Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes

Journal of Molecular Evolution

Volumn 81, Issue 1-2, 2015, Pages 34-53

  Bains, William ^a   Schulze Makuch, Dirk ^b,c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Cell function; Cellular evolution; Complexity; Gene control; Innovation; Transition

Indexed keywords

ANIMALIA; EUKARYOTA; PROKARYOTA;

BIOLOGICAL MODEL; EUKARYOTE; EUKARYOTIC CELL; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; PHYSIOLOGY; PROKARYOTIC CELL; STRUCTURE ACTIVITY RELATION;

BIOLOGICAL EVOLUTION; EUKARYOTA; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; MODELS, GENETIC; PROKARYOTIC CELLS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84939565893     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-015-9688-6     Document Type: Article

References (271)

1. Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H (2003) Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol 10:256–263
2. Albers S-V et al (2006) Production of recombinant and tagged proteins in the hyperthermophilic archaeon sulfolobus solfataricus. Appl Environ Microbiol 72:102–111. doi:10.1128/aem.72.1.102-111.2006
3. Allers T (2010) Overexpression and purification of halophilic proteins in Haloferax volcanii. Bioeng Bugs 1:288–290
4. Allers T, Barak S, Liddlell S, Wardell K, Mevarech M (2010) Improved strains and plasmid vectors for conditional overexpression of his-tagged proteins in Haloferax volcanii. Appl Environ Microbiol 76:1759–1769
5. Aravalli RN, Garrett RA (1997) Development of a simvastatin selection marker for a hyperthermophilic acidophile, sulfolobus islandicus. Extremophiles 1:183–191
6. Archibald JD (2011) Extinction and radiation: how the fall of the dinosaurs led to the rise of the mammals. The Johns Hopkins University Press, Baltimore
7. Argos P et al (1986) The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J 5:433–440
8. Bachellerie J-P, Cavaillé J, Hüttenhofer A (2002) The expanding snoRNA world. Biochimie 84:775–790. doi:10.1016/S0300-9084(02)01402-5
9. Bains W (1982) The structure of cloned histone genes from Xenopus borealis. University of Warwick, pp 223–238. http://wrap.warwick.ac.uk/67748
10. Bains W (2000) Statistical mechanic prediction of non-Gompertzian ageing in extremely aged populations. Mech Aging Dev 112:89–97
11. Bains W (2004) Paradoxes of non-trivial gene networks: how cancer-causing mutations can appear to be cancer-protective. Rejuvenation Res 7:199–210
12. Baliga NS, Goo YA, Ng WV, Hood L, Daniels CJ, DasSarma S (2000) Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol 36:1184–1185. doi:10.1046/j.1365-2958.2000.01916.x
13. Bartlett MS, Thomm M, Geiduschek EP (2000) The orientation of DNA in an archaeal transcription initiation complex. Nat Struct Mol Biol 7:782–785
14. Battesti A, Gottesman S (2013) Roles of adaptor proteins in regulation of bacterial proteolysis. Curr Opin Microbiol 16:140–147. doi:10.1016/j.mib.2013.01.002
15. Baumann H, Knapp S, Lundback T, Landstein R, Hard T (1994) Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus. Nat Struct Biol 1:808–819
16. Belew AT et al (2014) Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway. Nature 512:265–269. doi:10.1038/nature13429
17. Bell SD, Jackson SP (2001) Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4:208–213. doi:10.1016/S1369-5274(00)00190-9
18. Bentley SD, Parkhill J (2004) Comparative genomic structure of prokaryotes. Annu Rev Genet 38:771–791. doi:10.1146/annurev.genet.38.072902.094318
19. Bi S, Wang Y, Guan J, Sheng X, Meng J (2014) Three new Jurassic euharamiyidan species reinforce early divergence of mammals. Nature. doi:10.1038/nature13718
20. Bini E, Blum P (2001) Archaeal catabolite repression: a gene regulatory paradigm. In: Laskin AI, Bennett JW, Gadd GM (eds) Advances in applied microbiology, vol 50. Academic Press, San Diego, pp 339–362
21. Blackburn DG, Flemming AF (2012) Invasive implantation and intimate placental associations in a placentotrophic african lizard, Trachylepis ivensi (scincidae). J Morphol 273:137–159. doi:10.1002/jmor.11011
22. Blackstone NW (2013) Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation. Philos Trans R Soc B. doi:10.1098/rstb.2012.0266
23. Blankenship RE, Hartman H (1998) The origin and evolution of oxygenic photosynthesis. Trends Biochem Sci 23:94–97
24. Bouligand Y, Norris V (2001) Chromosome separation and segregation in dinoflagellates and bacteria may depend on liquid crystalline states. Biochimie 83:187–192. doi:10.1016/S0300-9084(00)01211-6
25. Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K (2006) Genome-wide mapping of polycomb target genes unravels their roles in cell fate transitions. Genes Dev 20:1123–1136. doi:10.1101/gad.381706
26. Braglia P, Percudani R, Dieci G (2005) Sequence context effects on oligo (dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 280:19551–19562. doi:10.1074/jbc.M412238200
