Genome Formatting For Properly Accessing Stored Information

(Spradling and Rubin 1983; Iborra, Jackson et al. 2001; van Driel, Fransz et al. 2003; Wray 2003; Istrail, De-Leon et al. 2007; Koch, Jourquin et al. 2008; Gilchrist, Fargo et al. 2009; Hager, McNally et al. 2009; van Hijum, Medema et al. 2009; van Vliet and Wren 2009; Dumay-Odelot, Durrieu-Gaillard et al. 2010; Lang, Weiche et al. 2010; Maatouk and Capel 2010; Papantonis, Larkin et al. 2010; de Nadal, Ammerer et al. 2011; Hackenberg, Carpena et al. 2011; Nikitina, Tischenko et al. 2011; Papantonis and Cook 2011; White 2011)

Transcription factor networks and dynamics

(Truss, Chalepakis et al. 1992; Swanson, Qiu et al. 2003; Yeger-Lotem, Sattath et al. 2004; Levine and Davidson 2005; Sommer 2005; Tonkiss and Calderwood 2005; Gilbert, Fuss et al. 2006; Ben-Tabou de-Leon and Davidson 2007; Hinman, Nguyen et al. 2007; Istrail, De-Leon et al. 2007; Busser, Bulyk et al. 2008; Daburon, Mella et al. 2008; Akalin, Fredman et al. 2009; Babu, Lang et al. 2009; Ben-Tabou de-Leon and Davidson 2009; Fullwood, Liu et al. 2009; Hager, McNally et al. 2009; Hinman, Yankura et al. 2009; Jacquier 2009; Li and Davidson 2009; Mak, Pillus et al. 2009; Peter and Davidson 2009; van Vliet and Wren 2009; White, Riles et al. 2009; Biddie, John et al. 2010; Botta, Haider et al. 2010; Carlberg and Seuter 2010; Charoensawan, Wilson et al. 2010; Cheung, Nayak et al. 2010; Eymery, Souchier et al. 2010; Fusco, Grassi et al. 2010; Goodrich and Tjian 2010; Lee, Min et al. 2010; McCauley, Weideman et al. 2010; Oler, Alla et al. 2010; Ragoczy and Groudine 2010; Ueki and Lovley 2010; Ueki and Lovley 2010; Wong Sak Hoi and Dumas 2010; Xu, Sankaran et al. 2010; Yankura, Martik et al. 2010; Bogdanove and Voytas 2011; Greenhill, Rocco et al. 2011; Harper, Finkenstadt et al. 2011; Helmlinger, Marguerat et al. 2011; Hong, Kim et al. 2011; Larson, Zenklusen et al. 2011; Scholze and Boch 2011; Suter, Molina et al. 2011; Wang, Chen et al. 2011; Wang, Lercher et al. 2011; Wei, Pelechano et al. 2011)

Nature Reviews Genetics, Modes of transcriptional regulation, http://www.nature.com/nrg/series/transcriptionalregulation/index.html

            Heat shock: (Jolly, Morimoto et al. 1997; Jolly, Usson et al. 1999; Arsene, Tomoyasu et al. 2000; Pirkkala, Nykanen et al. 2001; Tonkiss and Calderwood 2005; Zhao, Herrera-Diaz et al. 2005; Shamovsky, Ivannikov et al. 2006; Mariner, Walters et al. 2008; Shivaswamy and Iyer 2008; Kalmar and Greensmith 2009; Eymery, Souchier et al. 2010; Sakurai and Enoki 2010)

cis-Regulatory signals and modules

(Scarlato, Storlazzi et al. 1989; Truss, Chalepakis et al. 1992; Collado-Vides 1993; Collado-Vides 1993; Ludwig and Kreitman 1995; Collado-Vides 1996; Shen and Gigot 1997; Swanson, Qiu et al. 2003; Kel, Konovalova et al. 2006; Hinman and Davidson 2007; Simpson and Ayyar 2008; Tuch, Galgoczy et al. 2008; Veitia 2008; Akalin, Fredman et al. 2009; Gertz, Siggia et al. 2009; Han, Garcia et al. 2009; Hood, Neafsey et al. 2009; Lawless, Pearson et al. 2009; Moscou and Bogdanove 2009; Rach, Yuan et al. 2009; Wasson and Hartemink 2009; Bond, Peters et al. 2010; Cheung, Nayak et al. 2010; Goodrich and Tjian 2010; Gotea, Visel et al. 2010; Juven-Gershon and Kadonaga 2010; Oler, Alla et al. 2010; Raab and Kamakaka 2010; Bickel, Kopp et al. 2011; Bogdanove and Voytas 2011; Liu, Bushnell et al. 2011; Ludwig, Manu et al. 2011; Myers, Stamatoyannopoulos et al. 2011; Ong and Corces 2011; Patek and Nesvera 2011; Rada-Iglesias, Bajpai et al. 2011; Scholze and Boch 2011; Wei, Pelechano et al. 2011; Yokoyama, Thorne et al. 2011)

