Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.
Nucleic Acids Res
; 52(4): 1613-1627, 2024 Feb 28.
Article
en En
| MEDLINE
| ID: mdl-38296821
ABSTRACT
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.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Secuencias Reguladoras de Ácidos Nucleicos
/
Técnicas Genéticas
Tipo de estudio:
Prognostic_studies
Idioma:
En
Año:
2024
Tipo del documento:
Article