There is an increasing interest in understanding how three-dimensional(3D)organization of the genome is regulated.Different strategies have been employed to identify genome-wide chromatin interactions.However,due to c...There is an increasing interest in understanding how three-dimensional(3D)organization of the genome is regulated.Different strategies have been employed to identify genome-wide chromatin interactions.However,due to current limitations in resolving genomic contacts,visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date.Here,we describe Tn5 transposase-based Fluorescencein situhybridization(Tn5-FISH),a PCR-based,cost-effective imaging method,which can co-localize the genomic loci with sub-kilobase resolution,dissect genome architecture,and verify chromatin interactions detected by chromatin configuration capture(3C)-derived methods.To validate this method,short-range interactions in keratin-encoding gene(KRT)locus in topologically associated domain(TAD)were imaged by triple-color Tn5-FISH,indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD.Therefore,Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.展开更多
基金This work was supported in part by the State Key Research Development Program of China(2017YFA0505503)the National Natural Science Foundation of China(81890991 and 31671383)+4 种基金Beijing Advanced Innovation Center for Structural Bio logy,Tsinghua University(100300001)the fund from Foshan-Tsinghua Innovation Special Fund(FTISF,2019THFS0141)to J.G.,the National Natural Science Foundation of China(31871444)the program for Guangdong Introducing Innovative and Entrepreneurial Teams(2016ZT06S029)to J.W.Australia China Science and Research Fund Joint Research Centre for POCT(ACSRF65827)Shenzhen Science and Technology Program(KQTD 20170810110913065)to D.J.
文摘There is an increasing interest in understanding how three-dimensional(3D)organization of the genome is regulated.Different strategies have been employed to identify genome-wide chromatin interactions.However,due to current limitations in resolving genomic contacts,visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date.Here,we describe Tn5 transposase-based Fluorescencein situhybridization(Tn5-FISH),a PCR-based,cost-effective imaging method,which can co-localize the genomic loci with sub-kilobase resolution,dissect genome architecture,and verify chromatin interactions detected by chromatin configuration capture(3C)-derived methods.To validate this method,short-range interactions in keratin-encoding gene(KRT)locus in topologically associated domain(TAD)were imaged by triple-color Tn5-FISH,indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD.Therefore,Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.