Evo21 References.shtml

Targeting Of Natural Genetic Engineering Within The Genome

(Wu and Burgess 2004; Holmes, Kaykov et al. 2005; Winckler, Szafranski et al. 2005; Berry, Hannenhalli et al. 2006; Van Maele, Busschots et al. 2006; Kauppi, Jasin et al. 2007; Yamada-Inagawa, Klar et al. 2007; Brady, Agosto et al. 2009; Grey, Baudat et al. 2009; Mathas, Kreher et al. 2009; Rain, Cribier et al. 2009; Uchiyama, Fujino et al. 2009; Zhang and Saier 2009; Wu, Getun et al. 2010; Zhang, Yen et al. 2010; Zheng, Ao et al. 2010; Cooper, Bacolla et al. 2011; Siol, Spaller et al. 2011; Smagulova, Gregoretti et al. 2011; Steiner, Davidow et al. 2011)

Table II.11. Examples of targeted natural genetic engineering.
Example	Observed specificity (mechanism)	References
DNA import and export	Special DNA uptake signals; oriT sites for initiating conjugal transfer replication	DNA uptake signals in bacterial transformation (Smith, Gwinn et al. 1999; Wang, Goodman et al. 2002; Davidsen, Rodland et al. 2004; Findlay and Redfield 2009; Maughan, Wilson et al. 2010), oriT signals in conjugative plasmids and elements (Adams, Lyras et al. 2002; Grohmann, Muth et al. 2003; Parker, Becker et al. 2005; Garcillan-Barcia, Francia et al. 2009)
Homologous recombination	Special sequences stimulating DS breaks and other biochemical events in homologous exchange	(Cromie, Hyppa et al. 2007; Bagshaw, Pitt et al. 2008; Pryce and McFarlane 2009; Steiner, Steiner et al. 2009) – Chi-like sequences (Smith 1994; Sourice, Biaudet et al. 1998; El Karoui, Biaudet et al. 1999; El Karoui, Schaeffer et al. 2000; Amundsen and Smith 2007; Halpern, Chiapello et al. 2007; Dillingham and Kowalczykowski 2008); Spo11 targets and hotspots in S. cerevisiae (Fukuda, Kugou et al. 2008; Nicolas 2009; Tsai, Burt et al. 2010); M26 and other recombination hotspots in S. pombe (Smith 1994; Cromie, Hyppa et al. 2007; Pryce and McFarlane 2009; Steiner, Steiner et al. 2009); repeats in plant and animal genomes (Mezard 2006; Buard and de Massy 2007; Coop and Myers 2007; McVean 2010)
Transposon insertions at special DNA structures	Insertion at REP palindromes (transposase specificity), DNA replication forks (interaction with processivity factor)	(Tobes and Pareja 2006); (Jomantiene, Zhao et al. 2007);(Nunvar, Huckova et al.) (Peters and Craig 2000; Peters and Craig 2001) (Parks, Li et al. 2009)
IS200/IS605 family target site selection	DNA sequence homology	(Barabas, Ronning et al. 2008; Guynet, Achard et al. 2009)
IS911 target site selection	InsAB transposase binding to specific DNA sequences; regulated by synthesis of InsA transposase without specificity	(Rousseau, Loot et al. 2007)
Cassette replacement/conversion in antigenic variation	DNA sequence homology at cassette boundaries	(Barbour and Restrepo 2000; Brayton, Palmer et al. 2002; Palmer, Futse et al. 2006; Palmer and Brayton 2007; Palmer, Bankhead et al. 2009)
Site-specific recombination (phase variation, antigenic variation, insertions and excisions)	Protein recognition of DNA sequence; protein-protein interaction	(Nash 1981), (Silverman, Zieg et al. 1979; Komano, Kim et al. 1994; Komano 1999)
Diversity-generating retroelements	Localized mutagenesis at duplicated segment of coding region; reverse transcription, RNA-DNA sequence homology	(Medhekar and Miller 2007; Guo, Tse et al. 2008)
Mating type cassette switching (S. cerevisiae, S. pombe, Kluyveromyces lactis)	Protein recognition of DNA sequence (endonuclease or transposase cleavage at unique site), DNA sequence homology at cassette boundaries	(Haber 1998; Klar, Ivanova et al. 1998; Dalgaard and Klar 1999; Haber 2006; Klar 2007; Barsoum, Martinez et al. 2010); (Rusche and Rine 2010)
Immune system V(D)J joining	Cleavage at specific recombination signal sequences (recognition of RSSs by RAG1+2 transposase); flexible joining by non-homologous end joining (NHEJ) functions	(Bassing, Swat et al. 2002; Gellert 2002)
Immune system somatic hypermutation	5’ exons of immunoglobulin sequences (transcriptional specificity determinants), DIVAC element to suppress repair	(Honjo, Kinoshita et al. 2002; Inlay, Gao et al. 2006; Yang, Fugmann et al. 2006; Xiang and Garrard 2008; Blagodatski, Batrak et al. 2009)
Immune system class switching	Lymphokine-controlled choice of switch region transcription (promoter activation)	(Kinoshita and Honjo 2001; Honjo, Kinoshita et al. 2002)
