Amaral PP, Dinger ME, Mercer TR, Mattick JS: The eukaryotic genome as an RNA machine. Science 2008, 319: 1787–1789. 10.1126/science.1155472
Article
CAS
PubMed
Google Scholar
Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Mattick JS: SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 2011, 17: 878–891. 10.1261/rna.2528811
Article
PubMed Central
CAS
PubMed
Google Scholar
Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Faulkner GJ: Somatic retrotransposition alters the genetic landscape of the human brain. Nature 2011, 479: 534–537. 10.1038/nature10531
Article
PubMed Central
CAS
PubMed
Google Scholar
Behe MJ: A functional pseudogene: an open letter to Nature. 2003.http://www.discovery.org/a/1448
Google Scholar
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, de Jong PJ: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447: 799–816. 10.1038/nature05874
Article
CAS
PubMed
Google Scholar
Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999, 238: 115–134. 10.1016/S0378-1119(99)00227-9
Article
CAS
PubMed
Google Scholar
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Hayashizaki Y: The transcriptional landscape of the mammalian genome. Science 2005, 309: 1559–1563.
Article
CAS
PubMed
Google Scholar
Carroll SB: Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 2008, 134: 25–36. 10.1016/j.cell.2008.06.030
Article
CAS
PubMed
Google Scholar
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Gingeras TR: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308: 1149–1154. 10.1126/science.1108625
Article
CAS
PubMed
Google Scholar
Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Mattick JS: The reality of pervasive transcription. PLoS Biol 2011, 9: e1000625. 10.1371/journal.pbio.1000625
Article
PubMed Central
CAS
PubMed
Google Scholar
Collins FS: The Language of God: a Scientist Presents Evidence for Belief. Free Press, New York; 2006.
Google Scholar
Dawkins R: The Blind Watchmaker: Why the evidence of Evolution Reveals a Universe without Design. W. W, Norton & Company, Inc, New York; 1986.
Google Scholar
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Mattick JS: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008, 18: 1433–1445. 10.1101/gr.078378.108
Article
PubMed Central
CAS
PubMed
Google Scholar
Dinger ME, Amaral PP, Mercer TR, Mattick JS: Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomics Proteomics 2009, 8: 407–423. 10.1093/bfgp/elp038
Article
CAS
Google Scholar
Doolittle WF: Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 2013, 110: 5294–5300. 10.1073/pnas.1221376110
Article
PubMed Central
CAS
PubMed
Google Scholar
Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Birney E: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489: 57–74. 10.1038/nature11247
Article
CAS
Google Scholar
Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Carninci P: The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 2009, 41: 563–571. 10.1038/ng.368
Article
CAS
PubMed
Google Scholar
Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS: Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 2006, 312: 276–279. 10.1126/science.1124070
Article
CAS
PubMed
Google Scholar
Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Sandelin A: Evolutionary turnover of mammalian transcription start sites. Genome Res 2006, 16: 713–722. 10.1101/gr.5031006
Article
PubMed Central
CAS
PubMed
Google Scholar
Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E: On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013, 5: 578–590. 10.1093/gbe/evt028
Article
PubMed Central
PubMed
Google Scholar
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Chang HY: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464: 1071–1076. 10.1038/nature08975
Article
PubMed Central
CAS
PubMed
Google Scholar
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Lander ES: lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011, 477: 295–300. 10.1038/nature10398
Article
PubMed Central
CAS
PubMed
Google Scholar
Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ: The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res 2011, 71: 3852–3862. 10.1158/0008-5472.CAN-10-4460
Article
CAS
PubMed
Google Scholar
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Rinn JL: Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009, 106: 11667–11672. 10.1073/pnas.0904715106
Article
PubMed Central
CAS
PubMed
Google Scholar
Koziol MJ, Rinn JL: RNA traffic control of chromatin complexes. Curr Opin Genet Dev 2010, 20: 142–148. 10.1016/j.gde.2010.03.003
Article
PubMed Central
CAS
PubMed
Google Scholar
Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P, Thanos S, Prior H: Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav Brain Res 2004, 154: 273–289. 10.1016/j.bbr.2004.02.015
Article
CAS
PubMed
Google Scholar
Liu G, Mattick JS, Taft RJ: A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle 2013, 12: 127–138.
