Biology subjects

Figlerowicz, M.

Publications and source records attributed to Figlerowicz, M..

6 recordsLinked to original sources

bioRxiv2026

Machine learning-guided design of artificial microRNAs for targeted gene silencing

Artificial microRNAs (amiRNAs) offer a powerful strategy for targeted gene silencing, but their rational design is limited by complex sequence-structure-processing relationships and the lack of tools capable of optimizing efficacy and specificity. To address this need, we developed miRarchitect, a web-based platform that uses machine learning to support the customizable design of amiRNAs. miRarchitect integrates neural network-guided target-site selection, siRNA insert design, and scaffold choice, utilizing large-scale data from human primary microRNAs (pri-miRNAs) and next-generation sequencing. The platform generates molecules that closely resemble endogenous pri-miRNAs and includes comprehensive off-target analysis to enhance specificity. Experimental validation targeting TMPRSS2 and ACE-2 confirmed precise processing, robust knockdown, and high specificity of miRarchitect-designed amiRNAs. In comparative benchmarking, miRarchitect consistently produced functional amiRNAs, whereas only half of the top candidates generated by other tools showed measurable activity. miRarchitect is freely available at https://rnadrug.ichb.pl/mirarchitect and provides an intuitive interface with an automated workflow for generating, ranking, and selecting candidate amiRNAs for research and therapeutic applications.

bioinformatics↗

bioRxiv2025

APOBEC3A deaminase catalyzes site-specific editing of transfer RNAs

APOBEC3A is a cytidine deaminase that plays a crucial role in innate immunity; however, it can also drive oncogenesis when dysregulated. While its DNA editing activity is well-studied, the impact of APOBEC3A on RNA has only recently gained attention. Previous studies revealed that APOBEC3A deaminates mRNA stem-loop structures, however, its activity on other RNA classes remains unexplored. Given its likely evolutionary origin from tRNA adenosine deaminases and the prevalence of stem-loop structures in tRNA, we investigated APOBEC3As activity on tRNAs. We found that in vitro APOBEC3A efficiently deaminates a large spectrum of tRNA isoacceptors, primarily at anticodon positions. To assess whether the editing sites identified in vitro can be detected in tumor tissues, we analyzed data from The Cancer Genome Atlas. We identified six editing sites present in numerous patient samples. Our results point to a possible impact of APOBEC3A on tRNA decoding capacity, with potential relevance to mistranslation and cancer development.

molecular biology↗

bioRxiv2023

Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo

MicroRNAs (miRNAs) that share identical or near-identical sequences constitute miRNA families and are predicted to act redundantly. Yet recent evidence suggests that members of the same miRNA family with high sequence similarity might have different roles and that this functional divergence might be rooted in their precursors sequence. Current knock-down strategies such as antisense oligonucleotides (ASOs) or miRNA sponges cannot distinguish between identical or near identical miRNAs originating from different precursors to allow exploring unique functions of these miRNAs. We now develop a method based on short 2'-OMe/LNA-modified oligonucleotides to selectively target specific precursor molecules and ablate the production of individual members of miRNA families in vitro and in vivo. Using the highly conserved Xenopus miR-181a family as a proof-of-concept, we demonstrate that 2'-OMe/LNA-ASOs targeting pre-miRNA apical region elicit a precursor-selective inhibition of mature miRNA-5p production. The levels of miRNAs released from the 3'-arm of these precursors are not reduced, suggesting that our approach is also arm-selective. Overall, we show that this strategy can be successfully applied in vivo to achieve high target selectivity to study identical or highly similar miRNAs stemming from different precursors.

molecular biology↗

bioRxiv2022

Copy number variations shape the structural diversity of Arabidopsis metabolic gene clusters and are associated with the climatic gradient

Metabolic gene clusters (MGCs) encode at least three different enzymes for a common biosynthetic pathway. Comparative genome analyses highlighted the role of duplications, deletions and rearrangements in MGC formation. We hypothesized that these mechanisms also contribute to MGC intraspecies diversity and play a role in adaptation. We assessed copy number variations (CNVs) of four Arabidopsis thaliana MGCs in a population of 1,152 accessions, with experimental and bioinformatic approaches. The MGC diversity was lowest in marneral gene cluster (one private deletion CNV) and highest in the arabidiol/baruol gene cluster where 811 accessions had gene gains or losses, however, there were no presence/absence variations of the entire clusters. We found that the compact version of thalianol gene cluster was predominant in A. thaliana and more conserved than the noncontiguogus version. In arabidiol/baruol cluster we found a large insertion in 35% of analyzed accessions, that contained duplications of the reference genes CYP705A2 and BARS1. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. Unexpectedly, in accessions with the insertion, the arabidiol/baruol gene cluster was expressed not only in roots but also in leaves. Additionally, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. We also found that paired genes encoding terpene synthases and cytochrome P450 oxidases had higher copy number variability compared to non-paired ones. Our study highlights the importance of intraspecies variation and nonreference genomes for dissecting secondary metabolite biosynthesis pathways and understanding their role in adaptation and evolution.

genomics↗

bioRxiv2020

RNA and DNA G-quadruplexes bind to human Dicer and inhibit its activity

Guanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform-PAZ-Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation.

biochemistry↗

bioRxiv2019

Human PUM1 and PUM2 exhibit regulation of divergent mRNA targets in male germ cells

Mammalian Pumilio (PUM) proteins are sequence-specific, RNA-binding proteins with wide-ranging roles, including germ cell development that has functional implications in fertility. Although human PUM1 and PUM2 are closely related to each other and recognize the same RNA binding motif, there is some evidence for functional diversity, particularly related to their roles in fertility. Here, by RNA sequencing (RNA-Seq) approaches, we identified separate mRNA pools regulated by PUM1 and PUM2 proteins in human male germ cells. Using global mass spectrometry-based profiling, we identified distinct PUM1- and PUM2-bound putative protein cofactors, most of them involved in RNA processing. Combinatorial analysis of RNA-Seq and mass spectrometry findings revealed that PUM1 and PUM2 may form distinct RNA-regulatory networks, with different roles in human reproduction and testicular tumorigenesis. Our findings highlight the functional divergence and versatility of PUM paralogue-based post-transcriptional regulation, offering insight into the mechanisms underlying their diverse biological roles and diseases resulting from their dysfunction.

molecular biology↗