Cellular Regulation Of Natural Genetic Engineering

(Ebina and Levin 2007; Mittelman, Sykoudis et al. 2010; Mittelman and Wilson 2010; Hua-Van, Le Rouzic et al. 2011; Nagai, Davoodi et al. 2011; Newton and Bordenstein 2011; Vitale, Galluzzi et al. 2011)

Control of replication proofreading, repair and recombination functions (including mutator polymerases)

(Darmon, Lopez-Vernaza et al. 2007; Thorslund and West 2007; Cohen, Godoy et al. 2009; Galhardo, Do et al. 2009; Heidelberg, Nelson et al. 2009; Chen, Liu et al. 2010; Chen, Liu et al. 2010; Cohen, Lewis et al. 2010; Frisch, Su et al. 2010; Koskiniemi, Hughes et al. 2010; Wallace, Belancio et al. 2010; Cohen and Walker 2011; Debora, Vidales et al. 2011; Kang, Reardon et al. 2011; Lippert, Kim et al. 2011; Liu, Renault et al. 2011; Mischo, Gomez-Gonzalez et al. 2011; Storvik and Foster 2011; Takahashi, Burguiere-Slezak et al. 2011; Vader, Blitzblau et al. 2011)

Prokaryotic CRISPRs

(Bolotin, Quinquis et al. 2005; Haft, Selengut et al. 2005; Makarova, Grishin et al. 2006; Barrangou, Fremaux et al. 2007; Andersson and Banfield 2008; Beloglazova, Brown et al. 2008; Brouns, Jore et al. 2008; Carte, Wang et al. 2008; Deveau, Barrangou et al. 2008; Horvath, Romero et al. 2008; Sorek, Kunin et al. 2008; Vestergaard, Shah et al. 2008; Horvath, Coute-Monvoisin et al. 2009; Makarova, Wolf et al. 2009; Narberhaus and Vogel 2009; Rousseau, Gonnet et al. 2009; Shah, Hansen et al. 2009; van der Oost and Brouns 2009; van der Oost, Jore et al. 2009; van der Ploeg 2009; Wiedenheft, Zhou et al. 2009; Garneau, Dupuis et al. 2010; Haurwitz, Jinek et al. 2010; Horvath and Barrangou 2010; Sorokin, Gelfand et al. 2010; Sorokin, Gelfand et al. 2010; Al-Attar, Westra et al. 2011; Blower, Pei et al. 2011; Deltcheva, Chylinski et al. 2011; Garrett, Shah et al. 2011; Jore, Lundgren et al. 2011; Makarova, Aravind et al. 2011; Makarova, Haft et al. 2011; Makarova, Wolf et al. 2011; Semenova, Jore et al. 2011; Terns and Terns 2011; Wiedenheft, Lander et al. 2011)

RNA interference and epigenetic regulation in eukaryotes directed by piRNAs and other RNA molecules

(Dalmay, Hamilton et al. 2000; Miura, Yonebayashi et al. 2001; Kubis, Castilho et al. 2003; Sijen and Plasterk 2003; Sollars, Lu et al. 2003; Baulcombe 2004; Xie, Johansen et al. 2004; Kalmykova, Klenov et al. 2005; Onodera, Haag et al. 2005; Karpinets, Greenwood et al. 2006; Zambon, Vakharia et al. 2006; Brennecke, Aravin et al. 2007; Dramard, Heidmann et al. 2007; Murchison, Stein et al. 2007; Brennecke, Malone et al. 2008; Casas-Mollano, Rohr et al. 2008; Desset, Buchon et al. 2008; Devor, Huang et al. 2008; Girard and Hannon 2008; Pikaard, Haag et al. 2008; Siomi 2008; Chen 2009; Daxinger, Kanno et al. 2009; Halic and Moazed 2009; Huda and Jordan 2009; Jia, Lisch et al. 2009; Klattenhoff, Xi et al. 2009; Malone and Hannon 2009; Michalak 2009; Mourier and Willerslev 2009; Narberhaus and Vogel 2009; van der Heijden and Bortvin 2009; van Rij and Berezikov 2009; Cantu, Vanzetti et al. 2010; Huda, Marino-Ramirez et al. 2010; Khurana and Theurkauf 2010; Kirino, Vourekas et al. 2010; Nowacki, Haye et al. 2010; Patil and Kai 2010; Siomi, Mannen et al. 2010; Siomi, Miyoshi et al. 2010; Specchia, Piacentini et al. 2010; Takacs, Banati et al. 2010; De Fazio, Bartonicek et al. 2011; Gangaraju, Yin et al. 2011; Huda, Bowen et al. 2011; Ito, Gaubert et al. 2011; Kibanov, Egorova et al. 2011; Rigal and Mathieu 2011; Xie, Liang et al. 2011)

DNA transposons

(Fischer, van Luenen et al. 1999; Timakov, Liu et al. 2002; Chung, Okamura et al. 2008; O'Donnell and Boeke 2008; Rozhkov, Aravin et al. 2010; Wang, Wang et al. 2010; Guerreiro 2011)

Retrotransposons           

(Neumann, Yan et al. 2007; Siomi, Saito et al. 2008; Faulkner, Kimura et al. 2009; Guerreiro 2011)

            Retrovirus and LTR retrotransposons: (Errede, Company et al. 1985; Company and Errede 1987; Fulton, Rathjen et al. 1988; Bradshaw and McEntee 1989; Scheinker, Lozovskaya et al. 1990; Dupressoir and Heidmann 1996; Grandbastien, Lucas et al. 1997; Ke, Irwin et al. 1997; Takeda, Sugimoto et al. 1998; Kimura, Tosa et al. 2001; Barbot, Dupressoir et al. 2002; Scholes, Kenny et al. 2003; Sacerdot, Mercier et al. 2005; Sehgal, Lee et al. 2007; Cam, Noma et al. 2008; Desset, Buchon et al. 2008; Labrador, Sha et al. 2008; Saito, Keng et al. 2008; Mourier and Willerslev 2009; Brunmeir, Lagger et al. 2010; Kaneko-Ishino and Ishino 2010; Lu, Contreras et al. 2011)

            Non-LTR retrotransposons: