Evo21 References.shtml

Distinct Classes Of DNA In The Genome

(Wood, Gwilliam et al. 2002; Mrazek 2009; Janes, Organ et al. 2010; Mrazek 2010; Romiguier, Ranwez et al. 2010)

Triplet code, other codes, nested coding sequences and overlapping messages embedded 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; Itzkovitz and Alon 2007; Assis, Kondrashov et al. 2008; 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; Kumar 2009; Ma and Nussinov 2009; Prat, Fromer et al. 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; Sanjuan and Borderia 2011; Trifonov 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)

Heterochromatin

(Passarge 1979; Karpen 1994; Weiler and Wakimoto 1995; Zacharias 1995; Henikoff 2000; Lohe and Roberts 2000; Grewal and Elgin 2002; Pidoux and Allshire 2005; Scott, Merrett et al. 2006; Carchilan, Delgado et al. 2007; Durand-Dubief and Ekwall 2008; Ishii, Ogiyama et al. 2008; Ferree and Barbash 2009; Hughes and Hawley 2009; Kotnova, Salenko et al. 2009; Las Penas, Urdampilleta et al. 2009; Guetg, Lienemann et al. 2010; Martienssen 2010; Tamaru 2010)

“Non-coding” (“nc”) sequences

(Mattick 2001; Puertas 2002; Sleutels, Zwart et al. 2002; Shabalina and Spiridonov 2004; Gottesman 2005; Lockton and Gaut 2005; Tang, Polacek et al. 2005; Woolfe, Goodson et al. 2005; Goodrich and Kugel 2006; Ponting and Lunter 2006; Westenberger, Cerqueira et al. 2006; Mikkelsen, Wakefield et al. 2007; Vavouri, Walter et al. 2007; Costa 2008; Glinsky 2008; Royo and Cavaille 2008; Swiercz, Hindra et al. 2008; Tomilin 2008; Warnecke, Parmley et al. 2008; Blombach, Makarova et al. 2009; Bradley, Uzilov et al. 2009; Collins and Penny 2009; Duharcourt, Lepere et al. 2009; Forrest, Abdelhamid et al. 2009; Gieni and Hendzel 2009; Guttman, Amit et al. 2009; Hirota and Ohta 2009; Koerner, Pauler et al. 2009; Leeb, Steffen et al. 2009; Mercer, Dinger et al. 2009; Morris 2009; Morris 2009; Morris 2009; Navarro, Chantalat et al. 2009; Ponjavic, Oliver et al. 2009; Qureshi and Mehler 2009; Tuller, Ruppin et al. 2009; Bousios, Darzentas et al. 2010; Kapranov, St Laurent et al. 2010; Malecova and Morris 2010; Matsunami, Sumiyama et al. 2010; Pennisi 2010; Schoeftner and Blasco 2010; Subirana and Messeguer 2010; van Leeuwen and Mikkers 2010; Zhou, Hu et al. 2010; Gibb, Brown et al. 2011; Janes, Chapus et al. 2011; Orom and Shiekhattar 2011; Pek and Kai 2011)

Segmental duplications

(Samonte and Eichler 2002; Armengol, Pujana et al. 2003; Newman and Trask 2003; Stankiewicz, Shaw et al. 2004; Armengol, Marques-Bonet et al. 2005; Sharp, Locke et al. 2005; Bailey and Eichler 2006; Coulibaly, Lobo et al. 2007; Darai-Ramqvist, Sandlund et al. 2008; She, Cheng et al. 2008; Koszul and Fischer 2009; Marques-Bonet, Girirajan et al. 2009; Marques-Bonet, Kidd et al. 2009)

Inversions

(Lyttle and Haymer 1992; Caceres, Ranz et al. 1999; Mathiopoulos, della Torre et al. 1999; Singh 2001; Kuwahara, Yamashita et al. 2004; Puig, Caceres et al. 2004; Cerdeno-Tarraga, Patrick et al. 2005; Caceres, Sullivan et al. 2007; Coulibaly, Lobo et al. 2007; Tsuji, Ueda et al. 2007; Hoffmann and Rieseberg 2008; Delprat, Negre et al. 2009; Kojima and Okada 2009; Kolb, Chuzhanova et al. 2009; Swenson and Moret 2009; Kirkpatrick 2010; Kugelberg, Kofoid et al. 2010; Ling and Cordaux 2010; Lobo, Sangare et al. 2010; Lowry and Willis 2010; Furuta, Kawai et al. 2011)

Mobile genetic elements

(Smit 1999; Craig 2002; Gentles, Wakefield et al. 2007; Kordis 2009)

Retrotransposons and retrotransduced sequences: (Noma, Ohtsubo et al. 1999; Schmidt 1999; Gilbert and Labuda 2000; Ogiwara, Miya et al. 2002; Cardazzo, Bargelloni et al. 2003; Duvernell, Pryor et al. 2004; DeCerbo and Carmichael 2005; Kramerov and Vassetzky 2005; Schmitz, Roos et al. 2005; Wang, Xing et al. 2005; Kejnovsky, Kubat et al. 2006; Kordis, Lovsin et al. 2006; Piskurek, Austin et al. 2006; Gu, Ray et al. 2007; Kriegs, Churakov et al. 2007; Lee, Cordaux et al. 2007; Moller-Krull, Delsuc et al. 2007; Onami, Nikaido et al. 2007; Akagi, Li et al. 2008; Kojima and Kanehisa 2008; Nishihara and Okada 2008; Wang and Liu 2008; Hirakawa, Nishihara et al. 2009; Matveev and Okada 2009; Ray, Platt et al. 2009; Smykal, Kalendar et al. 2009; Walters, Kugel et al. 2009; Cioffi, Martins et al. 2010; Kawakami, Strakosh et al. 2010; Novikova, Smyshlyaev et al. 2010; Ragupathy, Banks et al. 2010; Neumann, Navratilova et al. 2011)

