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1.
Cell ; 176(1-2): 391-403.e19, 2019 01 10.
Article in English | MEDLINE | ID: mdl-30528433

ABSTRACT

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-related changes in the total proteome. In addition, we combine XRNAX with crosslinking immunoprecipitation sequencing (CLIP-seq) to validate the interaction of ncRNA with lamin B1 and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.


Subject(s)
High-Throughput Nucleotide Sequencing/methods , RNA-Binding Proteins/isolation & purification , RNA/isolation & purification , Binding Sites , Exosome Multienzyme Ribonuclease Complex/metabolism , Humans , Immunoprecipitation/methods , Lamin Type B/metabolism , Protein Binding/genetics , Protein Binding/physiology , Protein Biosynthesis/genetics , Protein Biosynthesis/physiology , Protein Processing, Post-Translational , Proteins/isolation & purification , Proteins/metabolism , Proteome/metabolism , Proteomics/methods , RNA/genetics , RNA/metabolism , RNA, Messenger/metabolism , RNA, Untranslated/metabolism , RNA-Binding Proteins/metabolism , Transcriptome
2.
Mol Cell ; 82(3): 696-708.e4, 2022 02 03.
Article in English | MEDLINE | ID: mdl-35090599

ABSTRACT

We have used a combination of chemical genetics, chromatin proteomics, and imaging to map the earliest chromatin transactions during vertebrate cell entry into mitosis. Chicken DT40 CDK1as cells undergo synchronous mitotic entry within 15 min following release from a 1NM-PP1-induced arrest in late G2. In addition to changes in chromatin association with nuclear pores and the nuclear envelope, earliest prophase is dominated by changes in the association of ribonucleoproteins with chromatin, particularly in the nucleolus, where pre-rRNA processing factors leave chromatin significantly before RNA polymerase I. Nuclear envelope barrier function is lost early in prophase, and cytoplasmic proteins begin to accumulate on the chromatin. As a result, outer kinetochore assembly appears complete by nuclear envelope breakdown (NEBD). Most interphase chromatin proteins remain associated with chromatin until NEBD, after which their levels drop sharply. An interactive proteomic map of chromatin transactions during mitotic entry is available as a resource at https://mitoChEP.bio.ed.ac.uk.


Subject(s)
Chromatin Assembly and Disassembly , Chromatin/metabolism , Chromosomes , DNA/metabolism , Lymphoma, B-Cell/metabolism , Nuclear Proteins/metabolism , Prophase , Proteome , Proteomics , Animals , CDC2 Protein Kinase/genetics , CDC2 Protein Kinase/metabolism , Cell Line, Tumor , Chickens , Chromatin/genetics , DNA/genetics , Lamin Type B/genetics , Lamin Type B/metabolism , Lymphoma, B-Cell/genetics , Lymphoma, B-Cell/pathology , Nuclear Proteins/genetics , Protein Binding , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism , Time Factors
3.
Cell ; 159(4): 829-43, 2014 Nov 06.
Article in English | MEDLINE | ID: mdl-25417159

ABSTRACT

Aging of immune organs, termed as immunosenescence, is suspected to promote systemic inflammation and age-associated disease. The cause of immunosenescence and how it promotes disease, however, has remained unclear. We report that the Drosophila fat body, a major immune organ, undergoes immunosenescence and mounts strong systemic inflammation that leads to deregulation of immune deficiency (IMD) signaling in the midgut of old animals. Inflamed old fat bodies secrete circulating peptidoglycan recognition proteins that repress IMD activity in the midgut, thereby promoting gut hyperplasia. Further, fat body immunosenecence is caused by age-associated lamin-B reduction specifically in fat body cells, which then contributes to heterochromatin loss and derepression of genes involved in immune responses. As lamin-associated heterochromatin domains are enriched for genes involved in immune response in both Drosophila and mammalian cells, our findings may provide insights into the cause and consequence of immunosenescence during mammalian aging. PAPERFLICK:


Subject(s)
Drosophila Proteins/metabolism , Drosophila melanogaster/metabolism , Fat Body/immunology , Lamin Type B/metabolism , Aging , Animals , Cell Proliferation , Drosophila melanogaster/chemistry , Drosophila melanogaster/immunology , Fat Body/growth & development , Fat Body/metabolism , Gastrointestinal Tract/growth & development , Gastrointestinal Tract/immunology , Gastrointestinal Tract/metabolism , Heterochromatin , Inflammation/immunology , Mammals/immunology , Models, Animal , Signal Transduction
4.
Nature ; 620(7975): 863-872, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37587336

ABSTRACT

Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function1-8. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.


