Biology subjects

Findlay, S. D.

Publications and source records attributed to Findlay, S. D..

6 recordsLinked to original sources

bioRxiv2025

Sequence based prediction of cell type specific microRNA binding and mRNA degradation for therapeutic discovery

MicroRNAs and RNA binding proteins are crucial elements of post-transcriptional gene regulation, which governs the fate of mRNA molecules in the cell. However, the landscape of these regulatory interactions, particularly across different mammalian cell types, remains underexplored. We describe REPRESS, a deep learning model that predicts cell-type-specific microRNA binding and mRNA degradation directly from RNA sequence. REPRESS was trained on AGO2-CLIP, miR-eCLIP and Degradome-Seq data profiling millions of microRNA binding and mRNA degradation sites across multiple cell types in human and mouse. It reveals biology that other state-of-the-art methods did not, such as identifying repressive non-canonical miRNA target sites and decoding the regulatory effects of sequence context and miRNA binding site multiplicity. REPRESS outperforms other advanced methods and neural architectures on a comprehensive suite of seven orthogonal tasks, including identifying genetic variants that affect microRNA binding, predicting out-of-distribution data from massively parallel reporter assays, and predicting canonical and non-canonical miRNA mediated repression. To demonstrate the general utility of REPRESS, we show that it provides insights into novel biology and the design of RNA therapeutics. Code is available at : https://github.com/deepgenomics/repress

genomics↗

bioRxiv2023

Regulatory features aid interpretation of 3'UTR variants

Our ability to determine the clinical impact of variants in 3 untranslated regions (UTRs) of genes remains poor. We provide a thorough analysis of 3UTR variants from several datasets. Variants in putative regulatory elements including RNA-binding protein motifs, eCLIP peaks, and microRNA sites are up to 16 times more likely than other variants to have gene expression and phenotype associations. Heterozygous variants in regulatory motifs result in allele-specific protein binding in cell lines and allele-specific gene expression differences in population studies. In addition, variants in shared regions of alternatively polyadenylated isoforms and those proximal to polyA sites are more likely to affect gene expression and phenotype. Finally, pathogenic 3UTR variants in ClinVar are 20 times more likely than benign variants to fall in a regulatory site. We incorporated these findings into RegVar, a software tool that interprets regulatory elements and annotations for any 3UTR variant, and predicts whether the variant is likely to affect gene expression or phenotype. This tool will help prioritize variants for experimental studies and identify pathogenic variants in patients.

genomics↗

bioRxiv2022

Quantifying negative selection in human 3' UTRs uncovers constrained targets of RNA-binding proteins

Many non-coding variants associated with phenotypes occur in 3 untranslated regions (3 UTRs) and may affect interactions with RNA-binding proteins (RBPs) to regulate post-transcriptional gene expression. However, identifying functional 3 UTR variants has proven difficult. We used allele frequencies from the Genome Aggregation Database (gnomAD) to identify classes of 3 UTR variants under strong negative selection in humans. We developed intergenic mutability-adjusted proportion singleton (iMAPS), a generalized measure related to MAPS, to quantify negative selection in non-coding regions. This approach, in conjunction with in vitro and in vivo binding data, identifies precise RBP binding sites, miRNA target sites, and polyadenylation signals (PASs) under strong selection. For each class of sites, we identified thousands of gnomAD variants under selection comparable to missense coding variants, and found that sites in core 3 UTR regions upstream of the most-used PAS are under strongest selection. Together, this work improves our understanding of selection on human genes and validates approaches for interpreting genetic variants in human 3 UTRs.

evolutionary biology↗

bioRxiv2019

Translational control of breast cancer plasticity

Plasticity of neoplasia, whereby cancer cells attain stem-cell-like properties, is required for disease progression and represents a major therapeutic challenge. We report that in breast cancer cells NANOG, SNAIL and NODAL transcripts manifest multiple isoforms characterized by different 5 Untranslated Regions (5UTRs), whereby translation of a subset of these isoforms is stimulated under hypoxia. This leads to accumulation of corresponding proteins which induce plasticity and \"fate-switching\" toward stem-cell like phenotypes. Surprisingly, we observed that mTOR inhibitors and chemotherapeutics induce translational activation of a subset of NANOG, SNAIL and NODAL mRNA isoforms akin to hypoxia, engendering stem cell-like phenotypes. Strikingly, these effects can be overcome with drugs that antagonize translational reprogramming caused by eIF2 phosphorylation (e.g. ISRIB). Collectively, our findings unravel a hitherto unappreciated mechanism of induction of plasticity of breast cancer cells, and provide a molecular basis for therapeutic strategies aimed at overcoming drug resistance and abrogating metastasis.

cancer biology↗

bioRxiv2018

Genetically regulated human NODAL splice variants are differentially post-transcriptionally processed and functionally distinct

NODAL is a morphogen essential for early embryonic development in vertebrates. Since much of our understanding of NODAL comes from model organisms, we aimed to directly assess post-transcriptional regulation of human NODAL with specific attention to a newly discovered human-specific NODAL splice variant. Selective depletion of the NODAL variant in human embryonic stem cells resulted in increased LIFR levels, while total NODAL knockdown resulted in a decrease of several markers of pluripotency. The NODAL variant did not transmit a canonical NODAL signal in zebrafish embryos, but may share some functional capability with canonical NODAL in cancer cells. At the protein level, disruption of disulfide bond formation dramatically enhanced proteolytic processing of NODAL. Disruption of NODAL N-glycosylation decreased its secretion but not extracellular stability, and a novel N-glycosylation in the NODAL variant contributed to enhanced secretion. Collectively, this work offers a direct and precise account of post-transcriptional regulation of human NODAL.

developmental biology↗

bioRxiv2018

Comprehensive characterization of transcript diversity at the human NODAL locus

NODAL, a morphogen belonging to the transforming growth factor beta (TG{beta}) superfamily, is essential during embryogenesis where it induces axis formation and left-right asymmetry. NODAL is also required for the maintenance of human embryonic stem cell pluripotency, and emerges in many cancer types concomitant with metastasis and therapy resistance. Several enhancer elements have been shown to regulate mouse Nodal expression and studies have delineated mechanisms by which mRNA splicing and translation of NODAL homologues are regulated in model organisms. However, little is known regarding the co-transcriptional and post-transcriptional processing of human NODAL. Herein, we describe hitherto unreported RNAs which are transcribed from the NODAL locus, including an antisense transcript, a circular transcript, and multiple splice variants. These transcripts demonstrate the complexity of NODAL expression and highlight the need to consider each NODAL variant when attempting to quantify or target this morphogen.

molecular biology↗