Biology subjects

Lanzuolo, C.

Publications and source records attributed to Lanzuolo, C..

7 recordsLinked to original sources

bioRxiv2026

LBR nucleoplasmic domains regulate X-chromosome solubility and nuclear organization

The nuclear lamina plays a central role in genome organization, yet how specific lamina-associated proteins regulate chromosome architecture during development remains unclear. Here, we show that the nucleoplasmic domains of the Lamin B Receptor (LBR) are essential for X-chromosome localization at the nuclear periphery and chromatin architecture during neural differentiation. Using genetic dissection of LBR function, combined with genome-wide chromatin solubility profiling and transcriptional analyses, we demonstrate that loss of LBR N-terminal domains impairs proper cell differentiation and X chromosome inactivation (XCI), selectively disrupting chromatin structure in neural progenitors but not in pluripotent cells. Strikingly, these effects are disproportionately concentrated - but not limited to - on the inactive X chromosome, which undergoes a pronounced shift toward a more soluble chromatin state. Our findings establish the nucleoplasmic function of LBR as a key determinant of X-chromosome functionality and identify chromatin solubility and accessibility as a previously underappreciated layer of genome regulation by the nuclear lamina in XCI. Finally, our work provides definitive genetic evidence that LBRs nuclear architectural functions are molecularly separable from its metabolic sterol reductase activity, which is preserved in our model, and are critically necessary for XCI in differentiating mouse female XX ESCs models.

genetics↗

bioRxiv2024

The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation

The transition of embryonic stem cells (ESCs) from pluripotency to lineage commitment is regulated by multiple mechanisms, including chromatin dynamics and both transcriptional and post-transcriptional processes. Recent advances have highlighted that these mechanisms often interact, forming intricate multi-layered regulatory networks that require detailed characterization. In this study, we demonstrate that the RNA-binding protein LIN28A plays a pivotal role in neuronal differentiation by mediating RNA-dependent interactions with the Polycomb repressive complex 2 (PRC2). This interaction facilitates the eviction of PRC2 from chromatin, thereby activating a neuronal lineage-specific transcriptional program. Proteomic analyses revealed that the LIN28A interactome undergoes substantial remodeling during differentiation, corresponding to changes in LIN28A localization. In ESCs, LIN28A is predominantly nuclear and interacts with several components of the PRC2 complex in an RNA-dependent manner, assisting in chromatin dynamics. Our findings show that in the absence of LIN28A, PRC2 remains associated with chromatin, impairing the expression of genes critical for neuronal differentiation in ESCs. Chromatin immunoprecipitation sequencing (ChIP-seq) further confirmed that loss of LIN28A results in preferential PRC2 occupancy at the promoters of differentiation-associated genes. This study uncovers a novel role for LIN28A in epigenetic remodeling, which is essential for the proper differentiation of ESCs into the neuronal lineage.

molecular biology↗

bioRxiv2024

The molecular basis of lamin-specific chromatin interactions

In the cell nucleus, chromatin is anchored to the nuclear lamina, a network of lamin filaments and binding proteins that underly the inner nuclear membrane. The nuclear lamina is involved in chromatin organisation through the interaction of lamina-associated domains (LADs) within the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction with cryo-electron tomography (cryo-ET), we analysed the distribution of nucleosomes at the lamin-chromatin interface. Depletion of lamin A/C reduced the concentration of nucleosomes at the nuclear periphery, suggesting that lamins are directly involved in the interaction with chromatin. Using cryo-electron microscopy (cryo-EM), we then identified the specific binding motif of the lamin A tail domain that interacts with nucleosomes, distinguishing it from the other lamin isoforms. Furthermore, we examined chromatin structure dynamics using a genome-wide analysis that revealed lamin-dependent macroscopic-scale alterations in gene expression and chromatin remodelling. Our findings provide detailed insights into the dynamic and structural interplay between lamin isoforms and chromatin, molecular interactions which are shaping chromatin architecture and epigenetic regulation.

cell biology↗

bioRxiv2024

Biochemical properties of chromatin domains define genome compartmentalization

Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10,000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their 3D compartmentalization in one single experiment.

genomics↗

bioRxiv2024

Sorafenib induces muscle wasting by disrupting the activity of distinct chromatin regulators

Adverse effects of chemotherapies can outweigh the benefits in cancer patients. Various chemotherapeutics are linked to muscle wasting or cachexia, drastically reducing the chance of survivability of cancer patients. Insights into the molecular basis of chemotherapy-induced cachexia is an unmet need to improve the treatment strategies. Here, we investigated the tyrosine kinase inhibitor class of chemotherapeutic agents for their effects on muscle function. Sorafenib, but not Nilotinib and Imatinib, triggered cachexia. System-wide transcriptome and proteome analyses revealed that Sorafenib alters the global transcriptional program and proteostasis in muscle cells. Mechanistically, Sorafenib treatment reduced active epigenetic mark H3K4 methylation on distinct muscle-specific genes due to the defective chromatin association of SET1/A, a catalytic component of the SET1/MLL complex. It favored transcriptionally incompetent chromatin, characterized by diminished association with RNA polymerase II. The transcriptional reorientation led to disrupted sarcomere organization, calcium homeostasis, and mitochondrial respiration. Consequently, the contractile ability of muscle cells was severely compromised. Collectively, we identified an unanticipated transcriptional mechanism underlying Sorafenib-induced cachexia. Our findings hold the potential to strategize therapy regimens to minimize chemotherapy-induced cachexia and improve treatment outcomes.

cell biology↗

bioRxiv2020

A ChIC solution for ChIP-seq quality assessment

Despite the widespread adoption of the ChIP-seq technique, there is still no consensus on quality assessment procedures. Quantitative metrics previously proposed in literature are not always effective in discriminating the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. Here we introduce ChIC, a new framework for ChIP-seq data quality assessment that overcomes the limitations of previous solutions. ChIC is the first method for ChIP-seq quality control directly considering the enrichment profile shape, thus achieving good performances on ChIP targets yielding sharp and broad peaks alike. We integrate a comprehensive set of quality control metrics into one single score reliably summarizing the sample quality. The ChIC score is based on a machine learning classifier trained on a compendium with thousands of ChIP-seq profiles, which can also be used as a reference for easier evaluation of new datasets. ChIC is implemented as a user-friendly R/Bioconductor package.

bioinformatics↗

bioRxiv2019

Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis

Hutchinson-Gilford progeria syndrome (HGPS) is characterized by the progressive accumulation of progerin, an aberrant form of Lamin A. This leads to chromatin structure disruption, in particular by interfering with Lamina Associated Domains. Although several cellular and molecular alterations have been characterized, it is still unclear how chromatin structural changes translate into premature senescence in HGPS. Moreover, early events in chromatin remodeling have not been detected so far. We developed a new high-throughput sequencing-based method, named SAMMY-seq, for genome-wide characterization of heterochromatin accessibility changes. Using SAMMY-seq, we detected early stage alterations of chromatin structure in HGPS primary fibroblasts. Of note, these structural changes do not disrupt the distribution of H3K9me3 but are associated with site-specific H3K27me3 variations and transcriptional dysregulation of Polycomb target genes. Our results show that SAMMY-seq represents a novel and sensitive tool to characterize heterochromatin alterations. Moreover, we found that the assembly of lamin associated domains is strictly connected to the correct Polycomb repression, rapidly lost in early HGPS pathogenesis.

molecular biology↗