Subject(s)
Cellular Reprogramming , Epigenesis, Genetic , Induced Pluripotent Stem Cells , Humans , Chromatin/genetics , Chromatin/metabolism , DNA Demethylation , DNA Methylation , DNA Transposable Elements , Induced Pluripotent Stem Cells/cytology , Induced Pluripotent Stem Cells/metabolism , Human Embryonic Stem Cells/cytology , Human Embryonic Stem Cells/metabolism , Lamin Type B
5.
Cell ; 154(3): 583-95, 2013 Aug 01.
Article in English | MEDLINE | ID: mdl-23911323

ABSTRACT

Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs. Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control. IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes. Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content. IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway. In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis. Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation.


Subject(s)
Granulocytes/metabolism , Hematopoiesis , RNA Splicing , Algorithms , Animals , Base Composition , Cell Nucleus/metabolism , Down-Regulation , Granulocytes/cytology , Humans , Introns , Lamin Type B/genetics , Mice , Mice, Inbred C57BL , Nonsense Mediated mRNA Decay
6.
Nature ; 607(7920): 790-798, 2022 07.
Article in English | MEDLINE | ID: mdl-35768505

ABSTRACT

Ageing is intimately connected to the induction of cell senescence1,2, but why this is so remains poorly understood. A key challenge is the identification of pathways that normally suppress senescence, are lost during ageing and are functionally relevant to oppose ageing3. Here we connected the structural and functional decline of ageing tissues to attenuated function of the master effectors of cellular mechanosignalling YAP and TAZ. YAP/TAZ activity declines during physiological ageing in stromal cells, and mimicking such decline through genetic inactivation of YAP/TAZ in these cells leads to accelerated ageing. Conversely, sustaining YAP function rejuvenates old cells and opposes the emergence of ageing-related traits associated with either physiological ageing or accelerated ageing triggered by a mechano-defective extracellular matrix. Ageing traits induced by inactivation of YAP/TAZ are preceded by induction of tissue senescence. This occurs because YAP/TAZ mechanotransduction suppresses cGAS-STING signalling, to the extent that inhibition of STING prevents tissue senescence and premature ageing-related tissue degeneration after YAP/TAZ inactivation. Mechanistically, YAP/TAZ-mediated control of cGAS-STING signalling relies on the unexpected role of YAP/TAZ in preserving nuclear envelope integrity, at least in part through direct transcriptional regulation of lamin B1 and ACTR2, the latter of which is involved in building the peri-nuclear actin cap. The findings demonstrate that declining YAP/TAZ mechanotransduction drives ageing by unleashing cGAS-STING signalling, a pillar of innate immunity. Thus, sustaining YAP/TAZ mechanosignalling or inhibiting STING may represent promising approaches for limiting senescence-associated inflammation and improving healthy ageing.


Subject(s)
Aging , Membrane Proteins , Nucleotidyltransferases , Stromal Cells , Transcriptional Coactivator with PDZ-Binding Motif Proteins , YAP-Signaling Proteins , Actin-Related Protein 2/metabolism , Aging/metabolism , Cellular Senescence , Extracellular Matrix , Healthy Aging , Immunity, Innate , Lamin Type B/metabolism , Mechanotransduction, Cellular/genetics , Membrane Proteins/metabolism , Nuclear Envelope/metabolism , Nucleotidyltransferases/metabolism , Signal Transduction , Stromal Cells/metabolism , Transcriptional Coactivator with PDZ-Binding Motif Proteins/antagonists & inhibitors , Transcriptional Coactivator with PDZ-Binding Motif Proteins/metabolism , YAP-Signaling Proteins/antagonists & inhibitors , YAP-Signaling Proteins/metabolism
7.
Cell ; 148(4): 752-64, 2012 Feb 17.
Article in English | MEDLINE | ID: mdl-22341447