DNA transposons: (Lovering, Harden et al. 1991; Poulter, Goodwin et al. 2003; Dooner and Weil 2007; Ray, Feschotte et al. 2008; Bao, Jurka et al. 2009; Bao, Kapitonov et al. 2010; Cioffi, Martins et al. 2010; Tomita, Okutani et al. 2011)

Repeats/repetitive DNA

(Orgel 1980; Wostemeyer and Kreibich 2002; Jurka, Kapitonov et al. 2007; Cermak, Kubat et al. 2008; Doggett 2008; Kazama and Matsunaga 2008; Lorenzi, Thiagarajan et al. 2008; Otto, Gomes et al. 2008; Richard, Kerrest et al. 2008; Wang, Lorenzen et al. 2008; Kejnovsky, Hobza et al. 2009; Cioffi, Martins et al. 2010; Cioffi, Martins et al. 2010; Habu 2010; Mravinac and Plohl 2010; O'Meally, Patel et al. 2010; Castoe, Hall et al. 2011; Cioffi, Camacho et al. 2011; Cioffi, Molina et al. 2011; de Koning, Gu et al. 2011; Delihas 2011; Pearson 2011)

Dispersed repeats (Kordis and Gubensek 1998; Borodulina and Kramerov 1999; Smit 1999; Herman and Heyndrickx 2000; Smith, Bringaud et al. 2009; Zhao, Qi et al. 2009; Clayton 2010; Tempel, Rousseau et al. 2010; Tomita, Okutani et al. 2011)

Ultraconserved elements: (Bejerano, Pheasant et al. 2004; Sandelin, Bailey et al. 2004; Glazov, Pheasant et al. 2005; Poulin, Nobrega et al. 2005; Siepel, Bejerano et al. 2005; Woolfe, Goodson et al. 2005; Bejerano, Lowe et al. 2006; Derti, Roth et al. 2006; Gardiner, Hirons et al. 2006; Papatsenko, Kislyuk et al. 2006; Venkatesh, Kirkness et al. 2006; Ahituv, Zhu et al. 2007; Chen, Wang et al. 2007; Katzman, Kern et al. 2007; Lareau, Inada et al. 2007; Ni, Grate et al. 2007; Vavouri, Walter et al. 2007; Voss, Gierga et al. 2007; Baira, Greshock et al. 2008; Chen, Gottlieb et al. 2008; Chiang, Derti et al. 2008; Elgar and Vavouri 2008; Hickey 2008; Lin, Ma et al. 2008; McLean and Bejerano 2008; Ovcharenko 2008; Sakuraba, Kimura et al. 2008; Stephen, Pheasant et al. 2008; Visel, Prabhakar et al. 2008; Woolfe and Elgar 2008; Zheng and Zhang 2008; Rodelsperger, Kohler et al. 2009; Vavouri and Lehner 2009; Vavouri, Semple et al. 2009; Wang, Lee et al. 2009; Amiel, Benko et al. 2010; Licastro, Gennarino et al. 2010; Martinez, Monfort et al. 2010; Ni, Shu et al. 2010; Tran, Wong et al. 2010; Woolfe, Mullikin et al. 2010; Cheong and Lufkin 2011; Halligan, Oliver et al. 2011; Lee, Kerk et al. 2011; McCormack, Faircloth et al. 2011; Sathirapongsasuti, Sathira et al. 2011; Tashiro, Teissier et al. 2011)

Tandem repeats (“satellites”) and microsatellites: (Csink and Henikoff 1998; Motta, Landsberger et al. 1998; Schlotterer 2000; Bois 2003; Muegge 2005; Grechko, Ciobanu et al. 2006; Hobza, Lengerova et al. 2006; Anmarkrud, Kleven et al. 2008; Cermak, Kubat et al. 2008; Kazama and Matsunaga 2008; Plohl, Luchetti et al. 2008; Tomilin 2008; Adega, Guedes-Pinto et al. 2009; Chadwick 2009; Eckert and Hile 2009; Kejnovsky, Hobza et al. 2009; Kuhn, Teo et al. 2009; Macas, Koblizkova et al. 2009; Pemberton, Sandefur et al. 2009; Castagnone-Sereno, Danchin et al. 2010; Nakamori and Thornton 2010; Rolland, Dujon et al. 2010; Rosloski, Jali et al. 2010; Thierry, Dujon et al. 2010; Tremblay, Alexander et al. 2010; Vicari, Nogaroto et al. 2010; Cioffi, Kejnovsky et al. 2011; Lam, Wu et al. 2011; Payseur, Jing et al. 2011; Pokorna, Kratochvil et al. 2011; Smith, Bomblies et al. 2011; Wojciechowska and Krzyzosiak 2011; Zu, Gibbens et al. 2011)