SHIP identifies genomic safe harbors in eukaryotic organisms using genomic general feature annotation.

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Tác giả: Sônia Nair Báo, Leila Maria Gomes Barros, Letícia Sousa Cabral, Cíntia Marques Coelho, Rosângela Vieira de Andrade, Karen Letycia Rodrigues de Paiva, Taísa Godoy Gomes, Matheus de Castro Leitão, Lídia Maria Pepe Moraes, Georgios Joannis Pappas Júnior, Ana Laura Alfonso Perez, Luiza Cesca Piva, Pedro Felipe de Sousa Queiroz, Viviane Castelo Branco Reis, Roberto Coiti Togawa, Fernando Araripe Gonçalves Torres

Ngôn ngữ: eng

Ký hiệu phân loại:

Thông tin xuất bản: England : Scientific reports , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 734171

Integrating foreign genes into loci, allowing their transcription without affecting endogenous gene expression, is the desirable strategy in genomic engineering. However, these loci, known as genomic safe harbors (GSHs), have been mainly identified by empirical methods. Furthermore, the most prominent available GSHs are localized within regions of high gene density, raising concerns about unstable expression. As synthetic biology is moving towards investigating polygenic modules rather than single genes, there is an increasing demand for tools to identify GSHs systematically. To expand the GSH repertoire, we present SHIP, an algorithm designed to detect potential GSHs in eukaryotes. Using the chassis organism Saccharomyces cerevisiae, five GSHs were experimentally curated based on data from DNA sequencing, stability, flow cytometry, qPCR, electron microscopy, RT-qPCR, and RNA-Seq assays. Our study places SHIP as a valuable tool for providing a list of promising candidates to assist in the experimental assessment of GSHs in eukaryotic organisms with available annotated genomes.
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