ABSTRACT

Local protein synthesis plays a key role in regulating stimulus-induced responses in dendrites and axons. Recent genome-wide studies have revealed that thousands of different transcripts reside in these distal neuronal compartments, but identifying those with functionally significant roles presents a challenge. We performed an unbiased screen to look for stimulus-induced, protein synthesis-dependent changes in the proteome of Xenopus retinal ganglion cell (RGC) axons. The intermediate filament protein lamin B2 (LB2), normally associated with the nuclear membrane, was identified as an unexpected major target. Axonal ribosome immunoprecipitation confirmed translation of lb2 mRNA in vivo. Inhibition of lb2 mRNA translation in axons in vivo does not affect guidance but causes axonal degeneration. Axonal LB2 associates with mitochondria, and LB2-deficient axons exhibit mitochondrial dysfunction and defects in axonal transport. Our results thus suggest that axonally synthesized lamin B plays a crucial role in axon maintenance by promoting mitochondrial function.


Subject(s)
Axons/metabolism , Lamin Type B/metabolism , Mitochondria/metabolism , Retinal Ganglion Cells/metabolism , Xenopus laevis/embryology , Animals , Axonal Transport , Embryo, Nonmammalian/metabolism , Protein Biosynthesis , Xenopus laevis/metabolism
8.
Proc Natl Acad Sci U S A ; 121(27): e2406946121, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38917015

ABSTRACT

Progerin, the protein that causes Hutchinson-Gilford progeria syndrome, triggers nuclear membrane (NM) ruptures and blebs, but the mechanisms are unclear. We suspected that the expression of progerin changes the overall structure of the nuclear lamina. High-resolution microscopy of smooth muscle cells (SMCs) revealed that lamin A and lamin B1 form independent meshworks with uniformly spaced openings (~0.085 µm2). The expression of progerin in SMCs resulted in the formation of an irregular meshwork with clusters of large openings (up to 1.4 µm2). The expression of progerin acted in a dominant-negative fashion to disrupt the morphology of the endogenous lamin B1 meshwork, triggering irregularities and large openings that closely resembled the irregularities and openings in the progerin meshwork. These abnormal meshworks were strongly associated with NM ruptures and blebs. Of note, the progerin meshwork was markedly abnormal in nuclear blebs that were deficient in lamin B1 (~50% of all blebs). That observation suggested that higher levels of lamin B1 expression might normalize the progerin meshwork and prevent NM ruptures and blebs. Indeed, increased lamin B1 expression reversed the morphological abnormalities in the progerin meshwork and markedly reduced the frequency of NM ruptures and blebs. Thus, progerin expression disrupts the overall structure of the nuclear lamina, but that effect-along with NM ruptures and blebs-can be abrogated by increased lamin B1 expression.


Subject(s)
Lamin Type A , Lamin Type B , Nuclear Lamina , Nuclear Lamina/metabolism , Lamin Type A/metabolism , Lamin Type A/genetics , Lamin Type B/metabolism , Lamin Type B/genetics , Humans , Progeria/metabolism , Progeria/genetics , Progeria/pathology , Animals , Protein Precursors/metabolism , Protein Precursors/genetics , Myocytes, Smooth Muscle/metabolism , Myocytes, Smooth Muscle/pathology , Mice
9.
PLoS Genet ; 19(6): e1010805, 2023 06.
Article in English | MEDLINE | ID: mdl-37347778

ABSTRACT

Pelger-Huët anomaly (PHA) in humans is an autosomal dominant hematological phenotype without major clinical consequences. PHA involves a characteristic hyposegmentation of granulocytes (HG). Human PHA is caused by heterozygous loss of function variants in the LBR gene encoding lamin receptor B. Bi-allelic variants and complete deficiency of LBR cause the much more severe Greenberg skeletal dysplasia which is lethal in utero and characterized by massive skeletal malformation and gross fetal hydrops. HG phenotypes have also been described in domestic animals and homology to human PHA has been claimed in the literature. We studied a litter of Australian Shepherd Dogs with four stillborn puppies in which both parents had an HG phenotype. Linkage analysis excluded LBR as responsible gene for the stillborn puppies. We then investigated the HG phenotype in Australian Shepherd Dogs independently of the prenatal lethality. Genome-wide association mapped the HG locus to chromosome 27 and established an autosomal recessive mode of inheritance. Whole genome sequencing identified a splice site variant in LMBR1L, c.191+1G>A, as most likely causal variant for the HG phenotype. The mutant allele abrogates the expression of the longer X2 isoform but does not affect transcripts encoding the shorter X1 isoform of the LMBR1L protein. The homozygous mutant LMBR1L genotype associated with HG is common in Australian Shepherd Dogs and was found in 39 of 300 genotyped dogs (13%). Our results point to a previously unsuspected function of LMBR1L in the myeloid lineage of leukocytes.


