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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