Biology subjects

Grisanti, L.

Publications and source records attributed to Grisanti, L..

5 recordsLinked to original sources

bioRxiv2026

Exploring Disordered Regions of Human Spliceosome Proteins

Introns are removed from messenger RNAs by the spliceosome, a protein-RNA machinery enriched with intrinsically disordered regions (IDRs). Lacking stable 3D structures, IDRs can adopt diverse conformations interlacing proteins and RNAs components of the spliceosome and regulating splicing. Here we performed a comprehensive bioinformatics analysis of the human spliceosome proteome revealing that many proteins contain over 40% of disordered residues. Spliceosome IDRs are mainly driven by compositional bias due to an excess of charged and RS-like sequences, with both the nature and extent of this disorder being broadly conserved evolutionarily. Additionally, these IDRs are frequent targets of post-translational modifications, especially phosphorylation, and are hotspots for cancer-associated mutations, implicated in different cancer types. Our results collectively underscore central role of IDRs in splicing regulation and disease. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/698225v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@a6ed0dorg.highwire.dtl.DTLVardef@11514b7org.highwire.dtl.DTLVardef@103387borg.highwire.dtl.DTLVardef@713fde_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Genetic silencing of KCa3.1 inhibits atherosclerosis in ApoE null mice

Increased expression of KCa3.1 has been found in vascular smooth muscle (SMC), macrophages, and T cells in atherosclerotic lesions from humans and mice. Proliferating SMC cells increase the expression of KCa3.1, such that it becomes a dominant K+ channel and contributes to SMC cell migration. The efficacy of pharmacological inhibition of KCa3.1 in limiting atherosclerosis progression has been demonstrated in mice and pigs, however direct, loss-of-function, i.e. gene silencing, studies are absent. To investigate the role of KCa3.1, we used CRISPR/Cas9 to generate KCa3.1-/-Apoe-/- (DKO) mice and assessed lesion development in the brachiocephalic artery (BCA) of DKO versus Apoe-/- mice on a Western diet for 3 months. Notably, the loss of KCa3.1 did not affect serum total cholesterol or body weight. In BCAs of DKO mice, lesion size (0.036 mm{superscript 2} vs. 0.118 mm{superscript 2}, p<0.05) and relative stenosis (13.9% vs. 43.0%, p<0.05) were reduced by 70% compared to Apoe-/- mice, with no effect on medial or lumen area. Additionally, DKO mice exhibited a significant reduction in macrophage content within atherosclerotic plaques compared to Apoe-/- mice, independent of sex. In vitro migration assays further showed a significant reduction in migration of bone marrow-derived macrophages (BMDMs) from DKO mice compared to those from Apoe-/- mice. Furthermore, in vitro experiments using rat aortic smooth muscle cells (RAOSMCs) revealed significant inhibition of PDGF-BB-induced MCP1/Ccl21 expression upon KCa3.1 inhibition, while activation of KCa3.1 further enhanced MCP1/Ccl21 expression. Both in vivo and in vitro analyses showed that silencing KCa3.1 and sex had no significant effect on the collagen content of plaque. RNAseq analysis of BCA samples from DKO and Apoe-/- mice revealed PPAR-dependent signaling as a potential key mediator of the reduction in atherosclerosis due to KCa3.1 silencing. Overall, this study provides the first genetic evidence that KCa3.1 is a critical regulator of atherosclerotic lesion development and composition and provides novel mechanistic insight into the link between KCa3.1 and atherosclerosis.

physiology↗

bioRxiv2020

Intrinsic fluorescence in non-aromatic peptide structures is induced by collective vibrations, charge reorganisation and short hydrogen bonds, as shown in a new glutamine-related structure

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, we show that specific hydrogen bonding networks can significantly affect fluorescence employing a combined experimental and computational approach. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared to L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease non-radiative transition probabilities. Our findings open the doors for the design of new photoactive materials with biophotonic applications. Significance statementIntrinsic fluorescence of non-aromatic amino acids is a puzzling phenomenon with an enormous potential for technological and biomedical applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds in the networks on the ensuing fluorescence and we provide a detailed molecular mechanism to explain this unusual non-aromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.

biophysics↗

bioRxiv2018

Fate Before Function: Specification of the Hair Follicle Niche Occurs Prior to its Formation and Is Progenitor Dependent

Cell fate transitions are essential for specialization of stem cells and their niches, but the precise timing and sequence of molecular events during embryonic development are largely unknown. Here, we show that dermal condensates (DC), signaling niches for epithelial progenitors in hair placodes, are specified before niche formation and function. With 3D/4D microscopy we identify unclustered DC precursors. With population-based and single-cell transcriptomics we define a molecular time-lapse of dynamic niche signatures and the developmental trajectory as the DC lineage emerges from fibroblasts. Co-expression of downregulated fibroblast and upregulated DC genes in niche precursors reveals a transitory molecular state following a proliferation shutdown. Waves of transcription factor and signaling molecule expression then consolidate DC niche formation. Finally, ablation of epidermal Wnt signaling and placode-derived FGF20 demonstrates their requirement for DC-precursor specification. These findings uncover a progenitor-dependent niche precursor fate and the transitory molecular events controlling niche formation and function.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/414839_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (78K):\norg.highwire.dtl.DTLVardef@13fa73aorg.highwire.dtl.DTLVardef@1fbd280org.highwire.dtl.DTLVardef@1b8f66borg.highwire.dtl.DTLVardef@3a1ef9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIPrecursors of the hair follicle niche are specified before niche cluster formation\nC_LIO_LIBulk/single cell RNA-seq defines early niche fate at molecular transitional state\nC_LIO_LISuccessive waves of transcription factor/signaling genes mark niche fate acquisition\nC_LIO_LINiche fate acquisition is not \"pre-programmed\" and requires FGF20 from progenitors\nC_LI

developmental biology↗

bioRxiv2016

Hydrogen Bond Networks and HydrophobicEffects in the Amyloid β30-35 Chain in Water: A Molecular Dynamics Study

We study the conformational landscape of the C-terminal fragment of the Amyloid protein A{beta}30-35 in water using well-tempered metadynamics simulations and find that it resembles an intrinsically disordered protein. The conformational fluctuations of the protein are facilitated by a collective reorganization of both protein and water hydrogen bond networks, combined with electrostatic interactions between termini as well as hydrophobic interactions of the side chains. The stabilization of hydrophobic interactions in one of the conformers involves a collective collapse of the sidechains along with a squeeze out of water sandwiched in between. The charged N and C termini play a critical role in stabilizing different types of protein conformations including those involving contact ion salt-bridges as well as solvent mediated interactions of the termini and amide backbone. We examine this by probing the distribution of directed water wires forming the hydrogen bond network enveloping the polypeptide. Water wires and their fluctuations form an integral part of structural signature of the protein conformation.

neuroscience↗