A comprehensive review on RNA subcellular localization prediction
Year: 2026
Type: article
Abstract: The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are predominantly associated with chromatin and act as regulators of gene transcription and chromatin structure, while mRNAs are distributed across the nucleus and cytoplasm, facilitating the transport of genetic information for protein synthesis. Understanding RNA localization sheds light on processes like gene expression regulation with spatial and temporal precision. However, traditional wet lab methods for determining RNA localization, such as in situ hybridization, are often time-consuming, resource-demanding, and costly. To overcome these challenges, computational methods leveraging artificial intelligence (AI) and machine learning (ML) have emerged as powerful alternatives, enabling large-scale prediction of RNA subcellular localization. This paper provides a comprehensive review of the latest advancements in AI-based approaches for RNA subcellular localization prediction, covering various RNA types and focusing on sequence-based, image-based, and hybrid methodologies that combine both data types. We highlight the potential of these methods to accelerate RNA research, uncover molecular pathways, and guide targeted disease treatments. Furthermore, we critically discuss the challenges in AI/ML approaches for RNA subcellular localization, such as data scarcity and lack of benchmarks, and opportunities to address them. This review aims to serve as a valuable resource for researchers seeking to develop innovative solutions in the field of RNA subcellular localization and beyond.
Source: Briefings in Functional Genomics
DOI: 10.1093/bfgp/elag011
Authors: Cece Zhang, Xuehuan Zhu, Nick Peterson, Jieqiong Wang, Shibiao Wan
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,700
Awards: G1263877917, Leveraging Heterogenous Common Fund Data Sets and Beyond for Identifying Lung Cancer Subtypes, G2011318139, SCH: A Multi-Modal Transfer Learning Framework to Maximize Health Outcomes for Breast Cancer, G5989231044, G676280546, Nebraska Research Network in Functional Genomics, G9000042892, G9000108264, Alcohol Center Of Research -- Nebraska (ACORN), Buffett Cancer Center Support Grant
OpenAlex ID: W6966675507