PK (2003) Genomic insulators: connecting properties to mechanism. Curr Opin Cell Biol 15:259–265

62.

Labrador M, Corces VG (2002) Setting the boundaries of chromatin domains and nuclear organization. Cell 111:151–154

63.

Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003) New microRNAs from mouse and human. RNA 9:175–179

64.

Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921

65.

Lee TI et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799–804

66.

Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424:147–151

67.

Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405:827–836

68.

Lopez RA, Schoetz S, DeAngelis K, ‘Neill DO, Bank A (2002) Multiple hematopoietic defects and delayed globin switching in Ikaros null mice. Proc Natl Acad Sci USA 99:602–607

69.

Lv X, Shi HZ, Liu DP, Hao DL, Zhang S, Xin L, Li XG, Xu HM, Liang CC (2005) High fidelity screening of regulatory sequences in apolipoprotein(a)-plasminogen cluster. Int J Biochem Cell Biol 37:1846–1857

70.

Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429:571–574

71.

Martens JH, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A (2002) Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes. Mol Cell Biol 22:2598–2606

72.

Martone R et al (2003) Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci USA 100:12247–12252

73.

Miller WJ, McDonald JF, Nouaud D, Anxolabehere D (1999) Molecular domestication—more than a sporadic episode in evolution. Genetica 107:197–207

74.

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB (2003) Position specific variation in the rate of evolution in transcription factorbinding sites. BMC Evol Biol 3:19

75.

Okada N, Takeda J (2004) Biological significance in transposon-mediated mutation and molecular evolution—special reference to the junk DNA. Tanpakushitsu Kakusan Koso 49: 2075–2079

76.

Pasquinelli AE, Hunter S, Bracht J (2005) MicroRNAs: a developing story. Curr Opin Genet Dev 15:200–205

77.

Pastinen T, Hudson TJ (2004) Cis-acting regulatory variation in the human genome. Science 306:647–650

78.

Pastinen T et al (2004) A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics 16:184–193

79.

Pennacchio LA, Rubin EM (2001) Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2:100–109

80.

Perier RC, Praz V, Junier T, Bonnard C, Bucher P (2000) The eukaryotic promoter database (EPD). Nucleic Acids Res 28:302–303

81.

Perkins DO, Jeffries C, Sullivan P (2005) Expanding the ‘central dogma’: the regulatory role of nonprotein coding genes and implications for the genetic liability to schizophrenia. Mol Psychia 10:69–78

82.

Prestridge DS (2000) Computer software for eukaryotic promoter analysis, Methods Mol Biol 130:265–295

83.

Ragoczy T, Telling A, Sawado T, Groudine M, Kosak ST (2003) A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res 11:513–525

84.

Rajewsky N, Vergassola M, Gaul U, Siggia ED (2002) Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3:30

85.

Rank G, Prestel M, Paro R (2002) Transcription through intergenic chromosomal memory elements of the Drosophila bithorax complex correlates with an epigenetic switch. Mol Cell Biol 22:8026–8034

86.

Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626

87.

Rhesus Macaque Genome Sequencing and Analysis Consortium et al (2007) Evolutionary and biomedical insights from the rhesus macaque genome, Science, 316:222–234

88.

Rinn JL et al (2003) The transcriptional activity of human chromosome 22. Genes Dev 17:529–540

89.

Rogan DF et al (2004) Analysis of intergenic transcription in the human IL-4/IL-13 gene cluster. Proc Natl Acad Sci USA 101:2446–2451

90.

Ruvkun G, Hobert O (1998) The taxonomy of developmental control in Caenorhabditis elegans. Science 282:2033–2041

91.

Saitoh N, Bell AC, Recillas-Targa F, West AG, Simpson M, Pikaart M, Felsenfeld G (2000) Structural and functional conservation at the boundaries of the chicken beta-globin domain. EMBO J 19:2315–2322

92.

Sawado T, Halow J, Bender MA, Groudine M (2003) The beta-globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev 17:1009–1018

93.

Schlitt T, Brazma A (2006) Modeling in molecular biology: describing transcription regulatory networks at different scales. Philos Trans R Soc Lond B Biol Sci 361:483–94

94.

Schmitt S, Paro R (2004) Gene regulation: a reason for reading nonsense. Nature 429:510–511

95.

Schmitt S, Prestel M, Paro R (2005) Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev 19:697–708

96.

Schramke V et al (2005) RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435:1275–1279

97.