27. Braun RE (2001) Packaging paternal chromosomes with protamine. Nat Genet 28:10–12
28. Breaker RR (2012) Riboswitches and the RNA world. Cold Spring Harb Perspect Biol 4:a003566
29. Brierley I, Digard P, Inglis SC (1989) Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot. Cell 57:537–547. doi:10.1016/0092-8674(89)90124-4
30. Brown JR, Doolittle WF (1997) Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev 61:456–502
31. Buhler M, Moazed D (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14:1041–1048
32. Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, Stutz F (2009) Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23:1534–1545. doi:10.1101/gad.522509
33. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131:706–717. doi:10.1016/j.cell.2007.09.014
34. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13:2212–2217. doi:10.1016/j.cub.2003.11.052
35. Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature. doi:10.1038/nature13802
36. 2 is required by complex life on habitable planets and the concept of planetary “Oxygenation Time”. Astrobiology 5:415–438
37. Cavalier-Smith T (2010) Deep phylogeny, ancestral groups and the four ages of life. Philos Trans R Soc B 365:111–132. doi:10.1098/rstb.2009.0161
38. Cech Thomas R, Steitz Joan A (2014) The noncoding RNA revolution: trashing old rules to forge new ones. Cell 157:77–94. doi:10.1016/j.cell.2014.03.008
39. Chalker DL, Yao M-C (2011) DNA elimination in ciliates: transposon domestication and genome surveillance. Annu Rev Genet 45:227–246. doi:10.1146/annurev-genet-110410-132432
40. Champoux JJ (2001) DNA topoisomerases: structure function, and mechanism. Annu Rev Biochem 70:369–413. doi:10.1146/annurev.biochem.70.1.369
41. Chan SW-L, Ziberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA silencing genes control de novo DNA methylation. Science 303:1336
42. Chandler M, Fayet O (1993) Translational frameshifting in the control of transposition in bacteria. Mol Microbiol 7:497–503. doi:10.1111/j.1365-2958.1993.tb01140.x
43. Chang C-H, Luse DS (1997) The H3/H4 tetramer blocks transcript elongation by RNA polymerase II in vitro. J Biol Chem 272:23427–23434. doi:10.1074/jbc.272.37.23427
44. Chang Y-j et al (2011) Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21(T)). Stand Genomic Sci 5:97–111. doi:10.4056/sigs.2114901
45. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I (1998) The transcriptional program of sporulation in budding yeast. Science 282:699–705. doi:10.1126/science.282.5389.699
46. Cliffe LJ, Kieft R, Southern T, Birkeland SR, Marshall M, Sweeney K, Sabatini R (2009) JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res 37:1452–1462. doi:10.1093/nar/gkn1067
47. Cobucci-Ponzano B, Rossi M, Moracci M (2005) Recoding in archaea. Mol Microbiol 55:339–348. doi:10.1111/j.1365-2958.2004.04400.x
48. Collin SP, Knight MA, Davies WL, Potter IC, Hunt DM, Trezise AEO (2003) Ancient colour vision: multiple opsin genes in the ancestral vertebrates. Curr Biol 13:R864–R865. doi:10.1016/j.cub.2003.10.044
49. Contursi P, Cannio R, Prato S, Fiorentino G, Rossi M, Bartolucci S (2003) Development of a genetic system for hyperthermophilic Archaea: expression of a moderate thermophilic bacterial alcohol dehydrogenase gene in Sulfolobus solfataricus. FEMS Microbiol Lett 218:115–120
50. Coppins RL, Hall KB, Groisman EA (2007) The intricate world of riboswitches. Curr Opin Microbiol 10:176–181. doi:10.1016/j.mib.2007.03.006
51. Corbett KD, Berger JM (2004) Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu Rev Biophys Biomol Struct 33:95–118. doi:10.1146/annurev.biophys.33.110502.140357
52. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845–1848. doi:10.1126/science.1162228
53. Dalle-Donne I, Rossi R, Colombo G, Giustarini D, Milzani A (2008) Protein S-glutathionylation: a regulatory device from bacteria to humans. Trends Biochem Sci 34:85–96
54. de Duve C (2005) Singularities. Landmarks on the pathways of life. Cambridge University Press, Cambridge
55. de Duve C (2007) The origin of eukaryotes: a reappraisal. Nat Rev Genet 8:395–403
56. de la Espina SMD, Alverca E, Cuadrado A, Franca S (2005) Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: the amazing dinoflagellates. Eur J Cell Biol 84:137–149. doi:10.1016/j.ejcb.2005.01.002
57. de Santa F et al (2009) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8:e1000384. doi:10.1371/journal.pbio.1000384
58. de Vries R (2010) DNA condensation in bacteria: interplay between macromolecular crowding and nucleoid proteins. Biochimie 92:1715–1721. doi:10.1016/j.biochi.2010.06.024
59. Dinman JD (2012) Mechanisms and implications of programmed translational frameshifting. Wiley Interdiscip Rev 3:661–673. doi:10.1002/wrna.1126
60. Domené S, Bumaschny VF, de Souza FSJ, Franchini LF, Nasif S, Low MJ, Rubinstein M (2013) Enhancer turnover and conserved regulatory function in vertebrate evolution. Philos Trans R Soc B. doi:10.1098/rstb.2013.0027
