Biology subjects

Foltz, D. R.

Publications and source records attributed to Foltz, D. R..

7 recordsLinked to original sources

bioRxiv2026

The dynamics of nucleolus-centromeres interaction in living cells

Nucleoli and centromeres play essential roles in cellular proliferation and homeostasis, and are structurally and functionally interconnected. Centromeres frequently cluster around nucleoli, and some centromere assembly factors are known to reside in the nucleoli. To investigate the spatial and temporal relationships between these nuclear domains, we examined their dynamics in living cells. We imaged HeLa cells stably expressing mCherry-NPM1 and GFP-CENP-A using time-lapse microscopy. The results show that a subset of centromeres exhibits dynamic behavior during interphase, migrating over micrometer-scale distances within two hours. On average, 40-50% of centromeres maintain an association with nucleoli throughout interphase, with some cells displaying nucleolar-centromere association and dissociation within hours. Upon entry into mitosis, nucleoli are disassembled, and NPM1 localizes to the periphery of mitotic chromosomes. Nucleolar-centromere interactions are re-established in early G1, coinciding with the assembly of new centromeres. Treatment with actinomycin D, an inhibitor of RNA polymerase I, significantly reduces nucleolar size, nucleolar-centromere interactions, and centromere dynamics. Furthermore, post-mitotic nucleolar reformation is impaired. These findings highlight the dynamic nature of centromeres in interphase nuclei and their interactions with nucleoli. This behavior is partially dependent on rDNA transcription and nucleolar integrity, underscoring the critical roles of nucleoli, centromeres, and their interaction in 4D genome organization.

cell biology↗

bioRxiv2025

Replication stress alters CENP-A nucleosome stability during S phase

1.The maintenance of centromere identity is essential for the proper segregation of chromosomes during cell division. Centromere identity is epigenetically specified by centromeric histone H3 variant CENP-A, and its retention during DNA replication is facilitated by HJURP chaperone. Replication stress disrupts replication fork progression and can negatively influence the interactions between histone chaperone network necessary for retention and deposition of parental and new histones, respectively. In this study we investigate the role of replication stress response on centromere inheritance. We define changes in centromere-associated proteins that govern stability of centromeric and canonical nucleosomes through proximity labeling coupled with affinity purification mass spectrometry. We identified that under replication stress, CENP-A-containing chromatin strongly enriches for SWI/SNF chromatin remodeling proteins ATRX. We show that depletion of ATRX and its associated histone H3.3 chaperone DAXX results in the loss CENP-A retention in S-phase and loss persists into the subsequent cell cycle. Altogether our findings provide insight into how replication stress negatively influences centromeric chromatin instability and delineates a function of DAXX-ATRX complex in maintaining centromere inheritance during DNA replication.

biochemistry↗

bioRxiv2025

Rate Limiting Enzymes in Nucleotide Metabolism Synchronize Nucleotide Biosynthesis and Chromatin Formation

Chromatin formation requires both an adequate nucleotide supply and sufficient availability of histones. Chromatin must be assembled following DNA-based fundamental cellular processes such as replication and transcription to preserve genome integrity. Chromatin assembly is regulated by the orderly engagement of histones with a series of histone chaperones that guide newly synthesized histones from ribosomes to DNA. Although the synthesis of nucleotides and the histone proteins are the two major biosynthetic processes that complete the formation of chromatin, how these processes are coordinated remains unknown. Phosphoribosyl pyrophosphate synthetases (PRPSs) catalyze the first and rate-limiting step in the nucleotide biosynthesis pathway. PRPS enzymes form a complex with PRPS-associated proteins (PRPSAPs). In the present study, we discover that PRPS-PRPSAP enzyme complex are part of histone chaperone network. We show that PRPS enzymes are essential not only for nucleotide biogenesis, but together with PRPSAP also play a key role in the early steps in the process of histone maturation by regulating the interaction of histone chaperones with histone H3 and H4. Importantly, this regulation is separate from PRPS nucleotide biosynthetic activity. Depletion of PRPS proteins leads to limited histone availability and impaired chromatin assembly. Our discovery bridges cellular metabolism and chromatin regulation and provides the evidence of how nucleotide biogenesis and histone deposition are coordinated.

cell biology↗

bioRxiv2025

Distinct Control of histone H1 expression within the Histone Locus body by CRAMP1

