The researchers speculated that this interaction data, because it offers clues about the position of and distances between various regions of the chromosome, might reveal how DNA sequences are grouped and lined up along entire chromosomes. They wondered if the interaction data could show them which regions of the genome are near each other on each chromosome.
Their investigation of this possibility led them to create what they named LACHESIS (an acronym for "ligating adjacent chromatin enables scaffolding in situ"). The map of physical interactions generated by Hi-C was interpreted by the LACHESIS computational program to assign, order and orient genomic sequences into their correct position along chromosomes, including DNA positioned close to the centromere, the "pinch waist" gap in the chromosome shape.
The researchers combined their new approach with other cheap and widely used sequencing methods to generate chromosome-scale assemblies of the human, mouse and fruit fly genomes. The researchers were able to cluster nearly all scaffolds -- collections of short DNA segments whose position relative to each other is unknown -- into groups that corresponded to individual chromosomes.
They then ordered and oriented the scaffolds assigned to each chromosome group, and validated their results by comparing them to the high-quality reference genomes for these species that were generated by the Human Genome Project. In the case of human genomes, they achieved 98 percent accuracy in assigning tens of thousands of sequences of contiguous DNA to chromosome groups and 99 percent accuracy in ordering and orienting these sequences within chromosome groups.
"We think the method may fundamentally change how
|Contact: Leila Gray|
University of Washington