61. Doolittle WF, Feng D-F, Tsang S, Cho G, Little E (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470–477
62. Drlica K, Rouviere-Yaniv J (1987) Histonelike proteins of bacteria. Microbiol Rev 51:301–319
63. Dumesic Phillip A et al (2013) Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 152:957–968. doi:10.1016/j.cell.2013.01.046
64. Edgell D, Chalamcharla V, Belfort M (2011) Learning to live together: mutualism between self-splicing introns and their hosts. BMC Biol 9:22
65. Eichler J, Adams MWW (2005) Posttranslational protein modification in archaea. Microbiol Mol Biol Rev 69:393–425. doi:10.1128/mmbr.69.3.393-425.2005
66. EMBL (2015a) Bacterial expression vectors. http://www.embl.de/pepcore/pepcore_services/strains_vectors/vectors/bacterial_expression_vectors/
67. EMBL (2015b) Insect cell expression vectors. http://www.embl.de/pepcore/pepcore_services/strains_vectors/vectors/insectcell_expression_vectors/index.html
68. Fang FC, Rimsky S (2008) New insights into transcriptional regulation by H-NS. Curr Opin Microbiol 11:113–120. doi:10.1016/j.mib.2008.02.011
69. Fernando Bazan J, Koch-Nolte F (1997) Sequence and structural links between distant adp-ribosyltransferase sfamilies. In: Haag F, Koch-Nolte F (eds) ADP-ribosylation in animal tissues, vol 419., Advances in experimental medicine and biologySpringer, NewYork, pp 99–107. doi:10.1007/978-1-4419-8632-0_12
70. FitzGerald PC, Sturgill D, Shyakhtenko A, Oliver B, Vinson C (2006) Comparative genomics of Drosophila and human core promoters. Genome Biol 7:R53
71. Frost B, Hemberg M, Lewis J, Feany MB (2014) Tau promotes neurodegeneration through global chromatin relaxation. Nat Neurosci 17:357–366. doi:10.1038/nn.3639
72. Fuerst JA (2005) Intracellular compartmentalization in Planctomycetes. Annu Rev Microbiol 59:299–328
73. Fuerst JA, Webb RI, Garson MJ, Hardy L, Reiswig HM (1998) Membrane-bounded nucleoids in microbial symbionts of marine sponges. FEMS Microbiol Lett 166:29–34. doi:10.1111/j.1574-6968.1998.tb13179.x
74. Gao Z, Lee P, Stafford JM, von Schimmelmann M, Schaefer A, Reinberg D (2014) An AUTS2-polycomb complex activates gene expression in the CNS. Nature 516:349–354. doi:10.1038/nature13921
75. Gaspin C, Cavaillé J, Erauso G, Bachellerie J-P (2000) Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol 297:895–906. doi:10.1006/jmbi.2000.3593
76. Geiduschek EP, Ouhammouch M (2005) Archaeal transcription and its regulators. Mol Microbiol 56:1397–1407. doi:10.1111/j.1365-2958.2005.04627.x
77. Geisler S, Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 14:699–712. doi:10.1038/nrm3679
78. Geiss-Friedlander R, Melchior F (2007) Concepts in sumoylation: a decade on. Nat Rev Mol Cell Biol 8:947–956
79. Geng F, Wenzel S, Tansey WP, Tansey WP (2012) Ubiquitin and proteasomes in transcription. Ann Rev Biochem 81:177–201
80. Ghaemmaghami S et al (2003) Global analysis of protein expression in yeast. Nature 425:737–741
81. Gilbert W (1986) The RNA world. Nature 319:618
82. Glansdorff N (2002) About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Mol Microbiol 38:177–185
83. Görke B, Vogel J (2008) Noncoding RNA control of the making and breaking of sugars. Genes Dev 22:2914–2925. doi:10.1101/gad.1717808
84. Gould SJ (1989) Wonderful life. The burgess shales and the nature of history. W. W. Norton and Co, New York
85. Gourdeau H, Fournier REK (1990) Genetic analysis of mammalian cell differentiation. Annu Rev Cell Biol 6:69–94. doi:10.1146/annurev.cb.06.110190.000441
86. Grewal SIS, Rice JC (2004) Regulation of heterochromatin by histone methylation and small RNAs. Curr Opin Cell Biol 16:230–238. doi:10.1016/j.ceb.2004.04.002
87. Griese M, Lange C, Soppa J (2011) Ploidy in cyanobacteria. FEMS Microbiol Lett 323:124–131
88. Grigg JC, Ke A (2013) Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 21:2025–2032
89. Guttman M et al (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28:503–510
90. Haasa PO, Hottinger MO (2008) The diverse biological roles of mammalian PARPs, a small but powerful family of poly-ADP-ribose polymerases. Front Biosci 13:3036–3082
91. Hale CR et al (2009) RNA-guided RNA cleavage by a CRISPR RNA-cas protein complex. Cell 139:945–956. doi:10.1016/j.cell.2009.07.040
92. Hallet B, Sherratt DJ (1997) Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol Rev 21:157–178. doi:10.1111/j.1574-6976.1997.tb00349.x
93. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144:646–674. doi:10.1016/j.cell.2011.02.013
94. Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M (2002) A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol 316:409–419. doi:10.1006/jmbi.2001.5343
95. Helmann JD, Chamberlin MJ (1988) Structure and function of bacterial sigma factors. Annu Rev Biochem 57:839–872. doi:10.1146/annurev.bi.57.070188.004203
96. Hendrix DA, Hong J-W, Zeitlinger J, Rokhsar DS, Levine MS (2008) Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci USA 105:7762–7767. doi:10.1073/pnas.0802406105
