TY - JOUR
T1 - Genome-wide purification of extrachromosomal circular DNA from eukaryotic cells
AU - Møller, Henrik D.
AU - Bojsen, Rasmus Kenneth
AU - Tachibana, Chris
AU - Parsons, Lance
AU - Botstein, David
AU - Regenberg, Birgitte
PY - 2016/2/12
Y1 - 2016/2/12
N2 - Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are found in other eukaryotes. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and environmental and biological factors that induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, high-throughput sequencing, and mapping. Extensive exonuclease treatment (more than 100 units) was typically required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by #29 polymerase enriched for circular DNA over linear DNA. Validation of theCircle-Seq method on three S. cerevisiae CEN.PK populations of 1010 cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30,HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
AB - Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are found in other eukaryotes. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and environmental and biological factors that induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, high-throughput sequencing, and mapping. Extensive exonuclease treatment (more than 100 units) was typically required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by #29 polymerase enriched for circular DNA over linear DNA. Validation of theCircle-Seq method on three S. cerevisiae CEN.PK populations of 1010 cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30,HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
U2 - 10.3791/54239
DO - 10.3791/54239
M3 - Journal article
C2 - 27077531
SN - 1940-087X
JO - Journal of Visualized Experiments
JF - Journal of Visualized Experiments
IS - 110
M1 - e54239
ER -