CAS
Google Scholar
Lunter G, Ponting CP, Hein J: Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2006, 2: e5. 10.1371/journal.pcbi.0020005
Article
PubMed Central
PubMed
Google Scholar
Mattick JS: Introns: evolution and function. Curr Opin Genet Dev 1994, 4: 823–831. 10.1016/0959-437X(94)90066-3
Article
CAS
PubMed
Google Scholar
Mattick JS: RNA regulation: a new genetics? Nat Rev Genet 2004, 5: 316–323. 10.1038/nrg1321
Article
CAS
PubMed
Google Scholar
Mattick JS: A new paradigm for developmental biology. J Exp Biol 2007, 210: 1526–1547. 10.1242/jeb.005017
Article
PubMed
Google Scholar
Mattick JS: Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms. Ann N Y Acad Sci 2009, 1178: 29–46. 10.1111/j.1749-6632.2009.04991.x
Article
CAS
PubMed
Google Scholar
Mattick JS: The genetic signatures of noncoding RNAs. PLoS Genet 2009, 5: e1000459. 10.1371/journal.pgen.1000459
Article
PubMed Central
PubMed
Google Scholar
Mattick JS: Has evolution learnt how to learn? EMBO Rep 2009, 10: 665. 10.1038/embor.2009.135
Article
PubMed Central
CAS
PubMed
Google Scholar
Mattick JS: The central role of RNA in human development and cognition. FEBS Lett 2011, 585: 1600–1616. 10.1016/j.febslet.2011.05.001
Article
CAS
PubMed
Google Scholar
Mattick JS, Gagen MJ: The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 2001, 18: 1611–1630. 10.1093/oxfordjournals.molbev.a003951
Article
CAS
PubMed
Google Scholar
Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF: RNA regulation of epigenetic processes. Bioessays 2009, 31: 51–59. 10.1002/bies.080099
Article
CAS
PubMed
Google Scholar
Mattick JS, Taft RJ, Faulkner GJ: A global view of genomic information–moving beyond the gene and the master regulator. Trends Genet 2010, 26: 21–28. 10.1016/j.tig.2009.11.002
Article
CAS
PubMed
Google Scholar
Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS: Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 2008, 105: 716–721. 10.1073/pnas.0706729105
Article
PubMed Central
CAS
PubMed
Google Scholar
Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF: Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 2010, 11: 14. 10.1186/1471-2202-11-14
Article
PubMed Central
PubMed
Google Scholar
Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Rinn JL: Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotech 2012, 30: 99–104.
Article
CAS
Google Scholar
Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P: The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008, 322: 1717–1720. 10.1126/science.1163802
Article
CAS
PubMed
Google Scholar
Ng SY, Johnson R, Stanton LW: Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. Embo J 2012, 31: 522–533.
Article
PubMed Central
CAS
PubMed
Google Scholar
Niu DK, Jiang L: Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun 2013, 430: 1340–1343. 10.1016/j.bbrc.2012.12.074
Article
CAS
PubMed
Google Scholar
Oldmeadow C, Mengersen K, Mattick JS, Keith JM: Multiple evolutionary rate classes in animal genome evolution. Mol Biol Evol 2010, 27: 942–953. 10.1093/molbev/msp299
Article
CAS
PubMed
Google Scholar
Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Kanduri C: Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 2008, 32: 232–246. 10.1016/j.molcel.2008.08.022
Article
CAS
PubMed
Google Scholar
Pang KC, Frith MC, Mattick JS: Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 2006, 22: 1–5. 10.1016/j.tig.2005.10.003
Article
CAS
PubMed
Google Scholar
Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS: Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol 2009, 182: 7738–7748. 10.4049/jimmunol.0900603
Article
CAS
PubMed
Google Scholar
Pheasant M, Mattick JS: Raising the estimate of functional human sequences. Genome Res 2007, 17: 1245–1253. 10.1101/gr.6406307
Article
CAS
PubMed
Google Scholar
Roberts A, Pachter L: RNA-Seq and find: entering the RNA deep field. Genome Med 2011, 3: 74. 10.1186/gm290
Article
PubMed Central
CAS
PubMed
Google Scholar
Scanlan J: The Designer’s Detritus: ENCODE, Junk DNA, and Intelligent Design Creationists. Scitable (Nature Education) 2012. http://www.nature.com/scitable/blog/student-voices/the_designers_detritus_encode_junk
Google Scholar
Smith NG, Brandstrom M, Ellegren H: Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics 2004, 84: 806–813. 10.1016/j.ygeno.2004.07.012
Article
CAS
PubMed
Google Scholar
Spitale RC, Tsai MC, Chang HY: RNA templating the epigenome: Long noncoding RNAs as molecular scaffolds. Epigenetics 2011, 6: 539–43. 10.4161/epi.6.5.15221
Article
PubMed Central
CAS
PubMed
Google Scholar
Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL: MEN ϵ/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 2009, 19: 347–359.
Article
PubMed Central
CAS
PubMed
Google Scholar
Taft RJ, Pheasant M, Mattick JS: The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29: 288–299. 10.1002/bies.20544
Article
CAS
PubMed
Google Scholar
Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA: Heterotachy in mammalian promoter evolution. PLoS Genet 2006, 2: e30. 10.1371/journal.pgen.0020030
Article
PubMed Central
PubMed
Google Scholar
van Bakel H, Nislow C, Blencowe BJ, Hughes TR: Most “dark matter” transcripts are associated with known genes. PLoS Biol 2010, 8: e1000371. 10.1371/journal.pbio.1000371
Article
PubMed Central
PubMed
Google Scholar
Wells J: The Myth of Junk DNA. Discovery Institute Press, Seattle; 2011.
Google Scholar
Comments
View archived comments (1)