Subject(s)
Genome-Wide Association Study , Pelger-Huet Anomaly , Female , Pregnancy , Dogs , Humans , Animals , Receptors, Cytoplasmic and Nuclear/genetics , Australia , Granulocytes , Genotype , Pelger-Huet Anomaly/genetics , Lamin Type B/genetics , Receptors, Cell Surface/genetics
10.
Hum Mol Genet ; 32(5): 745-763, 2023 02 19.
Article in English | MEDLINE | ID: mdl-36124691

ABSTRACT

Lamin B Receptor (LBR) is an inner nuclear membrane protein that assembles the nuclear envelope post mitosis. Here we show that LBR depletion induces mitotic defects accompanied by recurrent chromosomal losses. In addition, LBR knockdown results in nuclear aberrations such as nuclear blebs and micronuclei, with chromosomes showing higher frequency of losses, being enriched within the micronucleus. Furthermore, doxycycline-induced conditional depletion of LBR significantly increased tumor volumes that form within the subcutaneous xenografts of mice. Of note, the tumor-derived primary cells recapitulated chromosomal losses and gains, revealing a novel role for LBR as a tumor suppressor. Co-immunoprecipitation of LBR uncovered an association of LBR with telomere-associated factors. Interestingly, qPCR array-based gene expression profiling showed a significant upregulation of telomere repeat-binding factor 1 (TRF1) upon LBR depletion. Remarkably, TRF1 knockdown in the background of LBR depletion maintains chromosomal stability, unraveling a novel mechanism involving LBR and TRF in the maintenance of chromosomal stability in colorectal cancer cells.


Subject(s)
Nuclear Envelope , Receptors, Cytoplasmic and Nuclear , Humans , Animals , Mice , Nuclear Envelope/metabolism , Membrane Proteins/metabolism , Carcinogenesis , Chromosomal Instability , Lamin Type B/metabolism , Lamin B Receptor
11.
EMBO J ; 40(3): e105819, 2021 02 01.
Article in English | MEDLINE | ID: mdl-33300615

ABSTRACT

Neurogenesis in the adult hippocampus declines with age, a process that has been implicated in cognitive and emotional impairments. However, the mechanisms underlying this decline have remained elusive. Here, we show that the age-dependent downregulation of lamin B1, one of the nuclear lamins in adult neural stem/progenitor cells (ANSPCs), underlies age-related alterations in adult hippocampal neurogenesis. Our results indicate that higher levels of lamin B1 in ANSPCs safeguard against premature differentiation and regulate the maintenance of ANSPCs. However, the level of lamin B1 in ANSPCs declines during aging. Precocious loss of lamin B1 in ANSPCs transiently promotes neurogenesis but eventually depletes it. Furthermore, the reduction of lamin B1 in ANSPCs recapitulates age-related anxiety-like behavior in mice. Our results indicate that the decline in lamin B1 underlies stem cell aging and impacts the homeostasis of adult neurogenesis and mood regulation.


Subject(s)
Aging/metabolism , Anxiety/genetics , Down-Regulation , Hippocampus/cytology , Lamin Type B/genetics , Lamin Type B/metabolism , Aging/genetics , Animals , Cell Differentiation , Cell Line , Disease Models, Animal , Female , Hippocampus/metabolism , Male , Mice , Neural Stem Cells/cytology , Neural Stem Cells/metabolism , Neurogenesis , Rats
12.
J Cell Sci ; 136(7)2023 04 01.
Article in English | MEDLINE | ID: mdl-36825599

