Biology subjects

Pavesi, G.

Publications and source records attributed to Pavesi, G..

3 recordsLinked to original sources

bioRxiv2026

Transcription controls chromatin-nuclear lamina contacts through distinct Lamin A and LBR tethering mechanisms

Lamina-associated domains (LADs) are large genomic regions that interact with the nuclear lamina (NL). Much of the underlying "grammar" governing their positioning at the nuclear periphery remains unclear. LADs are composed of heterochromatin and typically harbor repressed genes, and their association with the NL is generally incompatible with strong transcriptional activity. The extent to which transcription globally shapes chromatin-NL interactions is not fully understood. Here, we combined acute transcription inhibition using Flavopiridol or Triptolide with genome-wide mapping of chromatin-NL contacts. We found that chromatin-NL interactions are rapidly rewired upon transcription inhibition. Changes in chromatin-NL contacts upon transcription shutdown are predictable based on transcriptional activity and the presence of H3K9me3-marked heterochromatin. This rewiring is reversible, as genome-NL interactions quickly return to baseline levels following drug wash-off. Notably, gain and loss of chromatin-NL interactions upon transcription shutdown reflect two distinct tethering mechanisms. Inter-LADs genomic regions (iLADs) enriched in highly active genes and located near stable LADs, which are tethered by Lamin A (LMNA/C), become re-attached to the NL following transcription inhibition. In parallel, H3K9-methylated regions tethered to the nuclear envelope by the Lamin B receptor (LBR) undergo extensive detachment from the NL. Strikingly, LMNA/C and LBR oppositely regulate transcription-sensitive LADs and are required for transcriptional control of chromatin-NL contacts. Together, our findings highlight the plasticity and dynamic nature of chromatin-NL interactions and provide the first evidence that LMNA/C- and LBR-mediated tethering mechanisms exhibit distinct sensitivities to transcription inhibition. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/738400v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@16781a2org.highwire.dtl.DTLVardef@6febd1org.highwire.dtl.DTLVardef@1e3220forg.highwire.dtl.DTLVardef@d137f7_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LITranscription inhibition alters chromatin-NL contacts rapidly and reversibly C_LIO_LIActive transcription prevents inter-LADs located near LMNA/C-tethered LADs from associating with the nuclear lamina. C_LIO_LILBR-tethered heterochromatin is repositioned away from the NL C_LIO_LITranscription-dependent modulation of chromatin-NL contacts is dependent on LMNA/C and partially on LBR C_LI

genomics↗

bioRxiv2024

Pathological PNPase variants with altered RNA binding and degradation activity affect the phenotype of bacterial and human cell models

Human PNPase (hPNPase) is an essential RNA exonuclease located in mitochondria, where it contributes to RNA import from the cytoplasm, degradation of mitochondrial RNA, and R-loop homeostasis. Biallelic mutations in the hPNPase PNPT1 gene cause different genetic diseases, ranging from hereditary hearing loss to Leigh syndrome. In this work, we used an Escherichia coli model we recently developed to test the effects of four pathological PNPT1 mutations associated with diseases of different severity. Moreover, we generated a new human cell model by introducing PNPT1 mutations into 293T cells via CRISPR-Cas editing. Notably, the bacterial cells expressing the different mutant alleles exhibited similar phenotypes consistent with hPNPase loss of function. In contrast, the human cell model responded differently to the two mutations tested, with responses correlating with the severity of the respective pathologies. We interpreted the data derived from both models in the light of the in vitro RNA binding and degradation activity of the purified wild-type and mutated hPNPase variants. We found that all pathogenic mutations tested caused defects in protein assembly and affected the degradation and RNA binding efficiency to varying degrees. However, the severity of the conditions caused by different mutations did not correlate with the catalytic activity of the mutant proteins. Also, we demonstrated that human PNPase, like its bacterial orthologue, is capable of trimming ssDNA and some mutations inhibit such activity.

genetics↗

bioRxiv2023

SOX2 and NR2F1 coordinate the gene expression program of the early postnatal visual thalamus

The thalamic dorsolateral geniculate nucleus, (dLGN) receives visual input from the retina via the optic nerve, and projects to the cortical visual area, where eye-derived signals are elaborated. The transcription factors SOX2 and NR2F1 are directly involved in the differentiation of dLGN neurons, based on mouse work and patient mutations leading to vision defects. However, whether they regulate each other, or control common targets is still unclear. By RNA-seq analysis of neonatal dLGN from thalamo-specific Sox2 and Nr2f1 mouse mutants, we found a striking overlap of deregulated genes. Among them, VGF, a cytokine transported along thalamic-cortical axons is strongly downregulated in both mutants. CUT&RUN analysis of SOX2 binding in dLGN chromatin identified a binding pattern characteristic of the dLGN. Collectively, the SOX2 and NR2F1- coregulated genes, and cognate SOX2 binding sites, contribute as a basis to understand the gene regulatory network driving the differentiation and connectivity of thalamic neurons.

developmental biology↗