DeepFM-Crispr: Prediction of CRISPR On-Target Effects via Deep Learning

• URL: http://arxiv.org/abs/2409.05938v1
• Date: Mon, 9 Sep 2024 17:33:54 GMT
• Title: DeepFM-Crispr: Prediction of CRISPR On-Target Effects via Deep Learning
• Authors: Condy Bao, Fuxiao Liu,
• Abstract summary: DeepFM-Crispr is a novel deep learning model developed to predict the on-target efficiency and evaluate the off-target effects of Cas13d. It harnesses a large language model to generate comprehensive representations rich in evolutionary and structural data, thereby enhancing predictions of RNA secondary structures and overall sgRNA efficacy.
• Score: 0.24554686192257422
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: Since the advent of CRISPR-Cas9, a groundbreaking gene-editing technology that enables precise genomic modifications via a short RNA guide sequence, there has been a marked increase in the accessibility and application of this technology across various fields. The success of CRISPR-Cas9 has spurred further investment and led to the discovery of additional CRISPR systems, including CRISPR-Cas13. Distinct from Cas9, which targets DNA, Cas13 targets RNA, offering unique advantages for gene modulation. We focus on Cas13d, a variant known for its collateral activity where it non-specifically cleaves adjacent RNA molecules upon activation, a feature critical to its function. We introduce DeepFM-Crispr, a novel deep learning model developed to predict the on-target efficiency and evaluate the off-target effects of Cas13d. This model harnesses a large language model to generate comprehensive representations rich in evolutionary and structural data, thereby enhancing predictions of RNA secondary structures and overall sgRNA efficacy. A transformer-based architecture processes these inputs to produce a predictive efficacy score. Comparative experiments show that DeepFM-Crispr not only surpasses traditional models but also outperforms recent state-of-the-art deep learning methods in terms of prediction accuracy and reliability.

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