Proper histone gene expression is critical to cell viability and maintaining genomic integrity. Multiple histone genes organized into three genomic loci encode for replication coupled core and linker histones. Histone gene expression and transcript processing is orchestrated in the histone locus body (HLB) within the nucleus. We identified human CRAMP1 as a selective regulator of linker histone H1 expression. CRAMP1 is recruited to the HLB in RPE1hTERT cells. Affinity purification shows that CRAMP1 physically associates the HLB component GON4L (a.k.a. YARP). We show that the PAH domains of GON4L interact with CRAMP1. CRAMP1 disruption results in a loss of histone H1 expression and a reduction in H1 protein. CRAMP1 occupies the unmethylated promoters of the replication coupled linker histone genes that reside within the histone locus body, and the replication independent histone H1 loci, which reside in a region of the genome without other histone genes. Together these data identify CRAMP1 as a novel and selective regulator of histone H1 gene expression.

genomics↗

bioRxiv2023

Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation

Proper chromosome segregation is required to ensure genomic and chromosomal stability. The centromere is a unique chromatin domain present throughout the cell cycle on each chromosome defined by the CENP-A nucleosome. Centromeres (CEN) are responsible for recruiting the kinetochore (KT) during mitosis, ultimately regulating spindle attachment and mitotic checkpoint function. Upregulation of many genes that encode the CEN/KT proteins is commonly observed in cancer. Here, we show although that FOXM1 occupies the promoters of many CEN/KT genes with MYBL2, occupancy is insufficient alone to drive the FOXM1 correlated transcriptional program. We show that CENP-F, a component of the outer kinetochore, functions with FOXM1 to coregulate G2/M transcription and proper chromosome segregation. Loss of CENP-F results in alteration of chromatin accessibility at G2/M genes, including CENP-A, and leads to reduced FOXM1-MBB complex formation. The FOXM1-CENP-F transcriptional coordination is a cancer-specific function. We observed that a few CEN/KT genes escape FOXM1 regulation such as CENP-C which when upregulated with CENP-A, leads to increased chromosome misegregation and cell death. Together, we show that the FOXM1 and CENP-F coordinately regulate G2/M gene expression, and this coordination is specific to a subset of genes to allow for proliferation and maintenance of chromosome stability for cancer cell survival.

cell biology↗

bioRxiv2022

Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer

Centromeres are known to cluster around nucleoli in drosophila and mammalian cells. However, the functional significance of nucleoli-centromere interaction remains underexplored. We hypothesize that if this conserved interaction is functionally important, it should be dynamic under different physiological and pathological conditions. We examined the nucleolar structure and centromeres at various differentiation stages using cell culture models. The results show dynamic changes of nucleolar number, area, and nucleoli-centromere interactions at differentiation stages and in cancer cells. Embryonic stem cells usually have a single large nucleolus, which associates with a high percentage of centromeres. As cells differentiate into intermediate states, the nucleolar number increases and the association with centromeres decreases. In terminally differentiated cells, including myotubes, neurons and keratinocytes, the number of nucleoli and their association with centromeres are at the lowest. Cancer cells demonstrate the pattern of nucleoli number and nucleoli-centromere association that is akin to proliferative less differentiated cell types, suggesting that nucleolar reorganization and changes in nucleoli-centromere interactions may help facilitate malignant transformation. This idea is supported in a case of pediatric rhabdomyosarcoma, in which induced differentiation inhibits cell proliferation and reduces nucleolar number and centromere association. These findings suggest active roles of nucleolar structure in centromere function and genome organization critical for cellular function in both normal development and cancer.

cell biology↗

bioRxiv2019

Coessential Genetic Networks Reveal the Organization and Constituents of a Dynamic Cellular Stress Response

The interrelated programs essential for cellular fitness in the face of stress are critical to understanding tumorigenesis, neurodegeneration, and aging. However, modelling the combinatorial landscape of stresses experienced by diseased cells is challenging, leaving functional relationships within the global stress response network incompletely understood. Here, we leverage genome-scale fitness screening data from 625 cancer cell lines, each representing a unique biological context, to build a network of "coessential" gene relationships centered around master regulators of the response to proteotoxic, oxidative, hypoxic, and genotoxic stress. This approach organizes the stress response into functional modules, identifies genes connecting distinct modules, and reveals mechanisms underlying cellular dependence on individual modules. As an example of the power of this approach, we discover that the previously unannotated HAPSTR (C16orf72) promotes resilience to diverse stressors as a stress-inducible regulator of the E3 ligase HUWE1. Altogether, we present a broadly applicable framework and interactive tool (http://fireworks.mendillolab.org/) to interrogate biological networks using unbiased genetic screens.

genetics↗