ABSTRACT

SUN domain proteins are conserved proteins of the nuclear envelope and key components of the LINC complexes (for 'linkers of the nucleoskeleton and the cytoskeleton'). Previous studies have demonstrated that the testis-specific SUN domain protein SUN4 (also known as SPAG4) is a vital player in the directed shaping of the spermatid nucleus. However, its molecular properties relating to this crucial function have remained largely unknown, and controversial data for the organization and orientation of SUN4 within the spermatid nuclear envelope have been presented so far. Here, we have re-evaluated this issue in detail and show robust evidence that SUN4 is integral to the inner nuclear membrane, sharing a classical SUN domain protein topology. The C-terminal SUN domain of SUN4 localizes to the perinuclear space, whereas the N-terminus is directed to the nucleoplasm, interacting with the spermiogenesis-specific lamin B3. We found that SUN4 forms heteromeric assemblies with SUN3 in vivo and regulates SUN3 expression. Together, our results contribute to a better understanding of the specific function of SUN4 at the spermatid nucleo-cytoplasmic junction and the process of sperm-head formation.


Subject(s)
Nuclear Envelope , Spermatids , Humans , Male , Membrane Proteins/metabolism , Nuclear Envelope/metabolism , Semen/metabolism , Spermatids/metabolism , Nuclear Proteins/metabolism , Lamin Type B
13.
Cell ; 143(2): 288-98, 2010 Oct 15.
Article in English | MEDLINE | ID: mdl-20946986

ABSTRACT

The size of the nucleus varies among different cell types, species, and disease states, but mechanisms of nuclear size regulation are poorly understood. We investigated nuclear scaling in the pseudotetraploid frog Xenopus laevis and its smaller diploid relative Xenopus tropicalis, which contains smaller cells and nuclei. Nuclear scaling was recapitulated in vitro using egg extracts, demonstrating that titratable cytoplasmic factors determine nuclear size to a greater extent than DNA content. Nuclear import rates correlated with nuclear size, and varying the concentrations of two transport factors, importin α and Ntf2, was sufficient to account for nuclear scaling between the two species. Both factors modulated lamin B3 import, with importin α increasing overall import rates and Ntf2 reducing import based on cargo size. Importin α also contributes to nuclear size changes during early X. laevis development. Thus, nuclear transport mechanisms are physiological regulators of both interspecies and developmental nuclear scaling.


Subject(s)
Cell Nucleus , Nucleocytoplasmic Transport Proteins/metabolism , Xenopus Proteins/metabolism , Xenopus laevis/metabolism , Xenopus/metabolism , alpha Karyopherins/metabolism , Active Transport, Cell Nucleus , Animals , Lamin Type B/metabolism , Xenopus/embryology , Xenopus laevis/embryology
14.
Cell Mol Life Sci ; 81(1): 141, 2024 Mar 14.
Article in English | MEDLINE | ID: mdl-38485766

ABSTRACT

Human papillomavirus (HPV) infection is a primary cause of cervical and head-and-neck cancers. The HPV genome enters the nucleus during mitosis when the nuclear envelope disassembles. Given that lamins maintain nuclear integrity during interphase, we asked to what extent their loss would affect early HPV infection. To address this question, we infected human cervical cancer cells and keratinocytes lacking the major lamins with a HPV16 pseudovirus (HP-PsV) encoding an EGFP reporter. We found that a sustained reduction or complete loss of lamin B1 significantly increased HP-PsV infection rate. A corresponding greater nuclear HP-PsV load in LMNB1 knockout cells was directly related to their prolonged mitotic window and extensive nuclear rupture propensity. Despite the increased HP-PsV presence, EGFP transcript levels remained virtually unchanged, indicating an additional defect in protein turnover. Further investigation revealed that LMNB1 knockout led to a substantial decrease in autophagic capacity, possibly linked to the persistent activation of cGAS by cytoplasmic chromatin exposure. Thus, the attrition of lamin B1 increases nuclear perviousness and attenuates autophagic capacity, creating an environment conducive to unrestrained accumulation of HPV capsids. Our identification of lower lamin B1 levels and nuclear BAF foci in the basal epithelial layer of several human cervix samples suggests that this pathway may contribute to an increased individual susceptibility to HPV infection.


