Ukr.Biochem.J. 2014; Volume 86, Issue 4, Jul-Aug, pp. 5-17

doi: http://dx.doi.org/10.15407/ubj86.04.005

System biology and the project Encode

19.06.2015   Uncategorized   No comments

M. Yu. Obolenskaya

Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;
e-mail: m.obolenska@gmail.com

The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

Keywords: , ,

References:

  1. Von Bertalanffy L. The theory of open systems in physics and biology. Science. 1950 Jan 13;111(2872):23-9. PubMed, CrossRef
  2. Hodgkin AL, Huxley AF.  A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol. 1952 Aug;117(4):500-44. PubMed, PubMedCentral, CrossRef
  3. Waddington C. H. The Nature of Life. London: George, Allen, & Unwin, 1961. 131 p.
  4. Noble D. Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature. 1960 Nov 5;188(4749):495-7. PubMed, CrossRef
  5. Mesarovic´ MD. Systems Theory and Biology–View of a Theoretician. In: System Theory and Biology, ed. M. D. Mesarovic, Vienna: Springer-Verlag. 1968. P. 59-87. CrossRef
  6. Kacser H, Burns JA. The control of flux. Symp Soc Exp Biol. 1973;27:65-104. PubMed
  7. Heinrich R, Rapoport TA. A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector. Eur J Biochem. 1974 Feb 15;42(1):97-105. PubMed,  CrossRef
  8. Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol. 1969 Mar;22(3):437-67. PubMed, CrossRef
  9. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931-45. PubMed, CrossRef
  10. Wolkenhauer O, Mesarovic M. Feedback dynamics and cell function: Why systems biology is called Systems Biology. Mol Biosyst. 2005 May;1(1):14-6. Epub 2005 Apr 8. PubMed,CrossRef
  11. International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. Integrating common and rare genetic variation in diverse human populations. Nature. 2010 Sep 2;467(7311):52-8. PubMed, PubMedCentral, CrossRef
  12. 1000 Genomes Project Consortium, Abe­casis G. R., Altshuler D., Auton A., Brooks L. D., Durbin R. M., Gibbs R. A., Hurles M. E., McVean G. A. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061–1073. doi:10.1038.nature09534.
  13.  1000 Genomes Project Consortium, Abe­casis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56-65. CrossRef
  14. Witte JS. Genome-wide association studies and beyond. Annu Rev Public Health. 2010;31:9-20 4 p following 20. PubMed, PubMedCentral, CrossRef
  15. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. PubMed, PubMedCentral
  16. Maher B. ENCODE: The human encyclopaedia. Nature. 2012 Sep 6;489(7414):46-8. PubMed, CrossRef
  17. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PubMed, PubMedCentral, CrossRef
  18. Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biol. 2012;13(9):R51.  PubMed, PubMedCentral, CrossRef
  19. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009 Mar;10(3):155-9. Review. PubMed, CrossRef
  20. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007 Jun;17(6):669-81. Review. PubMed, CrossRef
  21. Moran VA, Perera RJ, Khalil AM. Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res. 2012 Aug;40(14):6391-400. Epub 2012 Apr 5. Review. PubMed, PubMedCentral, CrossRef
  22. Wang YM, Zhou P, Wang LY, Li ZH, Zhang YN, Zhang YX. Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells. PLoS One. 2012;7(8):e42414. Epub 2012 Aug 10. PubMed, PubMedCentral, CrossRef
  23. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M., Dunn D, Ebersol A K, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H., Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M., Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Cra wford G. E., Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. PubMed,  PubMedCentral, CrossRef
  24. Zentner GE, Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol. 2013 Mar;20(3):259-66. Review. PubMed, CrossRef
  25. de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012 Nov;58(3):189-91. PubMed, PubMedCentral, CrossRef
  26. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O’Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. PubMed, PubMedCentral, CrossRef
  27. Zhou JX, Huang S. Understanding gene circuits at cell-fate branch points for rational cell reprogramming. Trends Genet. 2011 Feb;27(2):55-62. Epub 2010 Dec 14. Review. PubMed, CrossRef
  28. Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R., Rechtsteiner A, Ikegami K., Alves P., Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G., Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R., Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T., Henikoff JG, Henz SR, Hinrichs A., Holster H., Hyman T, Iniguez AL, Janettex J, Jensen M., Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierzx P, Lai EC, Latorre I, Leahey A., Lewis S., Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R., MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science. 2010 Dec 24;330(6012):1775-87.  PubMed, PubMedCentral, CrossRef
  29. modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N., Washington NL Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko A A, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K., Perry M., Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan K. H, Yang L, Yu C, Feingold E, Good P., Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin S C, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park P J, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-97. PubMed, PubMedCentral, CrossRef
  30. Obolenskaya MYu, Tokovenko BT, Kuklin AV, Frolova AA, Rodriguez RR, Dotsenko VA, Dragushchenko OO. The start of systems biology in Ukraine. Biopolym Cell. 2014;30(1):16–24.  CrossRef
Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License.