Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections

Fan, Cong, Chen, Ken, Wang, Yukai, Ball, Edward V., Stenson, Peter D., Mort, Matthew, Bacolla, Albino, Kehrer-Sawatzki, Hildegard, Tainer, John A., Cooper, David N. ORCID: https://orcid.org/0000-0002-8943-8484 and Zhao, Huiying 2023. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Human Genetics 142 , pp. 245-274. 10.1007/s00439-022-02500-6

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Abstract

Whilst DNA repeat expansions cause numerous heritable human disorders, their origins and underlying pathological mechanisms are often unclear. We collated a dataset comprising 224 human repeat expansions encompassing 203 different genes, and performed a systematic analysis with respect to key topological features at the DNA, RNA and protein levels. Comparison with controls without known pathogenicity and genomic regions lacking repeats, allowed the construction of the first tool to discriminate repeat regions harboring pathogenic repeat expansions (DPREx). At the DNA level, pathogenic repeat expansions exhibited stronger signals for DNA regulatory factors (e.g. H3K4me3, transcription factor-binding sites) in exons, promoters, 5′UTRs and 5′genes but were not significantly different from controls in introns, 3′UTRs and 3′genes. Additionally, pathogenic repeat expansions were also found to be enriched in non-B DNA structures. At the RNA level, pathogenic repeat expansions were characterized by lower free energy for forming RNA secondary structure and were closer to splice sites in introns, exons, promoters and 5′genes than controls. At the protein level, pathogenic repeat expansions exhibited a preference to form coil rather than other types of secondary structure, and tended to encode surface-located protein domains. Guided by these features, DPREx (http://biomed.nscc-gz.cn/zhaolab/geneprediction/#) achieved an Area Under the Curve (AUC) value of 0.88 in a test on an independent dataset. Pathogenic repeat expansions are thus located such that they exert a synergistic influence on the gene expression pathway involving inter-molecular connections at the DNA, RNA and protein levels.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Publisher:	Springer
ISSN:	0340-6717
Date of First Compliant Deposit:	21 December 2022
Date of Acceptance:	24 October 2022
Last Modified:	23 Feb 2023 13:24
URI:	https://orca.cardiff.ac.uk/id/eprint/155085

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