RNA processing, alternative, cis- and trans-splicing and nucleotide editing

(Chen and Manley 2009; Zhang, Campbell et al. 2009; Derelle, Momose et al. 2010; Douris, Telford et al. 2010; Pullirsch and Jantsch 2010; Woolfe, Mullikin et al. 2010; Carmi, Borukhov et al. 2011; Cheong and Lufkin 2011; George, Gan et al. 2011; Hogg, Paro et al. 2011; Iwata and Gotoh 2011; Michaeli 2011; Samuel 2011; Yang, Zhan et al. 2011)

Triplet code, other codes and overlapping messages in coding sequences

(Sanger, Air et al. 1977; Van der Avoort, Teertstra et al. 1983; Tramontano, Scarlato et al. 1984; Merino, Balbas et al. 1994; Trifonov 1999; Konecny, Schoniger et al. 2000; Peleg, Trifonov et al. 2003; Hosid, Trifonov et al. 2004; Johnson and Chisholm 2004; Peleg, Kirzhner et al. 2004; Makalowska, Lin et al. 2005; Cohanim, Trifonov et al. 2006; Firth and Brown 2006; Gabdank, Barash et al. 2006; Zhu and Freeland 2006; Bollenbach, Vetsigian et al. 2007; Hanada, Zhang et al. 2007; Itzkovitz and Alon 2007; Chung, Miller et al. 2008; Delaye, Deluna et al. 2008; Robins, Krasnitz et al. 2008; Sabath, Graur et al. 2008; Salih, Salih et al. 2008; Sanna, Li et al. 2008; Wang, Barr et al. 2008; Bettecken and Trifonov 2009; Ma and Nussinov 2009; Prat, Fromer et al. 2009; Tautz 2009; Woltering and Duboule 2009; Cheng, Yang et al. 2010; Chirico, Vianelli et al. 2010; Itzkovitz, Hodis et al. 2010; Sabath and Graur 2010; Firth, Wills et al. 2011; Hudson, Gu et al. 2011; Ladoukakis, Pereira et al. 2011; Sanjuan and Borderia 2011; Trifonov 2011; Xu, Wei et al. 2011; Yang, Tschaplinski et al. 2011)

(Lin, Kheradpour et al. 2011) (“We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.”)

            Ribosomal frameshifting to elongate fusion proteins: (Ivanov, Gesteland et al. 2000; Ivanov and Atkins 2007; Jacobs, Belew et al. 2007; Belew, Hepler et al. 2008; Chou, Lin et al. 2010; Firth, Blitvich et al. 2010)

Nuclear & genomic three-dimensional organization & subnuclear compartmentalization

 

(Jackson, Hassan et al. 1993; Gotta and Gasser 1996; Iborra, Pombo et al. 1996; Saurin, Shiels et al. 1998; Cremer, Kreth et al. 2000; Pombo, Jones et al. 2000; Denegri, Chiodi et al. 2001; Carter, Chakalova et al. 2002; Dekker, Rippe et al. 2002; Denegri, Moralli et al. 2002; Tolhuis, Palstra et al. 2002; Fomproix and Percipalle 2004; Iborra, Kimura et al. 2004; Metz, Soret et al. 2004; Osborne, Chakalova et al. 2004; Verschure 2004; Taddei, Gartenberg et al. 2005; Cremer and Cremer 2006; Dostie, Richmond et al. 2006; Ahmed and Brickner 2007; Fraser and Bickmore 2007; Goodier, Zhang et al. 2007; Lanctot, Cheutin et al. 2007; Mateos-Langerak, Goetze et al. 2007; Misteli 2007; Osborne, Chakalova et al. 2007; Sexton, Umlauf et al. 2007; Brown, Green et al. 2008; Dekker 2008; Fedorova and Zink 2008; Finlan, Sproul et al. 2008; Hu, Kwon et al. 2008; Kaiser, Intine et al. 2008; Kumaran, Thakar et al. 2008; Meaburn, Newbold et al. 2008; Mitchell and Fraser 2008; Morris 2008; Ruault, Dubarry et al. 2008; Schofer and Weipoltshammer 2008; Sinha, Banerjee et al. 2008; Bond and Fox 2009; Brickner 2009; Clemson, Hutchinson et al. 2009; Dhar, Ongwijitwat et al. 2009; Dorsett 2009; Fedorova and Zink 2009; Gladfelter and Berman 2009; Linnemann and Krawetz 2009; Louvet and Percipalle 2009; Mateos-Langerak, Bohn et al. 2009; Meaburn, Gudla et al. 2009; Ponjavic, Oliver et al. 2009; Redrup, Branco et al. 2009; Rino and Carmo-Fonseca 2009; Rouquette, Genoud et al. 2009; Sasaki and Hirose 2009; Schaaf, Misulovin et al. 2009; Solovei, Kreysing et al. 2009; Wendt and Peters 2009; Zeitz, Marella et al. 2009; Zheng, Han et al. 2009; Zlatanova and Caiafa 2009; Biamonti and Vourc'h 2010; Castano, Philimonenko et al. 2010; Cook 2010; Cope, Fraser et al. 2010; Duan, Andronescu et al. 2010; Ferrai, Xie et al. 2010; Fox and Lamond 2010; Harewood, Schutz et al. 2010; Hetzer 2010; Kagey, Newman et al. 2010; Lallemand-Breitenbach and de The 2010; Malyavantham, Bhattacharya et al. 2010; Mehta, Amira et al. 2010; Naumova and Dekker 2010; Pollock and Huang 2010; Ragoczy and Groudine 2010; Schoenfelder, Sexton et al. 2010; Solovei and Joffe 2010; Souquere, Beauclair et al. 2010; Williams, Spilianakis et al. 2010; Baker 2011; Bantignies, Roure et al. 2011; Hernandez-Verdun 2011; Keaton, Taylor et al. 2011; Mao, Sunwoo et al. 2011; Mirny 2011; Papantonis and Cook 2011; Rajapakse and Groudine 2011; Strukov, Sural et al. 2011; Wu, Chen et al. 2011) (Ruault, Dubarry et al. 2008; Lieberman-Aiden, van Berkum et al. 2009; Rouquette, Genoud et al. 2009; Torok, Ching et al. 2009; van Berkum and Dekker 2009; Zeitz, Marella et al. 2009; Kagey, Newman et al. 2010; van Berkum, Lieberman-Aiden et al. 2010; Bau and Marti-Renom 2011; Marti-Renom and Mirny 2011; Mirny 2011; Sanyal, Bau et al. 2011; Umbarger, Toro et al. 2011)

