Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.

Autor:	Liu J; Graduate Program in Cell & Developmental Biology, Rutgers, The State University of New Jersey, 604 Allison Rd, Piscataway, NJ 08854, USA.; Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA.; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, Piscataway, NJ 08854, USA., Ashuach T; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, 387 Soda Hall, Berkeley, CA 94720, USA., Inoue F; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Faculty of Medicine Building B, Yoshidatachibanacho, Sakyo Ward, Kyoto 606-8303, Japan., Ahituv N; Department of Bioengineering and Therapeutic Sciences, University of California, 1700 4th Street, San Francisco, CA 94158, USA.; Institute for Human Genetics, University of California, 513 Parnassus Ave, San Francisco, CA 94143, USA., Yosef N; Department of Systems Immunology, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel.; Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.; Department of Systems Immunology, Ragon Institute of MGH, MIT, and Harvard Institute of Science, 400 Technology Square, Cambridge, MA 02139, USA., Kreimer A; Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA.; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, Piscataway, NJ 08854, USA.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Feb 28; Vol. 52 (4), pp. 1613-1627.
DOI:	10.1093/nar/gkae012
Abstrakt:	The advent of perturbation-based massively parallel reporter assays (MPRAs) technique has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant to evaluate and establish guidelines for sequence design strategies for perturbation MPRAs. In this study, we propose a framework for evaluating and comparing various perturbation strategies for MPRA experiments. Within this framework, we benchmark three different perturbation approaches from the perspectives of alteration in motif-based profiles, consistency of MPRA outputs, and robustness of models that predict the activities of putative regulatory motifs. While our analyses show very similar results across multiple benchmarking metrics, the predictive modeling for the approach involving random nucleotide shuffling shows significant robustness compared with the other two approaches. Thus, we recommend designing sequences by randomly shuffling the nucleotides of the perturbed site in perturbation-MPRA, followed by a coherence check to prevent the introduction of other variations of the target motifs. In summary, our evaluation framework and the benchmarking findings create a resource of computational pipelines and highlight the potential of perturbation-MPRA in predicting non-coding regulatory activities. (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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