97. Holland HD (2006) The oxygenation of the atmosphere and oceans. Philos Trans R Soc B 361:903–915. doi:10.1098/rstb.2006.1838
98. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170. doi:10.1126/science.1179555
99. Houseley J (2012) Form and function of eukaryotic unstable non-coding RNAs. Biochem Soc Trans 40:836–840
100. Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M (2008) A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol Cell 32:685–695. doi:10.1016/j.molcel.2008.09.027
101. Houseley J, Tollervey D (2008) The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast? Biochim Biophys Acta 1779:239–246. doi:10.1016/j.bbagrm.2007.12.008
102. Huarte M et al (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142:409–419. doi:10.1016/j.cell.2010.06.040
103. Jacob F, Monod J (1961) On the regulation of gene activity. Cold Spring Harb Symp Quant Biol 26:193–211. doi:10.1101/sqb.1961.026.01.024
104. Jeong SW, Lang WH, Reeder RH (1995) The release element of the yeast polymerase I transcription terminator can function independently of Reb1p. Mol Cell Biol 15:5929–5936
105. Jin F et al (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503:290–294. doi:10.1038/nature12644
106. Jobe EM, McQuate AL, Zhao X (2012) Crosstalk among epigenetic pathways regulates neurogenesis. Front Neurosci. doi:10.3389/fnins.2012.00059
107. Jore MM, Brouns SJJ, van der Oost J (2012) RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb Perspect Biol 4:a003657
108. Joshua-Tor L, Hannon GJ (2010) Ancestral roles of small RNAs: an ago-centric perspective. Cold Spring Harb Perspect Biol. doi:10.1101/cshperspect.a003772
109. Khalil AM et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106:11667–11672. doi:10.1073/pnas.0904715106
110. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Noncoding RNA Gas5 Is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3:8. doi:10.1126/scisignal.2000568
111. Kireeva ML, Hancock B, Cremona GH, Walter W, Studitsky VM, Kashlev M (2005) Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell 18:97–108. doi:10.1016/j.molcel.2005.02.027
112. Kireeva ML, Walter W, Tchernajenko V, Bondarenko V, Kashlev M, Studitsky VM (2002) Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol Cell 9:541–552. doi:10.1016/S1097-2765(02)00472-0
113. Kiucho T et al (2014) A single female-specific piRNa is the primary determiner of sex in the silkworm. Nature 509:633–636
114. Komaki K, Ishikawa H (2000) Genomic copy number of intracellular bacterial symbionts of aphids varies in response to developmental stage and morph of their host. Insect Biochem Mol Biol 30:253–258. doi:10.1016/S0965-1748(99)00125-3
115. Komik Z (2005) Pax genes in eye development and evolution. Curr Opin Genet Dev 15:430–438
116. Kumar S, Cheng X, Klimasauskas S, Mi S, Posfai J, Roberts RJ, Wilson GG (1994) The DNA (cytosine-5) methyltransferases. Nucleic Acids Res 22:1–10
117. Kuo C-H, Ochman H (2010) The extinction dynamics of bacterial pseudogenes. PLoS Genet 6:e1001050
118. Lafontaine DLJ, Tollervey D (1998) Birth of the snoRNPs: the evolution of the modification-guide snoRNAs. Trends Biochem Sci 23:383–388. doi:10.1016/S0968-0004(98)01260-2
119. Lambowitz AM, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35
120. Land MF, Nilsson D-E (2012) Animal eyes, 2nd edn. Oxford University Press, Oxford
121. Landschulz W, Johnson P, McKnight S (1988) The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240:1759–1764. doi:10.1126/science.3289117
122. Lang BF et al (2014) Massive programmed translational jumping in mitochondria. Proc Natl Acad Sci 111:5926–5931. doi:10.1073/pnas.1322190111
123. Leblond CS et al (2012) Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders. PLoS Genet 8:e1002521
124. Lee TI et al (2006) Control of developmental regulators by polycomb in human embryonic stem cells. Cell 125:301–313. doi:10.1016/j.cell.2006.02.043
125. Lettice LA et al (2003) A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 12:1725–1735. doi:10.1093/hmg/ddg180
126. Levis RW, Ganesan R, Houtchens K, Tolar LA, Sheen F-M (1993) Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75:1083–1093. doi:10.1016/0092-8674(93)90318-K
127. Lewis S, Gellert M (1989) The mechanism of antigen receptor gene assembly. Cell 59:585–588. doi:10.1016/0092-8674(89)90002-0
128. Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128:707–719. doi:10.1016/j.cell.2007.01.015
129. Li J, Gilmour DS (2013) Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J 32:1829–1841
130. Li Y, Tergaonkar V (2014) Noncanonical functions of telomerase: implications in telomerase-targeted cancer therapies. Cancer Res 74:1639–1644. doi:10.1158/0008-5472.can-13-3568
131. Liu X, Bushnell DA, Kornberg RD (2013) RNA polymerase II transcription: structure and mechanism. Biochim Biophys Acta 1829:2–8. doi:10.1016/j.bbagrm.2012.09.003
132. Liu Y, Harrison PM, Kunin V, Gerstein M (2004) Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol 5:R64. doi:10.1186/gb-2004-1185-1189-r1164
