Biology subjects

Nieduszynski, C.

Publications and source records attributed to Nieduszynski, C..

4 recordsLinked to original sources

bioRxiv2025

Single-molecule landscape of DNA replication pausing

A pause in DNA synthesis that occurs when the replisome encounters an obstacle could lead to genome instability. Although important, systematic identification of replication pause sites is challenging due to their low frequency and delocalized nature. Here we present the first single-molecule identification of sites of replisome perturbation across a eukaryotic genome using long-read nanopore sequencing. For each single-molecule replication pause we determine the direction of replication, leading/lagging-strand identity, location and approximate duration, and whether the replisome resumed synthesis. Although pauses are largely diffuse over the genome, they are significantly enriched over transcribed features and correlate with transcription and R-loop levels. Transcription-replication conflicts are more numerous when head-on than co-directional. Finally, we identified genomic loci with a strong bias towards leading over lagging strand pauses, consistent with uncoupling of the helicase from polymerase epsilon. Our data support helicase-polymerase uncoupling resulting from replication pausing as the molecular trigger behind epigenetic switching. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/670160v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@79250forg.highwire.dtl.DTLVardef@1702a30org.highwire.dtl.DTLVardef@e1d9f4org.highwire.dtl.DTLVardef@1ac2ce1_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

Schizosaccharomyces versatilis represents a distinct evolutionary lineage.

The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties - S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% coding sequence identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with "metabolism" and "cellular assembly" ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the "type" strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis. Take-awayO_LIThe taxonomic status of Schizosaccharomyces versatilis is addressed. C_LIO_LIS. versatilis diverged from S. japonicus around 25 million years ago. C_LIO_LIS. versatilis does not produce viable progeny in crosses with S. japonicus. C_LIO_LIS. versatilis has a reciprocal translocation between chromosomes 1 and 2. C_LIO_LIThe Gene Ontology terms for genes in the translocations are enriched for terms connected to "metabolism" and "cellular assembly". C_LI

evolutionary biology↗

bioRxiv2023

Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as fission yeasts. As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available short-read genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNAs, transfer RNAs, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics. Take-awayO_LIA telomere-to-telomere genome assembly of the fission yeast S. japonicus C_LIO_LIChromosome 2 harbours a previously unknown second centromere-like region C_LIO_LIThe estimated genome size of S. japonicus may be up to 18.12 Mb C_LI

genomics↗

bioRxiv2018

The effectiveness of glass beads for plating cell cultures

Cell plating, the spreading out of a liquid suspension of cells on a surface followed by colony growth, is a common laboratory procedure in microbiology. Despite this, the exact impact of its parameters on colony growth has not been extensively studied. A common protocol involves the shaking of glass beads within a petri dish containing solid growth media. We investigated the effects of multiple parameters in this protocol - the number of beads, the shape of movement, and the number of movements. Standard suspensions of Escherichia coli were spread while varying these parameters to assess their impact on colony growth. Results were assessed by a variety of metrics - the number of colonies, the mean distance between closest colonies, and the variability and uniformity of their spatial distribution. Finally, we devised a mathematical model of shifting billiard to explain the heterogeneities in the observed spatial patterns. Exploring the parameters that affect the most fundamental techniques in microbiology allows us to better understand their function, giving us the ability to precisely control their outputs for our exact needs.

biophysics↗