Schubeler D, Francastel C, Cimbora DM, Reik A, Martin DI, Groudine M (2000) Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev 14:940–95

98.

Sinha S, van Nimwegen E, Siggia ED (2003) A probabilistic method to detect regulatory modules. Bioinformatics 19:i292–i301

99.

Sinha S, Liang Y, Siggia E (2006) Stubb: a program for discovery and analysis of cis-regulatory modules. Nucleic Acids Res 34:W555–W559

100.

Smolen P, Baxter DA, Byrne JH (2000) Modeling transcriptional control in gene networks-methods, recent results, and future directions. Bull Math Biol 62:247–292

101.

Stamatoyannopoulos JA (2004) The genomics of gene expression. Genomics 84:449–457

102.

Steven TK, Groudine M (2004) Gene order and dynamic domains. Science 306:644–647

103.

Strogatz SH (2001) Exploring complex networks. Nature 410:268–276

104.

Sunkar R, Girke T, Zhu JK (2005) Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res 33:4443–4454

105.

Szallasi Z, Liang S (1998) Modeling the normal and neoplastic cell cycle with ‘realistic Boolean genetic networks’: their application for understanding carcinogenesis and assessing therapeutic strategies. Pac Symp Biocomput, pp 66–76

106.

Szutorisz H, Canzonetta C, Georgiou A, Chow CM, Tora L, Dillon N (2005) Formation of an active tissue-specific chromatin domain initiated by epigenetic marking at the embryonic stem cell stage. Mol Cell Biol 25:1804–1820

107.

Takada S et al (2002) Epigenetic analysis of the Dlk1-Gtl2 imprinted domain on mouse chromosome 12: implications for imprinting control from comparison with Igf2-H19. Hum Mol Genet 11:77–86

108.

Tyson JJ, Csikasz-Nagy A, Novak B (2002) The dynamics of cell cycle regulation. Bioessays 24:1095–1109

109.

van Driel R, Wansink DG, van Steensel B, Grande MA, Schul W, de Jong L (1995) Nuclear domains and the nuclear matrix. Int Rev Cytol 162A:151–189

110.

Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5:276–287

111.

Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet 2:1123–1128

112.

Wei GH, Liu DP, Liang CC (2005) Chromatin domain boundaries: insulators and beyond. Cell Res 15:292–300

113.

Wei GH, Liu DP, Liang CC (2004) Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J 381:1–12

114.

Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28:316–319

115.

Wittkopp PJ (2005) Genomic sources of regulatory variation in cis and in trans. Cell Mol Life Sci 62:1779–1783

116.

Wray GA et al (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377–1419

117.

Wyrick JJ, Young RA (2002) Deciphering gene expression regulatory networks. Curr Opin Genet Dev 12:130–136

118.

Xu HM, Zhang S, Liu DP, Li XG, Hao DL, Liang CC (2002) Efficient isolation of regulatory sequences from human genome and BAC DNA. Biochem Biophys Res Commun 290:1079–1083

119.

Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T (2002) SATB1 targets chromatin remodelling to regulate genes over long distances. Nature 419:641–645

120.

Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594–596

121.

Zhan HC, Liu DP, Liang CC (2001) Insulator: from chromatin domain boundary to gene regulation. Hum Genet 109:471–478

122.

Zhang LH, Liu DP, Liang CC (2003) Finding regulatory sequences. Int J Biochem Cell Biol 35:95–103

Titel: Unravelling the world of cis-regulatory elements
verfasst von: Zhao Wang
Gong-Hong Wei
De-Pei Liu
Chih-Chuan Liang
Publikationsdatum: 01.08.2007
Verlag: Springer-Verlag
Erschienen in: Medical & Biological Engineering & Computing / Ausgabe 8/2007
Print ISSN: 0140-0118
Elektronische ISSN: 1741-0444
DOI: https://doi.org/10.1007/s11517-007-0195-9

Springer Professional

Abstract

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Weitere Artikel der Ausgabe 8/2007

Simulation of an anterior spine instrumentation in adolescent idiopathic scoliosis using a flexible multi-body model

Assessment of cerebrospinal fluid outflow resistance

Effects of head size and morphology on dynamic responses to impact loading

Microbubbling by co-axial electrohydrodynamic atomization

A newly developed tool for intra-tracheal temperature and humidity assessment in laryngectomized individuals: the Airway Climate Explorer (ACE)

Signal-dependent wavelets for electromyogram classification

Premium Partner