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New tools speed genome assembly, tests of gene function

by  /  23 March 2018
water droplets contain and concentrate the materials needed to synthesize genes.
Clean capture: In a new method, water droplets contain and concentrate the materials needed to synthesize genes.

ktsimage / iStock

Two new techniques could help reveal the molecular basis of conditions such as autism.

One of them provides a way to quickly sequence and assemble an entire genome1. The other helps scientists synthesize thousands of versions of a single gene to test its function2.

Typically, genome sequencing involves spelling out short segments of DNA, or ‘reads,’ and piecing them together to reconstruct the genome. But repetitive sequences that are similar or identical to those elsewhere in the genome can yield errors.

In one of the new methods, researchers combined careful extraction and handling of DNA with a state-of-the art portable sequencing device to produce a more accurate and complete genome sequence.

They first used various existing tools to carefully extract long sections of DNA from human blood cells. They analyzed the samples with a commercially available pocket-sized sequencing device called the MinION nanopore sequencer.

The combination produces reads up to 80 times the length of those produced by other methods. The longer reads enabled the researchers to bridge 12 gaps in the reference human genome.

The final result is the most complete contiguous human genome to date using a single sequencing method, the researchers wrote 29 January in Nature Biotechnology.

Beaded batch:

Another team has invented a way of efficiently creating many mutated versions of a single gene.

In the method, researchers first suspend short segments of DNA called oligos and tiny plastic beads in water. The beads are covered with DNA segments that stick only to the oligos needed to build a particular gene. The beads have a barcode that identifies the oligos as part of a specific gene.

The researchers add oil to create a mixture of water droplets encasing the beads with their attached oligos, concentrating the parts needed to build genes. They then add enzymes that release the barcoded oligos from the beads and assemble them into full-length genes.

Using oligos of varying lengths enables researchers to introduce many mutations into the final sequences. And the method drops the cost of a synthetic gene to less than $2, compared with $50 to $150 for a comparable gene from commercial suppliers.

The researchers tested their method on versions of two genes found in the bacterium Escherichia coli. They generated 5,775 mutated versions of a gene that helps with protein synthesis and 1,152 versions of a gene that helps build bacterial cell walls. And they were able to identify which regions of each gene are key to that gene’s function.

The approach, described 19 January in Science, could reveal how specific mutations disable genes linked to conditions such as autism.


References:
  1. Jain M. et al. Nat. Biotechnol. Epub ahead of print (2018) PubMed
  2. Plesa C. et al. Science 359, 343-347 (2018) PubMed
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