Biology subjects

Bersaglieri, C.

Publications and source records attributed to Bersaglieri, C..

6 recordsLinked to original sources

bioRxiv2026

Nucleolar buffering of lamina-associated heterochromatin restrains Progerin-induced ageing programs

Nucleolar enlargement is a conserved hallmark of physiological and premature ageing, including Hutchinson-Gilford Progeria Syndrome (HGPS), a disorder caused by LMNA mutations that produce Progerin and profoundly disrupt nuclear architecture. Although both the nuclear lamina and nucleolus organize repressive chromatin, how nucleolar remodelling contributes to genome reorganization during ageing driven by lamina dysfunction remains unclear. Here, we identify the nucleolus as a stress-responsive chromatin-organizing compartment that buffers the initial events of Progerin-induced ageing programs by sequestering lamina-associated domains (LADs). Despite widespread nuclear reorganization and robust transcriptional ageing signatures following Progerin expression, repression of LADs is preserved. This preservation results from an increased nucleolar association of lamina-released LADs, which can retain H3K9me2 and remain transcriptionally silent. Disrupting this compensatory pathway by depleting NPM1, a nucleolar factor required for nucleolar genome association, abolishes nucleolar buffering, leading to loss of H3K9me2 at relocated LADs, derepression of LAD-associated genes, exacerbation of transcriptional ageing programs, and increased DNA damage. Together, these findings establish the nucleolus as a structural fail-safe that preserves heterochromatin integrity and reveal stress-responsive nuclear compartmentalization as a fundamental mechanism safeguarding epigenome stability.

molecular biology↗

bioRxiv2024

LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis

In most eukaryotic cells, euchromatin is localized in the nuclear interior, whereas heterochromatin is enriched at the nuclear envelope (NE). This conventional chromatin organization is established by heterochromatin tethering to the NE, however its importance for cellular homeostasis is largely unexplored. Peripheral heterochromatin localization relies on redundant NE-tethering systems. One tether is constituted by the lamin B receptor (LBR) in mammals, but the enigmatic nature of the other tethers has hampered functional analyses. Here we demonstrate that the downregulation of abundant, ubiquitous NE proteins can induce the global detachment of heterochromatin from the NE. Among these factors, we identify LBR and LAP2 as major players in bulk heterochromatin attachment to the NE in pluripotent and differentiated mammalian cells. Their loss leads to repositioning of heterochromatin to the nuclear interior, changes in chromatin accessibility, deregulation of gene expression including activation of antiviral innate immunity, and defects in cell fate determination.

cell biology↗

bioRxiv2024

NPM1 mediates genome-nucleolus interactions and the establishment of their repressive chromatin states

Repressive chromatin domains are often located at the nuclear lamina (NL) or nucleolus. Although nucleolar associated domains (NADs) have been recently mapped, the mechanisms of NAD association with nucleoli and the functional significance of their localization remain unclear. Here, we show that NAD association with nucleoli is mediated by nucleophosmin (NPM1), a factor located within the granular component, the outer layer of the nucleolus. NPM1 binds NADs, interacts with the histone lysine methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of NPM1 mutant lacking the DNA binding domain (NPM1{Delta}DBD) caused NAD dissociation from nucleoli and H3K9me2 reduction specifically at NADs. G9a is dispensable for NAD contacts with nucleoli and interacts with NPM1{Delta}DBD, indicating that NADs acquire G9a-mediated H3K9me2 only after associating with NPM1 at nucleoli. The results provide mechanistic insights into how genomic domains associate with nucleoli and acquire their repressive chromatin state. Additionally, our findings suggest that the nucleolus not only serves as a scaffold for positioning repressive chromatin domains but also plays a direct role in establishing these chromatin states.

molecular biology↗

bioRxiv2022

PRAMEL7/CUL2 axis regulates NuRD stability to establish ground-state pluripotency in embryonic stem cells

Pluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, they only partially resemble the gene expression signature of developmental ground-state. Induced PRAMEL7 expression, a protein highly expressed in the ICM but lowly expressed in ESCs, reprograms developmentally advanced ESC+serum into ground-state pluripotency by causing DNA hypomethylation and gene expression signature close to developmental ground-state. However, how PRAMEL7 reprograms gene expression remains elusive. Here we show that PRAMEL7 associates with Cullin2 (CUL2) and this interaction is required to establish ground-state gene expression. PRAMEL7 recruits CUL2 to chromatin and targets for proteasomal degradation regulators of repressive chromatin, including NuRD complex. PRAMEL7 antagonizes NuRD-mediated repression of genes implicated in pluripotency by decreasing NuRD stability and promoter association in a CUL2-dependent manner. Our data link proteasome degradation pathways to ground-state gene expression, offering insights to generate in vitro models to reproduce the in vivo ground-state pluripotency.

developmental biology↗

bioRxiv2020

Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains

Eukaryotic chromosomes are folded into hierarchical domains, enabling the organization of the genome into functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks thought to contribute to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for genome-wide maps of nucleolar associated domains (NADs). Here we established a method based on a Dam-fused engineered nucleolar histone H2B that marks DNA contacting the nucleolus. NAD-maps of ESCs and neural progenitors revealed layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs showed higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation, chromosomes around the nucleolus acquire a more compact, rigid architecture whereas NADs specific for ESCs decrease their interaction strength within the repressive B-compartment strength, unlocking neural genes from repressive nuclear environment. The methodologies here developed will make possible to include the contribution of the nucleolus in future studies investigating the relationship between nuclear space and genome function.

genomics↗

bioRxiv2019

TIP5 safeguards genome architecture of ground-state pluripotent stem cells

Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. However, how genome compartmentalization is regulated remains elusive. We analyzed two closely and developmentally related pluripotent cell types: ground-state ESCs that have an open and active chromatin and developmentally advanced ESCs that display a more closed and repressed state. We show that these two ESC types differ in their regulation of genome organization due to their differential dependency on TIP5, a component of the chromatin remodeling complex NoRC. We show that TIP5 interacts on ESC chromatin with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. TIP5 associates with sub-domains within the active A compartment that strongly intersect through long-range contacts in ESCs. We found that only ground-state chromatin requires TIP5 to limit the invasion of active domains into repressive compartments. Depletion of TIP5 increased chromatin accessibility particularly at B compartments and decreased their repressive features. Furthermore, TIP5 acts as a barrier for the repressive H3K27me3 spreading, a process that also requires TOP2A activity. Finally, ground-state ESCs require TIP5 for growth, differentiation capacity, and correct expression of developmental genes. Our results revealed the propensity of open and active chromatin domains to invade repressive domains, an action counteracted by chromatin remodeling and the relief of chromatin torsional stress. This effort in controlling open/active chromatin domains is required to establish active and repressed genome partitioning and preserves cell function and identity.

molecular biology↗