133. Livny J, Brencic A, Lory S, Waldor MK (2006) Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 34:3484–3493. doi:10.1093/nar/gkl453
134. Loeb LA, Loeb KR, Anderson JP (2003) Multiple mutations and cancer. Proc Natl Acad Sci USA 100:776–781. doi:10.1073/pnas.0334858100
135. Lucas S et al (2002) Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol 68:5528–5535
136. Luijsterburg MS, White MF, Van Driel R, Dame RT (2008) The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43:1–26
137. Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV (2005) Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res 33:4626–4638. doi:10.1093/nar/gki775
138. Makarova KS, Wolf YI, van der Oost J, Koonin EV (2009) Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct 4:29. doi:10.1186/1745-6150-1184-1129
139. Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656–668
140. Mantovani R (1999) The molecular biology of the CCAAT-binding factor NF-Y. Gene 239:15–27. doi:10.1016/S0378-1119(99)00368-6
141. Marsh VL, Peak-Chew SY, Bell SD (2005) Sir2 and the acetyltransferase, pat, regulate the archaeal chromatin protein, alba. J Biol Chem 280:21122–21128
142. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445:666–670
143. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6:838–849
144. Martin W, Koonin EV (2006) Introns and the origin of nucleus–cytosol compartmentalization. Nature 440:41–45
145. Mattick JS, Gagen MJ (2001) The evolution of controlled multitasked gene networks: the role of introns and other noncoding rnas in the development of complex organisms. Mol Biol Evol 18:1611–1630
146. McCarty DM, Young SM, Samulski RJ (2004) Integration of adeno-associated virus (AAV) and recombinant AAV vectors. Annu Rev Genet 38:819–845. doi:10.1146/annurev.genet.37.110801.143717
147. Meister G, Tuschi T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343–349
148. Mello CC, Conte DJ (2004) Revealing the world of RNA interference. Nature 431:338–341
149. Mendell JE, Clements KD, Choat JH, Angert ER (2008) Extreme polyploidy in a large bacterium. Proc Natl Acad Sci USA 105:6730–6734. doi:10.1073/pnas.0707522105
150. Meng Q, Wang Y, Liu X-Q (2005) An intron-encoded protein assists RNA splicing of multiple similar introns of different bacterial genes. J Biol Chem 280:35085–35088. doi:10.1074/jbc.C500328200
151. Menssen A, Haupl T, Sittinger M, Delorme B, Charbord P, Ringe J (2011) Differential gene expression profiling of human bone marrow-derived mesenchymal stem cells during adipogenic development. BMC Genomics 12:461
152. Mercer TR, Mattick JS (2013) Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20:300–307
153. Merck Millipore Inc. (2015) Expression vectors. http://www.emdmillipore.com/
154. Messer W (2002) The bacterial replication initiator DnaA, DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 26:355–374. doi:10.1111/j.1574-6976.2002.tb00620.x
155. Mighell AJ, Smith NR, Robinson PA, Markham AF (2000) Vertebrate pseudogenes. FEBS Lett 468:109–114. doi:10.1016/S0014-5793(00)01199-6
156. Mikkelsen TS et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560
157. Miller AD (1992) Retroviral vectors. In: Muzyczka N (ed) Viral expression vectors, vol 158., Current topics in microbiology and immunologySpringer, Berlin, pp 1–24. doi:10.1007/978-3-642-75608-5_1
158. Miller G, Hahn S (2006) A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex. Nat Struct Mol Biol 13:603–610
159. Mischo HE, Proudfoot NJ (2013) Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. Biochim Biophys Acta 1829:174–185
160. Mizuguchi G, Shen X, Landry J, Wu W-H, Sen S, Wu C (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303:343–348. doi:10.1126/science.1090701
161. Moroz LL et al (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature. doi:10.1038/nature13400
162. Mossman HW (1937) Comparative morphogenesis of the fetal membranes and accessory uterine structures. Carnegie Inst Contr Embryol 26:129–246
163. Müller J, Kassis JA (2006) Polycomb response elements and targeting of polycomb group proteins in Drosophila. Curr Opin Genet Dev 16:476–484. doi:10.1016/j.gde.2006.08.005
164. Mumberg D, Müller R, Funk M (1995) Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156:119–122. doi:10.1016/0378-1119(95)00037-7
165. Muse GW et al (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39:1507–1511
166. Nagano T, Fraser P (2011) No-nonsense functions for long noncoding RNAs. Cell 145:178–181
167. Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I (2010) Genome-wide discovery of human heart enhancers. Genome Res 20:381–392
168. Navarre WW, McClelland M, Libby SJ, Fang FC (2007) Silencing of xenogeneic DNA by H-NS—facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev 21:1456–1471. doi:10.1101/gad.1543107
169. Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, Libby SJ, Fang FC (2006) Selective silencing of foreign DNA with low GC content by the H-NS protein in salmonella. Science 313:236–238. doi:10.1126/science.1128794
170. Nechaev S, Adelman K (2011) Pol II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta 1809:34–45
171. Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K (2010) Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of pol II in Drosophila. Science 327:335–338. doi:10.1126/science.1181421
172. Nykänen A, Haley B, Zamore PD (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway cell 107:309–321. doi:10.1016/S0092-8674(01)00547-5
173. Olave IA, Peck-Peterson SI, Crabtree GR (2002) Nuclear actin and actin-related proteins in chromatin remodelling. Annu Rev Biochem 71:755–781
174. Ørom UA et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:46–58. doi:10.1016/j.cell.2010.09.001
175. Pagel M, Johnstone RA (1992) Variation across Species in the size of the nuclear genome supports the junk-DNA explanation for the C-value paradox. Proc R Soc Lond Ser B 249:119–124. doi:10.1098/rspb.1992.0093
176. Pallen MJ, Lam AC, Loman NJ, McBride A (2001) An abundance of bacterial ADP-ribosyltransferases: implications for the origin of exotoxins and their human homologues. Trends Microbiol 9:302–307. doi:10.1016/S0966-842X(01)02074-1
177. Papenfort K, Vogel J (2010) Regulatory RNA in bacterial pathogens. Cell Host Microbe 8:116–127
178. Peirce V, Carobbio S, Vidal-Puig A (2014) The different shades of fat. Nature 510:76–83
179. Peng N et al (2012) A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon sulfolobus islandicus. Appl Environ Microbiol 79:5630–5637
180. Pickart CM (2001) Mechanisms underlying ubiquitination. Annu Rev Biochem 70:503–533
181. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033–1038
182. Pollux BJA, Pires MN, Banet AI, Reznick DN (2009) Evolution of placentas in the fish family poeciliidae: an empirical study of macroevolution. Annu Rev Ecol Evol Syst 40:271–289. doi:10.1146/annurev.ecolsys.110308.120209
183. Polyzos SA, Kountouras J, Zavos C, Deretzi G (2012) Nonalcoholic fatty liver disease: multimodal treatment options for a pathogenetically multiple-hit disease. J Clin Gastroenterol 46(272–284):2. doi:10.1097/MCG.1090b1013e31824587e31824580
184. Ponting CP, Hardison RC (2011) What fraction of the human genome is functional? Genome Res 21:1769–1776
185. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629–641. doi:10.1016/j.cell.2009.02.006
186. Promega Corp. (2015) Vectors. http://www.promega.co.uk/products/vectors/
187. Pyle AM (2012) Group II intron architecture and its implications for the development of eukaryotic splicing systems. FASEB J 26(217):213
188. Rabbani MA et al (2003) Monitoring expression profiles of rice genes under cold drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755–1767. doi:10.1104/pp.103.025742
189. Rebollo R, Romanish MT, Mager DL (2012) Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 46:21–42. doi:10.1146/annurev-genet-110711-155621
190. Reeve JN (2003) Archaeal chromatin and transcription. Mol Microbiol 48:587–598. doi:10.1046/j.1365-2958.2003.03439.x
191. Reisenauer A, Kahng LS, McCollum S, Shapiro L (1999) Bacterial DNA methylation: a cell cycle regulator? J Bacteriol 181:5135–5139
192. Rhee HS, Pugh F (2012) Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483:295–301
193. Rinn JLC, Chang HY (2012) Genome regulation by long noncoding RNAs. AnnU Rev Biochem 81:145–166
194. Rivas E, Klein RJ, Jones TA, Eddy SR (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:1369–1373. doi:10.1016/S0960-9822(01)00401-8
195. Rivier C, Goldschmidt-Clermont M, Rochaix J-D (2001) Identification of an RNA–protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J 20:1765–1773. doi:10.1093/emboj/20.7.1765
196. Roeben A, Kofler C, Nagy I, Nickell S, Ulrich Hartl F, Bracher A (2006) Crystal structure of an archaeal actin homolog. J Mol Biol 358:145–156. doi:10.1016/j.jmb.2006.01.096
197. Ross RJ, Weiner MM, Lin H (2014) PIWI proteins and PIWI-interacting RNAs in the soma. Nature 505:353–359. doi:10.1038/nature12987
198. Roy SW, Gilbert W (2006) The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet 7:211–221
199. Ruthenburg A, Kli H, Patel DJ, Allis CD (2007) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev 8:983–994
200. Salas M (1991) Protein-priming of DNA replication. Annu Rev Biochem 60:39–71
201. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi Pier P (2011) A ceRNA hypothesis: the rosetta stone of a hidden RNA language? Cell 146:353–358. doi:10.1016/j.cell.2011.07.014
202. Sandman K, Reeve JN (2005) Archaeal chromatin proteins: different structures but common function? Curr Opin Microbiol 8:656–661. doi:10.1016/j.mib.2005.10.007
203. Sandman K, Reevem JH (2001) Chromosome packaging by archael histones. In: Laskin AI, Bennett JW, Gadd GM (eds) Advances in applied microbiology, vol 50. Academic Press, San Diego, pp 73–100
