"Nuclear DNA is where all the biology is," said Noonan, a post-doctoral fellow in Rubin's research group who holds joint appointments with Berkeley Lab and JGI. "If you want to understand how traits like language and cognition are encoded, you have to study nuclear DNA."
Studying ancient genomes from fossilized material by directly sequencing the DNA, as has been done for the genomes of humans and other contemporary organisms, represents a major challenge. As a fossil ages, its DNA is degraded by chemical processes. It also becomes contaminated with DNA from the microbes that colonize both the fossil and its immediate environment, and by other organisms, including the humans who handle the fossil.
While a group led by co-author Pbo is attempting to directly sequence the Neanderthal genome, Rubin, Noonan and their colleagues are meeting the fossilized DNA challenge with a unique solution that's been described as a "targeted approach." Essentially, they "immortalize" all of the DNA in a fossil sample into metagenomic libraries where individual fragments of the ancient DNA are propagated in microbes. The DNA propagated in the microbes can either be sequenced or specific sequences can in a targeted manner be specifically fished out of the library and studied.
Said Noonan, "Since direct sequencing is random, you can't go after specific sequences for genes that might be different between humans and Neanderthals. Instead you
have to wait for the sequences to show up in the reads, which could take a long time. Also, with direct sequencing,
once the DNA has been sequenced, it's gone, and you have to go get more from the s
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Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
15-Nov-2006