Lada, A. G. | bioRxiv Science

bioRxiv2026

FuzzyClusTeR: a web server for analysis of tandem and diffuse DNA repeat clusters with application to telomeric-like repeats

DNA repeats constitute a large fraction of eukaryotic genomes and play important roles in genome stability and evolution. While tandem repeats such as microsatellites have been extensively studied, the genomic organization and potential functions of dispersed or loosely organized repeat patterns remain poorly understood. Here we present FuzzyClusTeR, a web server for the identification, visualization and enrichment analysis of DNA repeat clusters in genomic sequences. Using parameterized metrics, FuzzyClusTeR detects both classical tandem repeats and regions where related motifs occur in proximity without forming perfect tandem arrays, which we term diffuse (or fuzzy) repeat clusters. The server supports analysis of user-defined sequences as well as genome-scale datasets, including the T2T-CHM13 and GRCh38 human genome assemblies, and provides interactive visualization and statistical tools for assessing the genomic distribution of repetitive motifs and corresponding clusters. As a demonstration, we analyzed telomeric-like repeats in the T2T-CHM13v2.0 genome and identified families of diffuse clusters enriched in these motifs. Comparison with simulated sequences suggests that these clusters represent non-random genomic patterns with potential evolutionary and functional significance. FuzzyClusTeR enables systematic exploration of repeat clustering across genomic regions or entire genomes. It is available at https://utils.researchpark.ru/bio/fuzzycluster GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/712643v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1844091org.highwire.dtl.DTLVardef@1ab0e1dorg.highwire.dtl.DTLVardef@12bc717org.highwire.dtl.DTLVardef@11bbec9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2020

Compensation for the absence of the catalytically active half of DNA polymerase ε in yeast by positively selected mutations in CDC28 gene

DNA polymerase {varepsilon} (pol {varepsilon}) participates in the leading DNA strand synthesis in eukaryotes. The catalytic subunit of this enzyme, Pol2, is a fusion of two ancestral B-family DNA polymerases. Paradoxically, the catalytically active N-terminal pol is dispensable, and an inactive C-terminal pol is essential for yeast cell viability. Despite extensive studies of strains without the active N-terminal half (mutation pol2-16), it is still unclear how they survive and what is the mechanism of rapid recovery of initially miserably growing cells. The reason for the slow progress is in the difficultly of obtaining strains with the defect. We designed a robust method for constructing mutants with only the C-terminal part of Pol2 using allele pol2rc-{Delta}N with optimized codon usage. Colonies bearing pol2rc-{Delta}N appear three times sooner than colonies of pol2-16 but exhibit similar growth defects: sensitivity to hydroxyurea, chromosomal instability, and an elevated level of spontaneous mutagenesis. UV-induced mutagenesis is partially affected; it is lower only at high doses in some reporters. The analysis of the genomes of pol2rc-{Delta}N isolates revealed the prevalence of nonsynonymous mutations suggesting that the growth recovery was a result of positive selection for better growth fueled by variants produced by the elevated mutation rate. Mutations in the CDC28 gene, the primary regulator of the cell cycle, were repeatedly found in independent clones. Genetic analysis established that cdc28 alleles single-handedly improve the growth of pol2rc-{Delta}N strains and suppress sensitivity hydroxyurea. The affected amino acids are located on the Cdc28 molecules two surfaces that mediate contacts with cyclins or kinase subunits. Our work establishes the significance of the CDC28 gene for the resilience of replication and predicts that changes in mammalian homologs of cyclin-dependent kinases may play a role in remastering replication to compensate for the defects in the leading strand synthesis by the dedicated polymerase. Author SummaryThe catalytic subunit of the leading strand DNA polymerase {varepsilon}, Pol2, consists of two halves made of two different ancestral B-family DNA polymerases. Counterintuitively, the catalytically active N-terminal half is dispensable while the inactive C-terminal part is required for viability. The corresponding strains show a severe growth defect, sensitivity to replication inhibitors, chromosomal instability, and elevated spontaneous mutagenesis. Intriguingly, the slow-growing mutant strains rapidly produced fast-growing clones. We discovered that the adaptation to the loss of the catalytic N-terminal part of Pol2 occurs during evolution by positive selection for a better growth fueled by variants produced by elevated mutation rates. Mutations in the cell cycle-dependent kinase gene, CDC28, can single-handedly improve the growth of strains lacking the N-terminal part of Pol2. Our study predicts that changes in mammalian homologs of cyclin-dependent kinases may play a role in response to the defects of active leading strand polymerase.

genetics↗