Deregulation of mitochondrial gene expression in cancer: mechanisms and therapeutic opportunities

British Journal of Cancer, Год журнала: 2024, Номер 131(9), С. 1415 - 1424

Опубликована: Авг. 14, 2024

Язык: Английский

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A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

RNA-binding proteins (RBPs) are essential modulators in the regulation of mRNA processing. The binding patterns, interactions, and functions most RBPs not well-characterized. Previous studies have shown that motif context is an important contributor to RBP specificity, but its precise role remains unclear. Despite recent computational advances predict binding, existing methods challenging interpret largely lack a categorical focus on contexts RBP-RBP interactions. There need for interpretable predictive models disambiguate contextual determinants specificity vivo . Here, we present novel comprehensive pipeline address these knowledge gaps. We devise Natural Language Processing-based decomposition method deconstruct sequences into entities consisting central target k -mer flanking regions, then use this representation formulate prediction task as weakly supervised Multiple Instance Learning problem. To our predictions, introduce deterministic discovery algorithm designed handle data structure, recapitulating established motifs numerous validation. Importantly, characterize 71 RBPs, with many them being novel. Finally, through feature integration, transitive inference, new cross-prediction approach, propose cooperative competitive interaction partners hypothesize their potential regulatory functions. In summary, complete strategy investigating specific demonstrate significance findings delineating

Язык: Английский

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EASI-ORC: A pipeline for the efficient analysis and segmentation of smFISH images for organelle-RNA colocalization measurements in yeast

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Фев. 15, 2025

Analysis of single-molecule fluorescent in situ hybridization (smFISH) images is important to translate cellular image data into a quantifiable format. Although smFISH the gold standard for RNA localization measurements, there are no freely available, user-friendly applications assaying messenger (mRNA) organelles. EASI-ORC (Efficient and Segmentation Images Organelle-RNA Colocalization) novel pipeline automated analysis multiple yeast cells. automates segmentation cells organelles, identifies bona fide signals, measures mRNA-organelle colocalization. efficient, unbiased, plots colocalization statistical analyses. utilizes existing ImageJ plugins original scripts, thus allowing free access ease-of-use. To circumvent technical literacy issues, step-by-step user guide provided. offers robust solution - one that saves time, effort provides consistent measurements yeast.

Язык: Английский

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Functional analysis of the novel mitochondrial tRNA^Trp and tRNA^Ser(AGY) variants associated with type 2 diabetes mellitus

World Journal of Diabetes, Год журнала: 2024, Номер 15(8), С. 1753 - 1763

Опубликована: Июль 25, 2024

Mutations in mitochondrial tRNA (

Язык: Английский

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Proximity labeling reveals differential interaction partners of the human mitochondrial import receptor proteins TOMM20 and TOMM70

Опубликована: Окт. 25, 2024

Abstract Import of most mitochondrial proteins requires that their precursor are bound by the (peripheral) receptor TOM20, TOM22, and TOM70. For budding yeast TOM20 TOM70, there is evidence specific yet overlapping substrate recognition, but no such data available for metazoan cells. Using APEX2-based proximity labeling, we thus created association profiles human TOMM20 TOMM70 in HeLa We particularly focused on interaction with RNA-binding (RBPs) since RNA outer membrane (MOM) local translation at surface, these processes poorly understood. Our results show a preferred several RBPs factors over TOMM70. These include SYNJBP2, previously identified membrane-bound RBP binds protects mRNAs encoding proteins. Translational inhibition puromycin resulted an even increased compared to TOMM70, suggesting not might play role preserving cellular hemostasis during stress retaining protective translation-related MOM.

Язык: Английский

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Prediction of mitochondrial targeting signals and their cleavage sites

Methods in enzymology on CD-ROM/Methods in enzymology, Год журнала: 2024, Номер unknown, С. 161 - 192

Опубликована: Янв. 1, 2024

Язык: Английский

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Therapies that address altered gene regulation

Elsevier eBooks, Год журнала: 2024, Номер unknown, С. 263 - 292

Опубликована: Ноя. 1, 2024

Язык: Английский

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Screening for mitochondrial tRNA variants in 200 patients with systemic lupus erythematosus

Human Heredity, Год журнала: 2024, Номер 89(1), С. 84 - 97

Опубликована: Ноя. 13, 2024

Systemic lupus erythematosus (SLE) is a common autoimmune disease with unknown etiology. Recently, growing number of evidence suggested that mitochondrial dysfunctions played active roles in the pathogenesis SLE, but its detailed mechanism remains largely undetermined. The aim this study was to analyze frequencies tRNA (mt-tRNA) variants Chinese individuals SLE.

Язык: Английский

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