Budding yeast (S. cerevisaea) retroviral-like elements Ty1-Ty4	Strong preference for insertion upstream of RNA polymerase III initiation sites(protein-protein interaction of integrase with RNA polymerase III factors TFIIIB and TFIIIC).	(Kirchner, Connolly et al. 1995; Kim, Vanguri et al. 1998; Bushman 2003; Bachman, Gelbart et al. 2005; Mou, Kenny et al. 2006)
Budding yeast retroviral-like element Ty1	Preference for insertion upstream of RNA polymerase II initiation sites rather than exons.	(Eibel and Philippsen 1984)
Budding yeast retroviral-like element Ty5	Strong preference for insertion in transcriptionally silenced regions of the yeast genome (protein-protein interaction of integrase targeting domain (TD) with Sir4 silencing protein). Regulated in response to stress by modulation of integrase TD protein phosphorylation.	(Zou, Ke et al. 1996; Gai and Voytas 1998; Zhu, Zou et al. 1998; Xie, Gai et al. 2001; Bushman 2003; Zhu, Dai et al. 2003; Brady, Schmidt et al. 2008); (Dai, Xie et al. 2007)
Fission yeast (S. pombe) retroviral-like elements Tf1 & Tf2	Insertion almost exclusively in intergenic regions (>98% for Tf1); biased towards PolII promoter-proximal sites, 100 – 400 bp upstream of the translation start by protein-protein interaction with transcription activators; prefers chromosome 3.	(Behrens, Hayles et al. 2000; Singleton and Levin 2002; Bowen, Jordan et al. 2003); (Bushman 2003; Kordis 2005; Leem, Ripmaster et al. 2008); (Chatterjee, Leem et al. 2009) (Novikova 2009) (Guo and Levin 2010)
MAGGY (fungal Ty3/gypsy family) retrotransposon	Targeting to heterochromatin by chromodomain in integrase protein	(Gao, Hou et al. 2008)
Dictyostelium discoideum non-LTR retrotransposon TRE5-A	Insertion upstream of tRNA sequences by protein-protein interactions with RNA Pol III transcription factors	(Siol, Boutliliss et al. 2006; Chung, Siol et al. 2007)
Rapidly expanding mPing transposons in rice	Insertion upstream of coding sequences	(Naito, Zhang et al. 2009)
Drosophila ZAM LTR retrotransposons	Site-specific insertions by protein-DNA recognition	(Faye, Arnaud et al. 2008)
Murine Leukemia Virus (MLV)	Preference for insertion upstream of transcription start sites in human genome; role for IN (integrase) and GAG proteins	(Bushman 2003; Wu, Li et al. 2003; Mitchell, Beitzel et al. 2004); (Dunbar 2005; Lewinski, Yamashita et al. 2006)
HIV, SIV	Preference for insertion into actively transcribed regions of human genome; role for IN (integrase) and GAG proteins; HIV integrase interaction with LEDGF/p75 transcription factor	(Mitchell, Beitzel et al. 2004; Ciuffi, Llano et al. 2005; Dunbar 2005; Ciuffi and Bushman 2006; Ciuffi, Diamond et al. 2006; Lewinski, Yamashita et al. 2006; Llano, Saenz et al. 2006; Botbol, Raghavendra et al. 2008; Ciuffi 2008); (Engelman and Cherepanov 2008; Levin, Rosenbluh et al. 2010)
Gammaretroviral (but not lentiviral) vectors	Insertion at transcription factor binding sites; 21% recurrence rate at hotspots	(Cattoglio, Facchini et al. 2007; Deichmann, Hacein-Bey-Abina et al. 2007; Felice, Cattoglio et al. 2009)
Drosophila gypsy retrovirus	Site-specific insertion into Ovo locus regulatory region guided by Ovo protein binding sites	(Labrador and Corces 2001; Labrador, Sha et al. 2008)
Drosophila P-factors	Preference for insertion into the 5’ end of transcripts	(Spradling, Stern et al. 1995)
Drosophila P-factors	Targeting (“homing”) to regions of transcription factor function by incorporation of cognate binding site; region-specific	(Kassis, Noll et al. 1992; Taillebourg and Dura 1999; Bender and Hudson 2000) (Fauvarque and Dura 1983; Hama, Ali et al. 1990; Kassis 2002)
HeT-A and TART retrotransposons	Insertion at Drosophila telomeres	(Casacuberta and Pardue 2002; Casacuberta and Pardue 2003; Casacuberta and Pardue 2003; Pardue and DeBaryshe 2003)
R1 and R2 LINE element retrotransposons	Insertion in arthropod ribosomal 28S coding sequences (sequence-specific homing endonuclease)	(Xiong, Burke et al. 1988; Xiong and Eickbush 1988; Xiong and Eickbush 1988; Burke, Malik et al. 1989)
Group I homing introns (DNA based)	Site-specific insertion into coding sequences in bacteria and eukaryotes (sequence-specific endonuclease)	(Belfort and Perlman 1995)
Group II homing introns (RNA based)	Site-specific insertion into coding sequences in bacteria and eukaryotes (RNA recognition of DNA sequence motifs, reverse transcription)	(Mohr, Smith et al. 2000; Karberg, Guo et al. 2001)
Group II intron retroelements	Insertion after intrinsic transcriptional terminators.	(Robart, Seo et al. 2007)

