Biology subjects

Holub, E.

Publications and source records attributed to Holub, E..

4 recordsLinked to original sources

bioRxiv2025

Thymidylate synthase inhibitory drugs induce p53-dependent pathways differently

Thymidylate synthase (TS) is a key enzyme in thymidylate biosynthesis and an established target of chemotherapeutics such as 5-fluoro-2-deoxyuridine (5FdUR) and raltitrexed (RTX). Inhibition of TS disrupts the dUTP:dTTP balance, leading to uracil misincorporation, futile base excision repair cycles, DNA strand breaks, and ultimately cell death. Beyond its catalytic role, TS also binds RNA, autoregulating its own translation and interacting with transcripts such as p53 and c-myc, thereby linking TS activity to broader post-transcriptional regulatory networks. These interactions, together with regulation by miRNAs and lncRNAs, suggest that TS inhibition may provoke cellular responses extending beyond DNA metabolism. Non-coding RNAs, including miRNAs, snoRNAs, snRNAs, and lncRNAs, may play critical roles in shaping these outcomes. To dissect these mechanisms, we investigated the transcriptomic effects of TS inhibition in mismatch repair-deficient, UNG-inhibited HCT116 colon cancer cells treated with 5FdUR or RTX. Both drugs induced DNA damage responses and S-phase arrest, yet displayed distinct transcriptional signatures. Moreover, TS-RNA immunoprecipitation sequencing revealed direct RNA-binding targets of TS, highlighting its contribution as a post-transcriptional regulator. Our findings underscore the multifaceted impact of TS inhibition, linking enzymatic disruption to RNA-level regulation and revealing drug-specific differences in cellular responses.

cancer biology↗

bioRxiv2021

Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida recognition specificities

The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR)-genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Col-0 provides resistance to many but not all white rust races, and encodes a nucleotide-binding (NB), leucine-rich repeat (LRR) (NLR) immune receptor protein. Col-0 WRR4A resistance is broken by a Col-0-virulent isolate of A. candida race 4 (AcEx1). We identified an allele of WRR4A in Arabidopsis accession Oy-0 and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed as a transgene in the oilseed crop Camelina sativa. SignificanceA C-terminal extension in an allele of the Arabidopsis resistance-protein WRR4A changes effector recognition specificity, enabling the WRR4AOy-0 allele to confer immunity to Albugo candida races that overcome the WRR4ACol-0 allele. This resistance can be transferred to the oil-producing crop Camelina sativa. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/437434v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a68de6org.highwire.dtl.DTLVardef@ae0addorg.highwire.dtl.DTLVardef@4b3384org.highwire.dtl.DTLVardef@12330b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2020

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug-treatment in human cancer cell-line HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards more active/functional segments. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can also be applied to study the dynamic spatio-temporal nature of genomic uracil.

biochemistry↗

bioRxiv2019

Population genetics of the highly polymorphic RPP8 gene family

Plant NLR resistance genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from A. lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.

evolutionary biology↗