Biology subjects

Gatto, A.

Publications and source records attributed to Gatto, A..

5 recordsLinked to original sources

bioRxiv2024

HIRA defines early replication initiation zones independently of their genome compartment

Chromatin states and 3D architecture have been used as proxy to identify replication initiation zones (IZs) in mammalian cells. While they do often correlate, their functional interconnections remain a puzzle. Here, we dissect these relationships by focusing on the histone H3.3 chaperone HIRA, which plays a role in both early initiation zone (IZ) definition and higher-order organisation of active chromatin. We monitored in parallel early replication initiation, chromatin accessibility, histone post-translational modifications (PTMs) and 3D organisation in wild-type cells, HIRA knock-out cells and HIRA knock-out cells complemented with HIRA. In the absence of HIRA, impaired early firing at HIRA-dependent IZs does not correspond to changes in chromatin accessibility or patterns of histone H3 PTMs. With respect to 3D organisation, a small subset of early IZs initially in compartment A switched to B and lost early initiation in the absence of HIRA. Critically, HIRA complementation restores these early IZ (and H3.3 variant enrichment) without substantial compartment reversal. Thus, our work reveals that regulation of early replication initiation by HIRA can be uncoupled from accessibility, histone mark patterns and compartment organisation.

cell biology↗

bioRxiv2024

HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation

The mammalian genome, organised into chromatin, adopts a three-dimensional (3D) folding within the cell nucleus with spatially segregated active and repressed compartments, termed A and B. However, how nucleosome deposition impacts these levels of organisation is unknown. Here, we monitored changes in 3D genome folding by Hi-C after impairing the chaperone HIRA, involved in histone H3.3 deposition. In the absence of HIRA, H3.3 enrichment decreases in compartment A that also shows weaker interactions. At this scale, histone post-translational modifications (PTMs) do not follow H3.3 changes. In line with impaired H3.3 nucleosome maintenance, compartment A accessibility measured by ATAC-seq increases. Specifically, at active genes, accessibility increases in gene bodies but decreases at promoters where compensation by H3.1 reduces nucleosome turnover. Notably, regions flanking active genes show reduced insulation. We conclude that the HIRA-dependent pathway involved in H3.3 deposition is key to maintain higher order organisation in active regions and impact compartmentalisation independently of histone PTMs.

cell biology↗

bioRxiv2023

Tumor microenvironment-induced FOXM1 regulates ovarian cancer stemness

In ovarian tumors, the omental microenvironment profoundly influences the behavior of cancer cells and sustains the acquisition of stem-like traits, with major impacts on tumor aggressiveness and relapse. Here, we exploit a patient-derived platform of organotypic cultures to study the crosstalk between the tumor microenvironment and ovarian cancer stem cells. The pro-tumorigenic transcription factor FOXM1 is specifically induced by the microenvironment in ovarian cancer stem cells, through activation of FAK/YAP signaling. The microenvironment-induced FOXM1 sustains stemness, and its inactivation reduces cancer stem cells survival in the omental niche and enhances their response to the PARP inhibitor Olaparib. By unveiling the novel role of FOXM1 in ovarian cancer stemness, our findings highlight patient-derived organotypic co-cultures as a powerful tool to capture clinically relevant mechanisms of the microenvironment/stem cells crosstalk, contributing to the identification of tumor vulnerabilities.

cancer biology↗

bioRxiv2022

Regulation of replicative histone RNA metabolism by the histone chaperone ASF1

In S phase, duplication and assembly of the whole genome into chromatin requires upregulation of replicative histone gene expression. Here, we explored a potential role of histone chaperones in this process thereby linking chromatin assembly with histone production in human cells. Depletion of the ASF1 chaperone specifically decreased the pool of replicative histones both at the levels of soluble protein and total RNA, while depletion of CAF-1 did not. Most replicative histone genes decreased in their overall expression as revealed by total RNA-seq. In contrast, both their newly synthesized RNAs and nascent RNAs at transcription sites increased as shown by 4sU-labeled RNA-seq and single-molecule RNA FISH, respectively. Further inspection of the sequences corresponding to replicative histone RNAs showed a 3 processing defect, leading to unprocessed transcripts usually targeted for degradation. We discuss how this regulation of replicative histone RNA metabolism by ASF1 fine-tunes the histone dosage to avoid unbalanced situations deleterious for cell survival.

molecular biology↗

bioRxiv2020

CENP-A overexpression drives distinct cell fates depending on p53 status

Tumour evolution is driven by both genetic and epigenetic changes. CENP-A, the centromeric histone H3 variant, is an epigenetic mark that directly perturbs genetic stability and chromatin when overexpressed. Although CENP-A overexpression is a common feature of many cancers, how this impacts cell fate and response to therapy remains unclear. Here, we established a tunable system of inducible and reversible CENP-A overexpression combined with a switch in p53 status in human cell lines. Through clonogenic survival assays and single-cell RNA-sequencing over time, we uncover the tumour suppressor p53 as a key determinant of how CENP-A impacts cell state, cell identity and therapeutic response. If p53 is functional, CENP-A overexpression promotes senescence and radiosensitivity. But, when we inactivate p53, CENP-A overexpression instead promotes epithelial-mesenchymal transition, an essential precursor for tumour cell invasion and metastasis. Thus, CENP-A overexpression drives distinct cell fates depending on p53 status, with important implications for tumour evolution.

cancer biology↗