Title:	SHIP identifies genomic safe harbors in eukaryotic organisms using genomic general feature annotation.
Authors:	LEITÃO, M. de C. CABRAL, L. S. PIVA, L. C. QUEIROZ, P. F. de S. GOMES, T. G. ANDRADE, R. V. de PEREZ, A. L. A. PAIVA, K. L. R. de BÁO, S. N. REIS, V. C. B. MORAES, L. M. P. TOGAWA, R. C. BARROS, L. M. G. TORRES, F. A. G. PAPPAS JÚNIOR, G. J. COELHO, C. M.
Affiliation:	MATHEUS DE CASTRO LEITÃO, UNIVERSITY OF BRASILIA; LETÍCIA SOUSA CABRAL, UNIVERSITY OF BRASILIA; LUIZA CESCA PIVA, UNIVERSITY OF BRASILIA; PEDRO FELIPE DE SOUSA QUEIROZ, UNIVERSITY OF BRASILIA; TAÍSA GODOY GOMES, UNIVERSITY OF BRASILIA; ROSÂNGELA VIEIRA DE ANDRADE, CATHOLIC UNIVERSITY OF BRASILIA; ANA LAURA ALFONSO PEREZ, UNIVERSITY OF BRASILIA; KAREN LETYCIA RODRIGUES DE PAIVA, UNIVERSITY OF BRASILIA; SÔNIA NAIR BÁO, UNIVERSITY OF BRASILIA; VIVIANE CASTELO BRANCO REIS, UNIVERSITY OF BRASILIA; LÍDIA MARIA PEPE MORAES, UNIVERSITY OF BRASILIA; ROBERTO COITI TOGAWA, CENARGEN; LEILA MARIA GOMES BARROS, CENARGEN; FERNANDO ARARIPE GONÇALVES TORRES, UNIVERSITY OF BRASILIA; GEORGIOS JOANNIS PAPPAS JÚNIOR, UNIVERSITY OF BRASILIA; CÍNTIA MARQUES COELHO, UNIVERSITY OF BRASILIA.
Date Issued:	2025
Citation:	Scientific Reports, v. 15, 7193 2025.
Description:	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.
Keywords:	GSHs Chassi Saccharomyces cerevisiae SHIP Eukaryotic organisms
DOI:	https://doi.org/10.1038/s41598-025-91249-9
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Artigo em periódico indexado (CENARGEN)