204. Santangelo TJ, Čuboňová L, Reeve JN (2008) Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl Environ Microbiol 74:3099–3104. doi:10.1128/aem.00305-08
205. Sanyal A, Lajoie BR, Jain G, Dekker J (2012) The long-range interaction landscape of gene promoters. Nature 489:109–113
206. Sauer B (1994) Site-specific recombination: developments and applications. Curr Opin Biotechnol 5:521–527. doi:10.1016/0958-1669(94)90068-X
207. Schouten M, Buijink MR, Lucassen PJ, Fitzsimons CP (2012) New neurons in aging brains: molecular control by small non-coding RNAs. Front Neurosci. doi:10.3389/fnins.2012.00025
208. Schreier H, Robinson-Bidle KA, Romashko AM, Patel G (1999) Heterologous expression in the Archaea: transcription from Pyrococcus furiousus gdh and mlrA promoters in Haloferax volcanii. Extremophiles 3:11–19
209. Schulze-Makuch D, Irwin LN (2008) Life in the universe: expectations and constraints, 2nd edn. Springer, Berlin
210. Schwabe JWR, Chapman L, Finch JT, Rhodes D (1993) The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell 75:567–578. doi:10.1016/0092-8674(93)90390-C
211. Schwanhausser B et al (2011) Global quantification of mammalian gene expression control. Nature 473:337–342
212. Schwartz DC, Hochstrasser M (2003) A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends Biochem Sci 28:321–328. doi:10.1016/S0968-0004(03)00113-0
213. Schwartz YB, Kahn TG, Nix DA, Li X-Y, Bourgon R, Biggin M, Pirrotta V (2006) Genome-wide analysis of polycomb targets in Drosophila melanogaster. Nat Genet 38:700–705
214. Sesto N, Wurtzel O, Archambaud C, Sorek R, Cossart P (2013) The excludon: a new concept in bacterial antisense RNA-mediated gene regulation. Nat Rev Microbiol 11:75–82
215. Shabalina SA, Koonin EV (2008) Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol 23:578–587. doi:10.1016/j.tree.2008.06.005
216. Shen X, Mizuguchi G, Hamiche A, Wu C (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406:541–544
217. Singh DP et al (2014) Genome-defence small RNAs exapted for epigenetic mating-type inheritance. Nature 509:447–452. doi:10.1038/nature13318
218. Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ (2014) R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 516:436–439. doi:10.1038/nature13787
219. Smemo S et al (2014) Obesity-associated varients within FTO form long-range functional connections with IRX3. Nature 507:371–375
220. Smith JM, Szathmary E (1995) The major transitions in evolution. W H Freeman, Oxford
221. Smits WK, Grossman AD (2010) The transcriptional regulator rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PLoS Genet 6:e1001207
222. Soares D, Dahlke I, Li W-T, Sandman K, Hethke C, Thomm M, Reeve JN (1998) Archaeal histone stability, DNA binding, and transcription inhibition above 90 °C. Extremophiles 2:75–81. doi:10.1007/s007920050045
223. Song J-J, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of argonaute and its implications for RISC slicer activity. Science 305:1434–1437. doi:10.1126/science.1102514
224. Soppa J (2001) Basal and regulated transcription in archaea. In: Laskin AI, Bennett JW, Gadd GM (eds) Advances in applied microbiology, vol 50. Academic Press, San Diego, pp 171–217
225. Soppa J (2010) Protein Acetylation in Archaea. Bacteria Eukaryotes Archaea. doi:10.1155/2010/820681
226. Soppa J (2014) Polyploidy in archaea and bacteria: about desiccation resistance giant cell size, long-term survival, enforcement by a eukaryotic host and additional aspects. J Mol Microbiol Biotechnol 24:409–419
227. Spang A et al (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179. doi:10.1038/nature14447
228. Stedman KM, Schleper C, Rumpf E, Zilig W (1999) Genetic requirements for the function of the archaeal virus SSV1 in Sulfolobus solfataricus: construction and testing of viral shuttle vectors. Genetics 152:1397–1405
229. Swerdlow R (2012) Alzheimer’s disease pathologic cascades: who comes first what drives what. Neurotox Res 22:182–194. doi:10.1007/s12640-011-9272-9
230. Taher L et al (2011) Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res 21:1139–1149
231. Taher L, Narlikar L, Ovcharenko I (2012) CLARE: cracking the language of regulatory elements. Bioinformatics 28:581–583. doi:10.1093/bioinformatics/btr704
232. Tahiliani M et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935. doi:10.1126/science.1170116
233. Tay Y, Rinn J, Pandolfi PP (2014) The multilayered complexity of ceRNA crosstalk and competition. Nature 505:344–352. doi:10.1038/nature12986
234. Thebault P, Boutin G, Bhat W, Rufiange A, Martens J, Nourani A (2011) Transcription regulation by the noncoding RNA SRG1 requires Spt2-dependent chromatin deposition in the wake of RNA polymerase II. Mol Cell Biol 31:1288–1300. doi:10.1128/mcb.01083-10
235. Ulitsky I, Shkumatava A, Jan Calvin H, Sive H, Bartel David P (2011) Conserved function of lincrnas in vertebrate embryonic development despite rapid sequence evolution. Cell 147:1537–1550. doi:10.1016/j.cell.2011.11.055
