Efficient assembly of de novo human artificial chromosomes from large genomic loci.
BACKGROUND
Human artificial chromosomes (HACs) are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb) genomic loci have been reported to be successfully packaged into de novo HACs.


RESULTS
We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs) for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100-200 kb) genomic loci including therapeutically significant genes for human growth hormone (HGH), polycystic kidney disease (PKD1) and beta-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained beta-globin gene expression from HACs incorporating the entire 200 kb beta-globin genomic locus for over 90 days in the absence of selection.


CONCLUSIONS
Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci may be useful for identifying discrete functional elements that may be incorporated into future generations of HAC vectors.
Basu
Joydeep
J
Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA. joydeep.basu@duke.edu
Compitello
George
G
Stromberg
Gregory
G
Willard
Huntington F
HF
Van Bokkelen
Gil
G
D001709:Biotechnology / Q000379:methods*; D002460:Cell Line; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D022222:Chromosomes, Artificial, Human / Q000235:genetics*; D003001:Cloning, Molecular; D004247:DNA; D004276:DNA, Satellite; D005347:Fibroblasts / Q000166:cytology; D018014:Gene Transfer Techniques; D005821:Genetic Techniques; D005822:Genetic Vectors; D016678:Genome; D005914:Globins / Q000235:genetics; D019382:Human Growth Hormone / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008856:Microscopy, Fluorescence; D008957:Models, Genetic; D007690:Polycystic Kidney Diseases / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014162:Transfection
D004276:DNA, Satellite; D012333:RNA, Messenger; D019382:Human Growth Hormone; D005914:Globins; D004247:DNA