Biology subjects

Mbegbu, O.

Publications and source records attributed to Mbegbu, O..

3 recordsLinked to original sources

bioRxiv2026

Telomere Dysfunction in Human Astrocytes Drives Acrocentric Chromosome Instability and Nucleolar Reorganization

Loss of p53 and Rb enables continued cell division despite progressive telomere erosion, ultimately triggering telomere crisis. While recent work has clarified mechanisms of chromatin bridge resolution, the longitudinal dynamics of structural damage through crisis remain incompletely understood. We transduced normal human astrocyte (NHA) cells with HPV18 E6/E7 and tracked them across extended population doublings. NHA E6/E7 cells showed progressive telomere shortening, anaphase bridges, and a growth plateau consistent with crisis. Multicolor FISH revealed subclonal chromosomal abnormalities largely invisible to short-read sequencing, with acrocentric chromosomes disproportionately affected: chromosome 13 was abnormal in over 92% of metaphases, and chromosomes 21 and 22 were similarly enriched. Translocations involving chromosome 13 were transient, replaced at later passages, while numerical aberrations persisted. Immunofluorescence revealed compact spherical nucleoli replaced by dispersed necklace-like structures, indicating a large-scale reorganization of nucleolar structure in response to telomere dysfunction. To determine whether these changes reflected altered chromosomal organization in the nucleus, we performed Hi-C and deployed KaryoScope, our alignment-free k-mer-based approach that recovers trans-chromosomal signal from repetitive acrocentric short arms. Inter-chromosomal contacts among nucleolar organizing region-bearing acrocentric chromosomes were markedly and persistently depleted in E6/E7 cells. Together, cytogenetic, imaging, and chromatin-contact data identify the nucleolus as a structural nexus linking telomere dysfunction to large-scale genomic rearrangement.

cancer biology↗

bioRxiv2025

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance

Telomeres are essential for genome integrity, but the accurate, high-resolution mapping of their three-dimensional (3D) chromatin interactions, a process thought to mediate gene regulation and telomere maintenance, has been limited by the repetitive nature of subtelomeric DNA and shortcomings of traditional sequencing-based chromatin conformation capture methodologies. To overcome these challenges, we developed Telomere Conformation Capture by sequencing (Telomere-C), a novel high-throughput approach for the genome-wide identification of telomeric chromatin interactions. We applied Telomere-C to three normal fibroblast cell lines (BJ, IMR90, WI38), one telomerase-positive cancer cell line (HeLa S3) and two cancer cell lines (U2-OS and WI38-VA13) that maintain telomeres by alternative lengthening of telomeres (ALT). We generated millions of telomere-associated reads per sample and identified up to 41,026 interaction peaks. We successfully validated previously-described telomeric interaction sites (e.g., TERT and DUX4), and critically, revealed a novel class of ultra-long-range interactions extending over 5 Mb away from the telomere, which surprisingly constitute over 80% of all identified contacts. Contrary to prior studies focusing on protein coding gene interactions, we discovered that the telomeric 3D interactome is overwhelmingly anchored at repetitive element hubs, particularly interstitial telomeric sequence (ITS), telomere-associated repeat 1 (TAR1) and D20S16 elements. We found that the clustering of these interactions correlates strongly with cell-type-specific telomere maintenance. Most notably, D20S16 telomeric interactions were uniquely and highly enriched in ALT cancer cells, suggesting a mechanistic link. Taken together, our study effectively constructs the first high resolution maps of the telomeric 3D interactome, redefining its scope to be dominated by ultra-long-range contacts with repetitive elements. This work provides fundamental insights into telomeric nuclear organization and establishes the telomeric D20S16 interaction as a molecular signature for the ALT pathway.

genomics↗

bioRxiv2025

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing

Human cell lines are fundamental tools in biomedical research and are widely used in disease modeling, drug development, and many other domains. Here, we present chromosome-level, phased diploid genome assemblies of two popular human cell lines: the BJ foreskin fibroblast line and the IMR-90 fetal lung fibroblast line. Our high-quality assemblies, generated using long-read and Hi-C sequencing data, reveal substantial structural variation, including more than 50,000 insertions, deletions, duplications, and inversions compared to the recent T2T-CHM13v2.0 reference. Our assemblies provide detailed maps of genetic variation, enabling more accurate variant calling and the ability to phase reads when using newly generated or historical sequencing data on these cell lines or their derivatives. All assemblies and associated data have been made available as a resource for the research community. We envision that diploid genome assembly will become a cornerstone approach for personalized medicine in the near future.

genomics↗