 

Nucleoskeleton

 

(Hozak 1996; Zheng, Han et al. 2009; Zhong, Wilson et al. 2010; Simon and Wilson 2011)

“nc”RNA regulation:

(Morris 2005; Berezikov, Chung et al. 2007; Goodier, Zhang et al. 2007; Murchison, Stein et al. 2007; Chung, Okamura et al. 2008; Morris 2008; Okamura and Lai 2008; Tam, Aravin et al. 2008; Armisen, Gilchrist et al. 2009; Beisel and Smolke 2009; Dambach and Winkler 2009; Garst and Batey 2009; Ghildiyal and Zamore 2009; Jacquier 2009; Morris 2009; Morris 2009; Papaioannou, Pitetti et al. 2009; Ponjavic, Oliver et al. 2009; Redrup, Branco et al. 2009; Waters and Storz 2009; Wirth and Crespi 2009; Beisel and Storz 2010; Cheloufi, Dos Santos et al. 2010; Chen, Chen et al. 2010; Chiang, Schoenfeld et al. 2010; Chong, Zhang et al. 2010; Cifuentes, Xue et al. 2010; Ebhardt, Fedynak et al. 2010; Flynt, Greimann et al. 2010; Gottesman and Storz 2010; Gripenland, Netterling et al. 2010; Haussecker, Huang et al. 2010; Hawkins and Matzuk 2010; Khurana and Theurkauf 2010; Lau 2010; Lipovich, Johnson et al. 2010; Ma, Flemr et al. 2010; Malecova and Morris 2010; Miyoshi, Miyoshi et al. 2010; Muro and Andrade-Navarro 2010; Newman and Hammond 2010; Nicolas, Moxon et al. 2010; Nozawa, Miura et al. 2010; Ohnishi, Totoki et al. 2010; Romby and Charpentier 2010; Schnall-Levin, Zhao et al. 2010; Schwab and Voinnet 2010; Siomi and Siomi 2010; Souquere, Beauclair et al. 2010; Suh, Baehner et al. 2010; Svoboda and Flemr 2010; Tang 2010; Thomason and Storz 2010; Yang and Lai 2010; Yang, Maurin et al. 2010; Yassour, Pfiffner et al. 2010; Chung, Agius et al. 2011; Jouannet and Crespi 2011; Mao, Sunwoo et al. 2011; Phok, Moisan et al. 2011; Schnall-Levin, Rissland et al. 2011; Ulveling, Francastel et al. 2011; Volk and Shomron 2011; Wang, Yang et al. 2011; Wen, Zheng et al. 2011) (Ying and Lin 2005; Goodrich and Kugel 2006; Sexton, Umlauf et al. 2007; Kavi, Fernandez et al. 2008; Taft, Glazov et al. 2009; Hung and Chang 2010; Mattick, Taft et al. 2010; Berezikov 2011; Cernilogar, Onorati et al. 2011; Haag and Pikaard 2011; Jose, Garcia et al. 2011; Kaikkonen, Lam et al. 2011; Kogo, Shimamura et al. 2011; Wutz 2011; Zhang, Hou et al. 2011)

Nature Reviews Genetics, Non-coding RNA, http://www.nature.com/nrg/series/noncoding/index.html

RNA involvement in 3D genome organization

(Leung, Vallero et al. 2009; Redrup, Branco et al. 2009; Wang, Crutchley et al. 2011)

 

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