Homologous recombination

(Martini and Keeney 2002; Nishant and Rao 2006; Nicolas 2009; Parvanov, Ng et al. 2009; Ding, Haraguchi et al. 2010; Getun, Wu et al. 2010; Paigen and Petkov 2010; Szekvolgyi and Nicolas 2010; Wahls and Davidson 2010; Grey, Sommermeyer et al. 2011; Segurel, Leffler et al. 2011)

Chromosome fragile sites

(Le Beau 1986; Yunis 1987; Moriarty and Webster 2003; Ishii and Furukawa 2004; Arlt, Durkin et al. 2006; Glover 2006; O'Keefe and Richards 2006; Durkin and Glover 2007; Ruiz-Herrera and Robinson 2007; Smith, McAvoy et al. 2007; Pichiorri, Ishii et al. 2008; Burrow, Williams et al. 2009; Casper, Greenwell et al. 2009; Gericke 2010)

Viral integration

(Barr, Ciuffi et al. 2006; Moalic, Blanchard et al. 2006; Derse, Crise et al. 2007; Albanese, Arosio et al. 2008; Brady, Lee et al. 2009; Santoni, Hartley et al. 2010)

Agrobacterium T-DNA insertion

(Pelczar, Kalck et al. 2004; Muller, Atkinson et al. 2007; Lacroix and Citovsky 2009)

Diversity-generating retroelements

(Doulatov, Hodes et al. 2004; Medhekar and Miller 2007; Guo, Tse et al. 2008; Kojima and Kanehisa 2008; Miller, Le Coq et al. 2008; Baucom, Estill et al. 2009; Baucom, Estill et al. 2009; Guo, Tse et al. 2011)

