Molecular and experimental tools to design synthetic enhancers
I Vaknin, R Amit - Current Opinion in Biotechnology, 2022 - Elsevier
I Vaknin, R Amit
Current Opinion in Biotechnology, 2022•ElsevierHighlights•Characterized enhancer elements are in need for basic research, the pharma
and biotech industries.•Designing multiple synthetic enhancers in parallel is possible due to
oligo libraries technology.•Nowadays, DNA oligo library synthesis technologies capable of
various and complex library designs.•Oligo libraries are screened and tested using
massively parallel reporter assays.•A deep learning approach, with experimental data, can
be used to predict better enhancer candidates.Understanding the grammar of enhancers …
and biotech industries.•Designing multiple synthetic enhancers in parallel is possible due to
oligo libraries technology.•Nowadays, DNA oligo library synthesis technologies capable of
various and complex library designs.•Oligo libraries are screened and tested using
massively parallel reporter assays.•A deep learning approach, with experimental data, can
be used to predict better enhancer candidates.Understanding the grammar of enhancers …
Highlights
- Characterized enhancer elements are in need for basic research, the pharma and biotech industries.
- Designing multiple synthetic enhancers in parallel is possible due to oligo libraries technology.
- Nowadays, DNA oligo library synthesis technologies capable of various and complex library designs.
- Oligo libraries are screened and tested using massively parallel reporter assays.
- A deep learning approach, with experimental data, can be used to predict better enhancer candidates.
Understanding the grammar of enhancers and how they regulate gene expression is key for both basic research and for the pharma and biotech industries. The design and characterization of synthetic enhancers can expand the known regulatory space. This is achieved by the utilization of DNA Oligo Libraries (OLs), which facilitates screening of as many as millions of synthetic enhancer variants simultaneously. This review includes the latest commercial DNA OL synthesis technology and its capabilities, and a general ‘know-how’guide for the design, construction, and analysis of OL-based synthetic enhancer characterization experiments. Specifically, we focus on synthetic-enhancer-based massively parallel reporter assay, Sort-seq methodologies (eg flow cytometry, deep sequencing), and a brief description of machine learning-based attempts for OL-analysis and follow-up validation experiments.
Elsevier
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