Synthetic chromosome evolves the yeast genome
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摘要
<正>Genomic structural variations play a critical role in biological function and phenotypic diversity. Although smallscale variations, such as insertion, deletion, and point mutations, have been extensively investigated, studies on largescale structural variations such as segmental duplication,inversion, and chromosome-scale variations remain limited.In the recent decade, with the development of synthetic
引文
Blount,B.A.,Gowers,G.O.F.,Ho,J.C.H.,Ledesma-Amaro,R.,Jovicevic,D.,McKiernan,R.M.,Xie,Z.X.,Li,B.Z.,Yuan,Y.J.,and Ellis,T.(2018).Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome.Nat Commun 9,1932.
Dymond,J.S.,Richardson,S.M.,Coombes,C.E.,Babatz,T.,Muller,H.,Annaluru,N.,Blake,W.J.,Schwerzmann,J.W.,Dai,J.,Lindstrom,D.L.,et al.(2011).Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.Nature 477,471-476.
Jia,B.,Wu,Y.,Li,B.Z.,Mitchell,L.A.,Liu,H.,Pan,S.,Wang,J.,Zhang,H.R.,Jia,N.,Li,B.,et al.(2018).Precise control of SCRaMbLE in synthetic haploid and diploid yeast.Nat Commun 9,1933.
Hochrein,L.,Mitchell,L.A.,Schulz,K.,Messerschmidt,K.,and MuellerRoeber,B.(2018).L-SCRaMbLE as a tool for light-controlled Cremediated recombination in yeast.Nat Commun 9,1931.
Li,Y.X.,Wu,Y.,Ma,L.,Guo,Z.,Xiao,W.H.,Yuan,Y.J.(2019).Loss of heterozygosity by SCRaMbLEing.Sci China Life Sci 62,381-393.
Liu,W.,Luo,Z.,Wang,Y.,Pham,N.T.,Tuck,L.,Pérez-Pi,I.,Liu,L.,Shen,Y.,French,C.,Auer,M.,et al.(2018).Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods.Nat Commun 9,1936.
Luo,Z.,Wang,L.,Wang,Y.,Zhang,W.,Guo,Y.,Shen,Y.,Jiang,L.,Wu,Q.,Zhang,C.,Cai,Y.,et al.(2018).Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES.Nat Commun 9,1930.
Mitchell,L.A.,Wang,A.,Stracquadanio,G.,Kuang,Z.,Wang,X.,Yang,K.,Richardson,S.,Martin,J.A.,Zhao,Y.,Walker,R.,et al.(2017).Synthesis,debugging,and effects of synthetic chromosome consolidation:synVI and beyond.Science 355,eaaf4831.
Richardson,S.M.,Mitchell,L.A.,Stracquadanio,G.,Yang,K.,Dymond,J.S.,DiCarlo,J.E.,Lee,D.,Huang,C.L.V.,Chandrasegaran,S.,Cai,Y.,et al.(2017).Design of a synthetic yeast genome.Science 355,1040-1044.
Shen,M.J.,Wu,Y.,Yang,K.,Li,Y.,Xu,H.,Zhang,H.,Li,B.Z.,Li,X.,Xiao,W.H.,Zhou,X.,et al.(2018).Heterozygous diploid and interspecies SCRaMbLEing.Nat Commun 9,1934.
Shen,Y.,Stracquadanio,G.,Wang,Y.,Yang,K.,Mitchell,L.A.,Xue,Y.,Cai,Y.,Chen,T.,Dymond,J.S.,Kang,K.,et al.(2016).SCRaMbLEgenerates designed combinatorial stochastic diversity in synthetic chromosomes.Genome Res 26,36-49.
Shen,Y.,Wang,Y.,Chen,T.,Gao,F.,Gong,J.,Abramczyk,D.,Walker,R.,Zhao,H.,Chen,S.,Liu,W.,et al.(2017).Deep functional analysis of synII,a 770-kilobase synthetic yeast chromosome.Science 355,eaaf4791.
Wang,J.,Xie,Z.X.,Ma,Y.,Chen,X.R.,Huang,Y.Q.,He,B.,Bin Jia,B.,Li,B.Z.,and Yuan,Y.J.(2018).Ring synthetic chromosome VSCRaMbLE.Nat Commun 9,3783.
Wu,Y.,Li,B.Z.,Zhao,M.,Mitchell,L.A.,Xie,Z.X.,Lin,Q.H.,Wang,X.,Xiao,W.H.,Wang,Y.,Zhou,X.,et al.(2017).Bug mapping and fitness testing of chemically synthesized chromosome X.Science 355,eaaf4706.
Wu,Y.,Zhu,R.Y.,Mitchell,L.A.,Ma,L.,Liu,R.,Zhao,M.,Jia,B.,Xu,H.,Li,Y.X.,Yang,Z.M.,et al.(2018).In vitro DNA SCRaMbLE.Nat Commun 9,1935.
Xie,Z.X.,Li,B.Z.,Mitchell,L.A.,Wu,Y.,Qi,X.,Jin,Z.,Jia,B.,Wang,X.,Zeng,B.X.,Liu,H.M.,et al.(2017).“Perfect”designer chromosome Vand behavior of a ring derivative.Science 355,eaaf4704.
