메뉴 건너뛰기




Volumn 110, Issue 14, 2013, Pages 5294-5300

Is junk DNA bunk? A critique of ENCODE

Author keywords

Evolution; Human genome

Indexed keywords

DEOXYRIBONUCLEASE I; DNA; SPACER DNA; TRANSCRIPTION FACTOR FOXP2;

EID: 84875847924     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1221376110     Document Type: Review
Times cited : (303)

References (58)
  • 1
    • 84889064130 scopus 로고    scopus 로고
    • Bits of mystery DNA, far from 'junk', play crucial role
    • September 5, Section A
    • Kolata G (September 5, 2002) Bits of mystery DNA, far from 'junk', play crucial role. The New York Times, Section A, p. 1.
    • (2002) The New York Times , pp. 1
    • Kolata, G.1
  • 2
    • 84865772716 scopus 로고    scopus 로고
    • Genomics: ENCODE explained
    • Ecker JR, et al. (2012) Genomics: ENCODE explained. Nature 489(7414):52-55.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 52-55
    • Ecker, J.R.1
  • 3
    • 84866941784 scopus 로고    scopus 로고
    • Cracking ENCODE
    • Anonymous
    • Anonymous (2012) Cracking ENCODE. Lancet 380(9846):950.
    • (2012) Lancet , vol.380 , Issue.9846 , pp. 950
  • 4
    • 84865812140 scopus 로고    scopus 로고
    • Genomics. ENCODE project writes eulogy for junk DNA
    • Pennisi E (2012) Genomics. ENCODE project writes eulogy for junk DNA. Science 337(6099):1159-1161.
    • (2012) Science , vol.337 , Issue.6099 , pp. 1159-1161
    • Pennisi, E.1
  • 5
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Dunham I, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
    • Dunham, I.1
  • 6
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145-166.
    • (2012) Annu Rev Biochem , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 7
    • 84866535949 scopus 로고    scopus 로고
    • The role of regulatory RNA in cognitive evolution
    • Barry G, Mattick JS (2012) The role of regulatory RNA in cognitive evolution. Trends Cogn Sci 16(10):497-503.
    • (2012) Trends Cogn Sci , vol.16 , Issue.10 , pp. 497-503
    • Barry, G.1    Mattick, J.S.2
  • 8
    • 84868550433 scopus 로고    scopus 로고
    • The C-value paradox, junk DNA and ENCODE
    • Eddy SR (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol 22(21):R898-R899.
    • (2012) Curr Biol , vol.22 , Issue.21
    • Eddy, S.R.1
  • 9
    • 84872861423 scopus 로고    scopus 로고
    • Can ENCODE tell us how much junk we carry in our genome?
    • Niu DK, Jiang L (2013) Can ENCODE tell us how much junk we carry in our genome? Biochem Biophys Res Commun 430(4): 1340-1343.
    • (2013) Biochem Biophys Res Commun , vol.430 , Issue.4 , pp. 1340-1343
    • Niu, D.K.1    Jiang, L.2
  • 10
    • 0015271630 scopus 로고
    • So much "junk" DNA in our genome
    • Ohno S (1972) So much "junk" DNA in our genome. Brookhaven Symp Biol 23:366-370.
    • (1972) Brookhaven Symp Biol , vol.23 , pp. 366-370
    • Ohno, S.1
  • 11
    • 0035090476 scopus 로고    scopus 로고
    • Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma
    • Gregory TR (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc 76(1):65-101.
    • (2001) Biol Rev Camb Philos Soc , vol.76 , Issue.1 , pp. 65-101
    • Gregory, T.R.1
  • 12
    • 2442606761 scopus 로고    scopus 로고
    • Macroevolution, hierarchy theory and the C-value enigma
    • Gregory TR (2004) Macroevolution, hierarchy theory and the C-value enigma. Paleobiology 30:179-202.
    • (2004) Paleobiology , vol.30 , pp. 179-202
    • Gregory, T.R.1
  • 13
    • 19544384334 scopus 로고    scopus 로고
    • Economy, speed and size matter: Evolutionary forces driving nuclear genome miniaturization and expansion
    • Cavalier-Smith T (2005) Economy, speed and size matter: Evolutionary forces driving nuclear genome miniaturization and expansion. Ann Bot (Lond) 95(1):147-175.
    • (2005) Ann Bot (Lond) , vol.95 , Issue.1 , pp. 147-175
    • Cavalier-Smith, T.1
  • 14
    • 23944504276 scopus 로고    scopus 로고
    • Synergy between sequence and size in largescale genomics
    • Gregory TR (2005) Synergy between sequence and size in largescale genomics. Nat Rev Genet 6(9):699-708.
    • (2005) Nat Rev Genet , vol.6 , Issue.9 , pp. 699-708
    • Gregory, T.R.1
  • 15
    • 84867761085 scopus 로고    scopus 로고
    • Evolution of the Australian lungfish (Neoceratodus forsteri ) genome: A major role for CR1 and L2 LINE elements
    • Metcalfe CJ, Filée J, Germon I, Joss J, Casane D (2012) Evolution of the Australian lungfish (Neoceratodus forsteri ) genome: A major role for CR1 and L2 LINE elements. Mol Biol Evol 29(11):3529-3539.
    • (2012) Mol Biol Evol , vol.29 , Issue.11 , pp. 3529-3539
    • Metcalfe, C.J.1    Filée, J.2    Germon, I.3    Joss, J.4    Casane, D.5
  • 16
    • 0027507739 scopus 로고
    • Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome
    • Brenner S, et al. (1993) Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366 (6452):265-268.
    • (1993) Nature , vol.366 , Issue.6452 , pp. 265-268
    • Brenner, S.1
  • 17
    • 0038129545 scopus 로고    scopus 로고
    • Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma
    • Gregory TR (2003) Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma. Biol J Linn Soc Lond 79:329-339.
    • (2003) Biol J Linn Soc Lond , vol.79 , pp. 329-339
    • Gregory, T.R.1
  • 18
    • 0016289595 scopus 로고
    • Chromosomes, DNA sequences, and evolution in salamaders of the genus Plethodon
    • Mizuno S, Macgregor HC (1974) Chromosomes, DNA sequences, and evolution in salamaders of the genus Plethodon. Chromosoma 48:239096.
    • (1974) Chromosoma , vol.48 , pp. 239096
    • Mizuno, S.1    MacGregor, H.C.2
  • 19
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Schnable PS, et al. (2009) The B73 maize genome: Complexity, diversity, and dynamics. Science 326(5956):1112-1115.
    • (2009) Science , vol.326 , Issue.5956 , pp. 1112-1115
    • Schnable, P.S.1
  • 20
    • 0018199859 scopus 로고
    • Nuclear volume control by nucleoskeletal DAN, selection for cell volme and cell growth rate, and the solution of the DNA C-value paradox
    • Cavalier-Smith T (1978) Nuclear volume control by nucleoskeletal DAN, selection for cell volme and cell growth rate, and the solution of the DNA C-value paradox. J Cell Sci 43:247-278.
    • (1978) J Cell Sci , vol.43 , pp. 247-278
    • Cavalier-Smith, T.1
  • 21
    • 0018894384 scopus 로고
    • Selfish genes, the phenotype paradigm and genome evolution
    • Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284(5757):601-603.
    • (1980) Nature , vol.284 , Issue.5757 , pp. 601-603
    • Doolittle, W.F.1    Sapienza, C.2
  • 22
    • 0018857680 scopus 로고
    • Selfish DNA: The ultimate parasite
    • Orgel LE, Crick FHC (1980) Selfish DNA: The ultimate parasite. Nature 284(5757):604-607.
    • (1980) Nature , vol.284 , Issue.5757 , pp. 604-607
    • Orgel, L.E.1    Crick, F.H.C.2
  • 23
    • 84859964614 scopus 로고    scopus 로고
    • Evolution of genome content: Population dynamics of transposable elements in flies and humans
    • González J, Petrov DA (2012) Evolution of genome content: Population dynamics of transposable elements in flies and humans. Methods Mol Biol 855:361-383.
    • (2012) Methods Mol Biol , vol.855 , pp. 361-383
    • González, J.1    Petrov, D.A.2
  • 25
    • 79959543603 scopus 로고    scopus 로고
    • Non-adaptive origins of interactome complexity
    • Fernández A, Lynch M (2011) Non-adaptive origins of interactome complexity. Nature 474(7352):502-505.
    • (2011) Nature , vol.474 , Issue.7352 , pp. 502-505
    • Fernández, A.1    Lynch, M.2
  • 26
    • 0022870264 scopus 로고
    • Polite DNA: Functional density and functional compatibility in genomes
    • Zuckerkandl E (1986) Polite DNA: Functional density and functional compatibility in genomes. J Mol Evol 24(1-2):12-27.
    • (1986) J Mol Evol , vol.24 , Issue.1-2 , pp. 12-27
    • Zuckerkandl, E.1
  • 27
    • 0023520847 scopus 로고
    • What introns have to tell us: Hierarchy in genome evolution
    • Doolittle WF (1987) What introns have to tell us: Hierarchy in genome evolution. Cold Spring Harb Symp Quant Biol 52:907-913.
    • (1987) Cold Spring Harb Symp Quant Biol , vol.52 , pp. 907-913
    • Doolittle, W.F.1
  • 28
    • 79957992453 scopus 로고    scopus 로고
