Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology

Gene regulatory networks are now at the forefront of precision biology, which can help researchers better understand how genes and regulatory elements interact to control cellular gene expression, offering a more promising molecular mechanism in biological research. Interactions between the genes and regulatory elements involve different promoters, enhancers, transcription factors, silencers, insulators, and long-range regulatory elements, which occur at a similar to 10 mu m nucleus in a spatiotemporal manner. In this way, three-dimensional chromatin conformation and structural biology are critical for interpreting the biological ef-fects and the gene regulatory networks. In the review, we have briefly summarized the latest processes in three-dimensional chromatin conformation, microscopic imaging, and bioinformatics, and we have pre-sented the outlook and future directions for these three aspects.(c) 2023 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creative-commons.org/licenses/by-nc-nd/4.0/).

Automated summary

Gene regulatory networks are critical in precision biology, offering insights into how genes and regulatory elements interact to control gene expression. The interactions involve various elements such as promoters, enhancers, transcription factors, silencers, insulators, and long-range regulatory elements, occurring within the nucleus. Understanding three-dimensional chromatin conformation and structural biology is essential for interpreting biological effects and gene regulatory networks. This review summarizes the latest advancements in three-dimensional chromatin conformation, microscopic imaging, and bioinformatics, and provides an outlook on future directions.