Zhang,W.,Zhao,G.,Luo,Z.,Lin,Y.,Wang,L.,Guo,Y.,Wang,A.,Jiang,S.,Jiang,Q.,Gong,J.,et al.(2017).Engineering the ribosomal DNA in a megabase synthetic chromosome.Science 355,eaaf3981.
Dymond,J.S.,Richardson,S.M.,Coombes,C.E.,Babatz,T.,Muller,H.,Annaluru,N.,Blake,W.J.,Schwerzmann,J.W.,Dai,J.,Lindstrom,D.L.,et al.(2011).Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.Nature 477,471-476.
Jia,B.,Wu,Y.,Li,B.Z.,Mitchell,L.A.,Liu,H.,Pan,S.,Wang,J.,Zhang,H.R.,Jia,N.,Li,B.,et al.(2018).Precise control of SCRaMbLE in synthetic haploid and diploid yeast.Nat Commun 9,1933.
Hochrein,L.,Mitchell,L.A.,Schulz,K.,Messerschmidt,K.,and MuellerRoeber,B.(2018).L-SCRaMbLE as a tool for light-controlled Cremediated recombination in yeast.Nat Commun 9,1931.
Li,Y.X.,Wu,Y.,Ma,L.,Guo,Z.,Xiao,W.H.,Yuan,Y.J.(2019).Loss of heterozygosity by SCRaMbLEing.Sci China Life Sci 62,381-393.
Liu,W.,Luo,Z.,Wang,Y.,Pham,N.T.,Tuck,L.,Pérez-Pi,I.,Liu,L.,Shen,Y.,French,C.,Auer,M.,et al.(2018).Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods.Nat Commun 9,1936.
Luo,Z.,Wang,L.,Wang,Y.,Zhang,W.,Guo,Y.,Shen,Y.,Jiang,L.,Wu,Q.,Zhang,C.,Cai,Y.,et al.(2018).Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES.Nat Commun 9,1930.
Mitchell,L.A.,Wang,A.,Stracquadanio,G.,Kuang,Z.,Wang,X.,Yang,K.,Richardson,S.,Martin,J.A.,Zhao,Y.,Walker,R.,et al.(2017).Synthesis,debugging,and effects of synthetic chromosome consolidation:synVI and beyond.Science 355,eaaf4831.
Richardson,S.M.,Mitchell,L.A.,Stracquadanio,G.,Yang,K.,Dymond,J.S.,DiCarlo,J.E.,Lee,D.,Huang,C.L.V.,Chandrasegaran,S.,Cai,Y.,et al.(2017).Design of a synthetic yeast genome.Science 355,1040-1044.
Shen,M.J.,Wu,Y.,Yang,K.,Li,Y.,Xu,H.,Zhang,H.,Li,B.Z.,Li,X.,Xiao,W.H.,Zhou,X.,et al.(2018).Heterozygous diploid and interspecies SCRaMbLEing.Nat Commun 9,1934.
Shen,Y.,Stracquadanio,G.,Wang,Y.,Yang,K.,Mitchell,L.A.,Xue,Y.,Cai,Y.,Chen,T.,Dymond,J.S.,Kang,K.,et al.(2016).SCRaMbLEgenerates designed combinatorial stochastic diversity in synthetic chromosomes.Genome Res 26,36-49.
Shen,Y.,Wang,Y.,Chen,T.,Gao,F.,Gong,J.,Abramczyk,D.,Walker,R.,Zhao,H.,Chen,S.,Liu,W.,et al.(2017).Deep functional analysis of synII,a 770-kilobase synthetic yeast chromosome.Science 355,eaaf4791.
Wang,J.,Xie,Z.X.,Ma,Y.,Chen,X.R.,Huang,Y.Q.,He,B.,Bin Jia,B.,Li,B.Z.,and Yuan,Y.J.(2018).Ring synthetic chromosome VSCRaMbLE.Nat Commun 9,3783.
Wu,Y.,Li,B.Z.,Zhao,M.,Mitchell,L.A.,Xie,Z.X.,Lin,Q.H.,Wang,X.,Xiao,W.H.,Wang,Y.,Zhou,X.,et al.(2017).Bug mapping and fitness testing of chemically synthesized chromosome X.Science 355,eaaf4706.
Wu,Y.,Zhu,R.Y.,Mitchell,L.A.,Ma,L.,Liu,R.,Zhao,M.,Jia,B.,Xu,H.,Li,Y.X.,Yang,Z.M.,et al.(2018).In vitro DNA SCRaMbLE.Nat Commun 9,1935.
Xie,Z.X.,Li,B.Z.,Mitchell,L.A.,Wu,Y.,Qi,X.,Jin,Z.,Jia,B.,Wang,X.,Zeng,B.X.,Liu,H.M.,et al.(2017).“Perfect”designer chromosome Vand behavior of a ring derivative.Science 355,eaaf4704.
Zhang,W.,Zhao,G.,Luo,Z.,Lin,Y.,Wang,L.,Guo,Y.,Wang,A.,Jiang,S.,Jiang,Q.,Gong,J.,et al.(2017).Engineering the ribosomal DNA in a megabase synthetic chromosome.Science 355,eaaf3981.