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1. DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions

   https://doi.org/10.1038/s41467-024-48718-y  

   Li, Yi; Lee, James; Bai, Lu (May 2024, Nature Communications)

   NA (Ed.)

   Abstract 3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we presentMethyltransferaseTargeting-based chromosomeArchitectureCapture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization. 

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2. Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales

   https://doi.org/10.1093/nar/gkaf670  

   Corrette, John; Li, Jiachun; Shao, Hanjuan; Veerasubramanian, Praveen Krishna; Spakowitz, Andrew; Downing, Timothy L.; Allard, Jun (July 2025, Nucleic Acids Research)

   Abstract The 3D organization of the genome—in particular, which two regions of DNA are in contact with each other—plays a role in regulating gene expression. Several factors influence genome 3D organization. Nucleosomes (where ∼100 base pairs of DNA wrap around histone proteins) bend, twist, and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And to what extent are polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATAC-seq data in regions of high accessibility. Most of the genome is low accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no fit parameters in the biophysical model. We apply this method to IL-6, IL-15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after inflammatory stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500-kb genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100 kb scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g. a macrophage during inflammatory stimulation). 

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3. TIGER: inferring DNA replication timing from whole-genome sequence data

   https://doi.org/10.1093/bioinformatics/btab166  

   Koren, Amnon; Massey, Dashiell J; Bracci, Alexa N (March 2021, Bioinformatics)

   Robinson, Peter (Ed.)

   Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online 

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4. Chromosome segregation dynamics during the cell cycle of Staphylococcus aureus

   https://doi.org/10.1101/2025.02.18.638847  

   Izquierdo-Martinez, Adrian; Schäper, Simon; Brito, António D; Liao, Qin; Tesseur, Coralie; Sorg, Moritz; Botinas, Daniela S; Wang, Xindan; Pinho, Mariana G (February 2025, bioRxiv)

   Abstract Research on chromosome organization and cell cycle progression in spherical bacteria, particularlyStaphylococcus aureus, remains limited and fragmented. In this study, we established a working model to investigate chromosome dynamics inS. aureususing a Fluorescent Repressor-Operator System (FROS), which enabled precise localization of specific chromosomal loci. This approach revealed that theS. aureuscell cycle and chromosome replication cycle are not coupled, with cells exhibiting two segregated origins of replication at the start of the cell cycle. The chromosome has a specific origin-terminus-origin conformation, with origins localizing near the membrane, towards the tip of each hemisphere, or the “cell poles”. We further used this system to assess the role of various proteins with a role inS. aureuschromosome biology, focusing on the ParB-parSand SMC-ScpAB systems. Our results demonstrate that ParB binds fiveparSchromosomal sequences and the resulting complexes influence chromosome conformation, but play a minor role in chromosome compaction and segregation. In contrast, the SMC-ScpAB complex plays a key role inS. aureuschromosome biology, contributing to chromosome compaction, segregation and spatial organization. Additionally, we systematically assessed and compared the impact of proteins linking chromosome segregation to cell division—Noc, FtsK, SpoIIIE and XerC—on origin and terminus number and positioning. This work provides a comprehensive study of the factors governing chromosome dynamics and organization inS. aureus, contributing to our knowledge on chromosome biology of spherical bacteria. 

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5. Telomere Roles in Fungal Genome Evolution and Adaptation

   https://doi.org/10.3389/fgene.2021.676751  

   Rahnama, Mostafa; Wang, Baohua; Dostart, Jane; Novikova, Olga; Yackzan, Daniel; Yackzan, Andrew; Bruss, Haley; Baker, Maray; Jacob, Haven; Zhang, Xiaofei; et al (August 2021, Frontiers in Genetics)

   Telomeres form the ends of linear chromosomes and usually comprise protein complexes that bind to simple repeated sequence motifs that are added to the 3′ ends of DNA by the telomerase reverse transcriptase (TERT). One of the primary functions attributed to telomeres is to solve the “end-replication problem” which, if left unaddressed, would cause gradual, inexorable attrition of sequences from the chromosome ends and, eventually, loss of viability. Telomere-binding proteins also protect the chromosome from 5′ to 3′ exonuclease action, and disguise the chromosome ends from the double-strand break repair machinery whose illegitimate action potentially generates catastrophic chromosome aberrations. Telomeres are of special interest in the blast fungus, Pyricularia , because the adjacent regions are enriched in genes controlling interactions with host plants, and the chromosome ends show enhanced polymorphism and genetic instability. Previously, we showed that telomere instability in some P. oryzae strains is caused by novel retrotransposons (MoTeRs) that insert in telomere repeats, generating interstitial telomere sequences that drive frequent, break-induced rearrangements. Here, we sought to gain further insight on telomeric involvement in shaping Pyricularia genome architecture by characterizing sequence polymorphisms at chromosome ends, and surrounding internalized MoTeR loci (relics) and interstitial telomere repeats. This provided evidence that telomere dynamics have played historical, and likely ongoing, roles in shaping the Pyricularia genome. We further demonstrate that even telomeres lacking MoTeR insertions are poorly preserved, such that the telomere-adjacent sequences exhibit frequent presence/absence polymorphism, as well as exchanges with the genome interior. Using TERT knockout experiments, we characterized chromosomal responses to failed telomere maintenance which suggested that much of the MoTeR relic-/interstitial telomere-associated polymorphism could be driven by compromised telomere function. Finally, we describe three possible examples of a phenomenon known as “Adaptive Telomere Failure,” where spontaneous losses of telomere maintenance drive rapid accumulation of sequence polymorphism with possible adaptive advantages. Together, our data suggest that telomere maintenance is frequently compromised in Pyricularia but the chromosome alterations resulting from telomere failure are not as catastrophic as prior research would predict, and may, in fact, be potent drivers of adaptive polymorphism. 

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