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Genetic engineering: Lassoing genomic libraries

Nature Biomedical Engineering volume 1, Article number: 0098 (2017) Cite this article

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Long single-stranded DNA probes enable the capture and multiplexed cloning of DNA at the megabase scale.

Determining the relationships between DNA sequence and function is central for understanding and engineering biology. Technologies that improve the ability to explore these relationships are thus broadly enabling. Recently, the development of a suite of multiplexed assays has allowed the search for individual biological functions in thousands of DNA sequences in a single pooled experiment1. In general, these methods use barcoding, that is, the addition of a short DNA tag that uniquely identifies a particular DNA sequence and ties that sequence to its function via next-generation sequencing (NGS). For example, massively parallel reporter assays were first developed to examine enhancers and promoters of transcription2,3. By linking each variant to be tested to a barcoded transcript, NGS can measure the relative RNA expression levels of all the barcodes in the library, thereby mapping the strength of each promoter or enhancer. In this manner, a pooled set of thousands of DNA constructs can be evaluated in a single experiment. Since then, many other multiplexed assays have been developed to examine DNA fragments controlling transcription, translation, mRNA stability, splicing, protein function, and other genetic processes4,5.

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Figure 1: DNA libraries used in multiplexed assays.
Figure 2: Target capture via a LASSO probe.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, UCLA, Charles E. Young Drive, Los Angeles, 90095, California, USA

    Nathan B. Lubock & Sriram Kosuri

  2. UCLA-DOE Institute of Genomics and Proteomics, Charles E. Young Drive, Los Angeles, 90095, California, USA

    Nathan B. Lubock & Sriram Kosuri

  3. Molecular Biology Institute, Charles E. Young Drive, Los Angeles, 90095, California, USA

    Nathan B. Lubock & Sriram Kosuri

Authors
  1. Nathan B. Lubock
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  2. Sriram Kosuri
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Correspondence to Sriram Kosuri.

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Lubock, N., Kosuri, S. Genetic engineering: Lassoing genomic libraries. Nat Biomed Eng 1, 0098 (2017). https://doi.org/10.1038/s41551-017-0098

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