    • Selected effects and causal role functions in the brain: The case for and etiological approach to neuroscience
    • Garson J (2011) Selected effects and causal role functions in the brain: The case for and etiological approach to neuroscience. Biol Philos 26:547-565.
    • (2011) Biol Philos , vol.26 , pp. 547-565
    • Garson, J.1
  • 29
    • 0000103250 scopus 로고
    • A modern history theory of functions
    • Godfrey-Smith P (1994) A modern history theory of functions. Nous 28:344-362.
    • (1994) Nous , vol.28 , pp. 344-362
    • Godfrey-Smith, P.1
  • 30
    • 23344443359 scopus 로고    scopus 로고
    • Proper function and recent selection
    • Schwartz PH (1999) Proper function and recent selection. Philos Sci 66:S210-S222.
    • (1999) Philos Sci , vol.66
    • Schwartz, P.H.1
  • 31
    • 85050417424 scopus 로고
    • Teleological explanations in evolutionary biology
    • Ayala FJ (1970) Teleological explanations in evolutionary biology. Philos Sci 37:1-15.
    • (1970) Philos Sci , vol.37 , pp. 1-15
    • Ayala, F.J.1
  • 32
    • 79959436430 scopus 로고    scopus 로고
    • Evo-devo, deep homology and FoxP2: Implications for the evolution of speech and language
    • Scharff C, Petri J (2011) Evo-devo, deep homology and FoxP2: Implications for the evolution of speech and language. Philos Trans R Soc Lond B Biol Sci 366(1574):2124-2140.
    • (2011) Philos Trans R Soc Lond B Biol Sci , vol.366 , Issue.1574 , pp. 2124-2140
    • Scharff, C.1    Petri, J.2
  • 33
    • 0020402387 scopus 로고
    • Exaptation-A missing term in the science of form
    • Gould SJ, Vrba E (1982) Exaptation-a missing term in the science of form. Paleobiology 8:4-15.
    • (1982) Paleobiology , vol.8 , pp. 4-15
    • Gould, S.J.1    Vrba, E.2
  • 34
    • 0018692402 scopus 로고
    • The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme
    • Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205(1161):581-598.
    • (1979) Proc R Soc Lond B Biol Sci , vol.205 , Issue.1161 , pp. 581-598
    • Gould, S.J.1    Lewontin, R.C.2
  • 35
    • 0019830772 scopus 로고
    • Secondary structure of 16S ribosomal RNA
    • Noller HF, Woese CR (1981) Secondary structure of 16S ribosomal RNA. Science 212(4493):403-411.
    • (1981) Science , vol.212 , Issue.4493 , pp. 403-411
    • Noller, H.F.1    Woese, C.R.2
  • 36
    • 84866775366 scopus 로고    scopus 로고
    • Evidence of abundant purifying selection in humans for recently acquired regulatory functions
    • Ward LD, Kellis M (2012) Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science 337(6102):1675-1678.
    • (2012) Science , vol.337 , Issue.6102 , pp. 1675-1678
    • Ward, L.D.1    Kellis, M.2
  • 37
    • 80555142991 scopus 로고    scopus 로고
    • What fraction of the human genome is functional?
    • Ponting CP, Hardison RC (2011) What fraction of the human genome is functional? Genome Res 21(11):1769-1776.
    • (2011) Genome Res , vol.21 , Issue.11 , pp. 1769-1776
    • Ponting, C.P.1    Hardison, R.C.2
  • 38
    • 77949775195 scopus 로고    scopus 로고
    • Repeat expansion disease: Progress and puzzles in disease pathogenesis
    • La Spada AR, Taylor JP (2010) Repeat expansion disease: Progress and puzzles in disease pathogenesis. Nat Rev Genet 11(4):247-258.
    • (2010) Nat Rev Genet , vol.11 , Issue.4 , pp. 247-258
    • La Spada, A.R.1    Taylor, J.P.2
  • 39
    • 34547396004 scopus 로고    scopus 로고
    • The frailty of adaptive hypotheses for the origins of organismal complexity
    • Lynch M (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104(Suppl 1): 8597-8604.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.SUPPL. 1 , pp. 8597-8604
    • Lynch, M.1
  • 40
    • 84862755029 scopus 로고    scopus 로고
    • Accessed December 11, 2012
    • An introduction to the gene ontology. Available at http://www. geneontology.org/GO.doc.shtml#molecular-function. Accessed December 11, 2012.
    • An Introduction to the Gene Ontology
  • 41
    • 84865859048 scopus 로고    scopus 로고
    • What does our genome encode?
    • Stamatoyannopoulos JA (2012) What does our genome encode? Genome Res 22(9):1602-1611.
