High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors.

Autor:	Crawford KD; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA., Khan AG; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA., Lopez SC; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA., Goodarzi H; Arc Institute, Palo Alto, CA, USA.; Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.; Department of Urology, University of California, San Francisco, CA, USA., Shipman SL; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.; Chan Zuckerberg Biohub, San Francisco, CA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 09. Date of Electronic Publication: 2024 Jul 09.
DOI:	10.1101/2024.07.08.602561
Abstrakt:	The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applications. In these technologies, a natural retron non-coding RNA (ncRNA) is modified to encode a template for the production of custom DNA sequences by reverse transcription. The efficiency of reverse transcription is a major limiting step for retron technologies, but we lack systematic knowledge of how to improve or maintain reverse transcription efficiency while changing the retron sequence for custom DNA production. Here, we test thousands of different modifications to the retron-Eco1 ncRNA and measure DNA production in pooled variant library experiments, identifying regions of the ncRNA that are tolerant and intolerant to modification. We apply this new information to a specific application: the use of the retron to produce a precise genome editing donor in combination with a CRISPR-Cas9 RNA-guided nuclease (an editron). We use high-throughput libraries in S. cerevisiae to additionally define design rules for editrons. We extend our new knowledge of retron DNA production and editron design rules to human genome editing to achieve the highest efficiency retron-Eco1 editrons to date. Competing Interests: Competing Interests S. L. S. is a co-founder of Retronix Bio and Sprint synthesis.
Databáze:	MEDLINE
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