236. Vaillasante A, de Pablos B, Mendez-Lago M, Abad JP (2008) Telomere maintenance in drosophila cell. Cycle 7:2134–2138
237. Vaishnaw AK et al (2010) Review A status report on RNAi therapeutics. Silence 1. doi:10.1186/1758-1907X-1181-1114
238. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20:515–524. doi:10.1101/gad.1399806
239. Vanin EF (1985) Processed pseudogenes: characteristics and evolution. Ann Rev Genetics 19:253–272
240. Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L (2004) Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci 101:9257–9262
241. Vockenhuber M-P et al (2011) Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 8:468–477
242. Wang D, Rendon A, Wernisch L (2013) Transcription factor and chromatin features predict genes associated with eQTLs. Nucleic Acids Res 41:1450–1463. doi:10.1093/nar/gks1339
243. Wang KC, Chang HY (2011) Molecular mechanisms of long noncoding RNAs. Cell 43:904–914
244. Wang W, Li G-W, Chen C, Xie XS, Zhuang X (2011) Nucleoid-associated protein in live bacteria. Science 333:1445–1449
245. Ward WS, Coffey DS (1991) DNA packaging and organization in mammalian spermatozoa: comparison with somatic cells. Biol Reprod 44:569–574. doi:10.1095/biolreprod44.4.569
246. Wardleworth BN, Russell RJM, Bell SD, Taylor GL, White MF (2002) Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J 21:4654–4662. doi:10.1093/emboj/cdf465
247. Washietl S et al (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17:852–864. doi:10.1101/gr.5650707
248. Wassarman KM (2007) 6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol 10:164–168. doi:10.1016/j.mib.2007.03.008
249. Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136:615–628. doi:10.1016/j.cell.2009.01.043
250. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 11:R31
251. Weinzierl ROJ (2013) The RNA polymerase factory and archaeal transcription. Chem Rev 113:8350–8376
252. Weiss M (1982) Cell hybridization: a tool for the study of cell differentiation. In: Caskey CT, Robbins DC (eds) ***Somatic cell genetics, vol 50., NATO Advanced Study Institutes SeriesSpringer, New York, pp 169–182. doi:10.1007/978-1-4684-4256-4_10
253. White MF, Bell SD (2002) Holding it together: chromatin in the Archaea. Trends Genetics 18:621–626. doi:10.1016/S0168-9525(02)02808-1
254. Whitehouse I, Rando OJ, Delrow J, Tsukiyama T (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature 450:1031–1035
255. Williams S et al (2005) CpG-island fragments from the HNRPA2B1/CBX3 genomic locus reduce silencing and enhance transgene expression from the hCMV promoter/enhancer in mammalian cells. BMC Biotechnol. doi:10.1186/1472-6750-1185-1117
256. Williams TA, Foster PG, Cox CJ, Embley TM (2014) An archeal origin of eukaryotes supports only two primary domains of life. Nature 504:231–236
257. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23:1494–1504
258. Wion D, Casadesus J (2006) N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev Micro 4:183–192
259. Wong JTY, New DC, Wong JCW, Hung VKL (2003) Histone-like proteins of the dinoflagellate crypthecodinium cohnii have homologies to bacterial DNA-binding proteins. Eukaryot Cell 2:646–650. doi:10.1128/ec.2.3.646-650.2003
260. Wourms JP, Lombardi J (1992) Reflections on the evolution of piscine viviparity. Am Zool 32:276–293. doi:10.1093/icb/32.2.276
261. Xie Y, Reeve JN (2004) Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome. J Bacteriol 186:3492–3498. doi:10.1128/jb.186.11.3492-3498.2004
262. Yadon AN, Van de Mark D, Basom R, Delrow J, Whitehouse I, Tsukiyama T (2010) Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol Cell Biol 30:5110–5122. doi:10.1128/mcb.00602-10
263. Yamashita T et al (2000) Comprehensive gene expression profile of a normal human liver. Biochem Biophys Res Commun 269:110–116. doi:10.1006/bbrc.2000.2272
264. Yao H, Brick K, Evrard Y, Xiao T, Camerini-Otero RD, Felsenfeld G (2010) Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 24:2543–2555. doi:10.1101/gad.1967810
265. Yoon J-H et al (2012) LincRNA-p21 suppresses target mRNA translation. Mol Cell 47:648–655. doi:10.1016/j.molcel.2012.06.027
266. Yun M, Wu J, Workman JL, Li B (2011) Readers of histone modifications. Cell Res 21:564–578
267. Zerulla K, Soppa J (2014) Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 5:274. doi:10.3389/fmicb.2014.00274
268. Zhang A, Rimsky S, Reaban ME, Buc H, Belfort M (1996) Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics. EMBO J 15:1340–1349
269. Zheng D, Gerstein MB (2007) The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet 23:219–224. doi:10.1016/j.tig.2007.03.003
270. Zheng T, Hunag Q, Zhang C, Ni J, She Q, Shen Y (2012) Development of a simvastatin selection marker for a hyperthermophilic acidophile Sulfolobus islandicus. Appl Environ Microbiol 78:568–574
271. Zimmerman SB, Murphy LD (1996) Macromolecular crowding and the mandatory condensation of DNA in bacteria. FEBS Lett 390:245–248