    • (2012) Genome Res , vol.22 , Issue.9 , pp. 1602-1611
    • Stamatoyannopoulos, J.A.1
  • 42
    • 84859241661 scopus 로고    scopus 로고
    • Expressing genes do not forget their LINEs: Transposable elements and gene expression
    • Kines KJ, Belancio VP (2012) Expressing genes do not forget their LINEs: Transposable elements and gene expression. Front Biosci 17:1329-1344.
    • (2012) Front Biosci , vol.17 , pp. 1329-1344
    • Kines, K.J.1    Belancio, V.P.2
  • 43
    • 84887606485 scopus 로고    scopus 로고
    • Non-coding but functional
    • Barroso I (2012) Non-coding but functional. Nature 489:54.
    • (2012) Nature , vol.489 , pp. 54
    • Barroso, I.1
  • 44
    • 77951115595 scopus 로고    scopus 로고
    • RNA dust: Where are the genes?
    • Carninci P (2010) RNA dust: Where are the genes? DNA Res 17(2):51-59.
    • (2010) DNA Res , vol.17 , Issue.2 , pp. 51-59
    • Carninci, P.1
  • 45
    • 78049308870 scopus 로고    scopus 로고
    • Long non-coding RNAs: Guardians of development
    • van Leeuwen S, Mikkers H (2010) Long non-coding RNAs: Guardians of development. Differentiation 80(4-5):175-183.
    • (2010) Differentiation , vol.80 , Issue.4-5 , pp. 175-183
    • Van Leeuwen, S.1    Mikkers, H.2
  • 46
    • 84865463232 scopus 로고    scopus 로고
    • NcDNA and drift drive binding site accumulation
    • Ruths T, Nakhleh L (2012) ncDNA and drift drive binding site accumulation. BMC Evol Biol 12:159.
    • (2012) BMC Evol Biol , vol.12 , pp. 159
    • Ruths, T.1    Nakhleh, L.2
  • 47
    • 0037549394 scopus 로고    scopus 로고
    • Refuge of spandrels
    • Brenner S (1998) Refuge of spandrels. Curr Biol 8(19):R669.
    • (1998) Curr Biol , vol.8 , Issue.19
    • Brenner, S.1
  • 48
    • 37249030834 scopus 로고    scopus 로고
    • Is evolvability evolvable?
    • Pigliucci M (2008) Is evolvability evolvable? Nat Rev Genet 9(1): 75-82.
    • (2008) Nat Rev Genet , vol.9 , Issue.1 , pp. 75-82
    • Pigliucci, M.1
  • 50
    • 70349279977 scopus 로고    scopus 로고
    • Altruistic functions for selfish DNA
    • Faulkner GJ, Carninci P (2009) Altruistic functions for selfish DNA. Cell Cycle 8(18):2895-2900.
    • (2009) Cell Cycle , vol.8 , Issue.18 , pp. 2895-2900
    • Faulkner, G.J.1    Carninci, P.2
  • 51
    • 84868534630 scopus 로고    scopus 로고
    • Presidential address. Transposable elements, epigenetics, and genome evolution
    • Fedoroff NV (2012) Presidential address. Transposable elements, epigenetics, and genome evolution. Science 338(6108):758-767.
    • (2012) Science , vol.338 , Issue.6108 , pp. 758-767
    • Fedoroff, N.V.1
  • 54
    • 84867319960 scopus 로고    scopus 로고
    • Constructive neutral evolution: Exploring evolutionary theory's curious disconnect
    • Stoltzfus A (2012) Constructive neutral evolution: Exploring evolutionary theory's curious disconnect. Biol Direct 7:35.
    • (2012) Biol Direct , vol.7 , pp. 35
    • Stoltzfus, A.1
  • 55
    • 84856001089 scopus 로고    scopus 로고
    • Evolutionary biology: A ratchet for protein complexity
    • Doolittle WF (2012) Evolutionary biology: A ratchet for protein complexity. Nature 481(7381):270-271.
    • (2012) Nature , vol.481 , Issue.7381 , pp. 270-271
    • Doolittle, W.F.1
  • 56
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali S, et al. (2012) Landscape of transcription in human cells. Nature 489(7414):101-108.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 101-108
    • Djebali, S.1
  • 57
    • 84865844316 scopus 로고    scopus 로고
    • Decoding the human genome
    • Frazer KA (2012) Decoding the human genome. Genome Res 22(9):1599-1601.
    • (2012) Genome Res , vol.22 , Issue.9 , pp. 1599-1601
    • Frazer, K.A.1
  • 58
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: "function" in the human genome according to the evolutionfree gospel of ENCODE
    • 10.1093/gbe/evt028
    • Graur D, et al. (2013) On the immortality of television sets: "Function" in the human genome according to the evolutionfree gospel of ENCODE. Genome Biol Evol, 10.1093/gbe/evt028.
    • (2013) Genome Biol Evol
    • Graur, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.