Group II retrohoming introns

(Mohr, Smith et al. 2000; Karberg, Guo et al. 2001; Dai and Zimmerly 2002; Zhong, Karberg et al. 2003; Jones, Kierlin et al. 2005; Yao and Lambowitz 2007; Mastroianni, Watanabe et al. 2008; Toor, Rajashankar et al. 2008; Zhuang, Mastroianni et al. 2009)

DNA transposition

(Craig 1991; Wolkow, DeBoy et al. 1996; Ketting, Fischer et al. 1997; Akagi, Yokozeki et al. 2001; Lee, Neiditch et al. 2002; Timakov, Liu et al. 2002; Preclin, Martin et al. 2003; Tsai, Chatterji et al. 2003; Loot, Turlan et al. 2004; Walser, Chen et al. 2006; Kiss, Nagy et al. 2007; Linheiro and Bergman 2008; Chandler 2009; Liu, Yeh et al. 2009; Post and Hall 2009; Zhang and Saier 2009; Gangadharan, Mularoni et al. 2010; Levy, Schwartz et al. 2010; Rawal and Ramaswamy 2011)

Tn7: (Nnalue 1990; Craig 1991; Hagemann and Craig 1993; Wolkow, DeBoy et al. 1996; Peters and Craig 2000; Peters and Craig 2001; Finn, Parks et al. 2007; Shi, Parks et al. 2008; Parks and Peters 2009)

Retrovirus and retrotransposon insertion

(Zou and Voytas 1997; Cost and Boeke 1998; Jurka, Klonowski et al. 1998; Huang, Hong et al. 1999; Szafranski, Glockner et al. 1999; Beck, Dingermann et al. 2002; De Palma, Montini et al. 2005; Johnson and Levy 2005; Repanas, Zingler et al. 2007; Brady, Fuerst et al. 2008; Hare and Cherepanov 2009; Levy, Schwartz et al. 2010; Santoni, Hartley et al. 2010; Rawal and Ramaswamy 2011; Siol, Spaller et al. 2011)

Somatic hypermutation and class switching

(Chaudhuri, Tian et al. 2003; Odegard, Kim et al. 2005; Odegard and Schatz 2006; Yang and Schatz 2007; Hackney, Misaghi et al. 2009; Maul and Gearhart 2010; Maul and Gearhart 2010; Tanaka, Shen et al. 2010)

Ciliate macronuclear rearrangements: (Gortz, Kuhlmann et al. 1999; Prescott 2000; Betermier 2004; Juranek and Lipps 2007; Lepere, Betermier et al. 2008; Baudry, Malinsky et al. 2009; Duharcourt, Lepere et al. 2009; Clark 2010)

Synthetic targeting: (Beck, Dingermann et al. 2002; Sandrin, Russell et al. 2003; Egli, Hafen et al. 2004; Hematti, Hong et al. 2004; Horn and Handler 2005; Ciuffi, Diamond et al. 2006; Garcia-Otin and Guillou 2006; Cui and Davis 2007; Ivics, Katzer et al. 2007; Frecha, Szecsi et al. 2008; Voigt, Izsvak et al. 2008; Yu and Kim 2008; Ziegler, Yang et al. 2008; Cai, Doyon et al. 2009; Deyle and Russell 2009; Feng, Bednarz et al. 2009; Foley, Yeh et al. 2009; Galvan, Nakazawa et al. 2009; Kim, Lee et al. 2009; Weng, Chen et al. 2009; Christian, Cermak et al. 2010; Craigie 2010; Karan, Frederick et al. 2010; Lim, Klimczak et al. 2010; Urnov, Rebar et al. 2010; Vasquez 2010; Weinthal, Tovkach et al. 2010; Zhang, Kutner et al. 2010; Bogdanove and Voytas 2011; Huda, Bowen et al. 2011; Li, Huang et al. 2011; Mahfouz, Li et al. 2011)