Subject(s)
Lamin Type B , Papillomavirus Infections , Female , Humans , Lamin Type B/genetics , Lamin Type B/metabolism , Papillomavirus Infections/genetics , Nuclear Envelope/metabolism , Mitosis , Chromosomes/metabolism , Lamin Type A/genetics , Lamin Type A/metabolism
15.
Proc Natl Acad Sci U S A ; 119(17): e2121816119, 2022 04 26.
Article in English | MEDLINE | ID: mdl-35439057

ABSTRACT

The ability of a cell to regulate its mechanical properties is central to its function. Emerging evidence suggests that interactions between the cell nucleus and cytoskeleton influence cell mechanics through poorly understood mechanisms. Here we conduct quantitative confocal imaging to show that the loss of A-type lamins tends to increase nuclear and cellular volume while the loss of B-type lamins behaves in the opposite manner. We use fluorescence recovery after photobleaching, atomic force microscopy, optical tweezer microrheology, and traction force microscopy to demonstrate that A-type lamins engage with both F-actin and vimentin intermediate filaments (VIFs) through the linker of nucleoskeleton and cytoskeleton (LINC) complexes to modulate cortical and cytoplasmic stiffness as well as cellular contractility in mouse embryonic fibroblasts (MEFs). In contrast, we show that B-type lamins predominantly interact with VIFs through LINC complexes to regulate cytoplasmic stiffness and contractility. We then propose a physical model mediated by the lamin­LINC complex that explains these distinct mechanical phenotypes (mechanophenotypes). To verify this model, we use dominant negative constructs and RNA interference to disrupt the LINC complexes that facilitate the interaction of the nucleus with the F-actin and VIF cytoskeletons and show that the loss of these elements results in mechanophenotypes like those observed in MEFs that lack A- or B-type lamin isoforms. Finally, we demonstrate that the loss of each lamin isoform softens the cell nucleus and enhances constricted cell migration but in turn increases migration-induced DNA damage. Together, our findings uncover distinctive roles for each of the four major lamin isoforms in maintaining nucleocytoskeletal interactions and cellular mechanics.


Subject(s)
Fibroblasts , Nuclear Lamina , Animals , Cell Nucleus/metabolism , Cytoskeleton/metabolism , Fibroblasts/metabolism , Lamin Type A/genetics , Lamin Type A/metabolism , Lamin Type B/genetics , Lamin Type B/metabolism , Mice , Nuclear Lamina/metabolism , Nuclear Matrix/metabolism , Protein Isoforms/genetics , Protein Isoforms/metabolism
16.
J Cell Physiol ; 239(5): e31213, 2024 May.
Article in English | MEDLINE | ID: mdl-38308641

ABSTRACT

Recent studies have shown that nucleophagy can mitigate DNA damage by selectively degrading nuclear components protruding from the nucleus. However, little is known about the role of nucleophagy in neurons after spinal cord injury (SCI). Western blot analysis and immunofluorescence were performed to evaluate the nucleophagy after nuclear DNA damage and leakage in SCI neurons in vivo and NSC34 expression in primary neurons cultured with oxygen-glucose deprivation (OGD) in vitro, as well as the interaction and colocalization of autophagy protein LC3 with nuclear lamina protein Lamin B1. The effect of UBC9, a Small ubiquitin-related modifier (SUMO) E2 ligase, on Lamin B1 SUMOylation and nucleophagy was examined by siRNA transfection or 2-D08 (a small-molecule inhibitor of UBC9), immunoprecipitation, and immunofluorescence. In SCI and OGD injured NSC34 or primary cultured neurons, neuronal nuclear DNA damage induced the SUMOylation of Lamin B1, which was required by the nuclear Lamina accumulation of UBC9. Furthermore, LC3/Atg8, an autophagy-related protein, directly bound to SUMOylated Lamin B1, and delivered Lamin B1 to the lysosome. Knockdown or suppression of UBC9 with siRNA or 2-D08 inhibited SUMOylation of Lamin B1 and subsequent nucleophagy and protected against neuronal death. Upon neuronal DNA damage and leakage after SCI, SUMOylation of Lamin B1 is induced by nuclear Lamina accumulation of UBC9. Furthermore, it promotes LC3-Lamin B1 interaction to trigger nucleophagy that protects against neuronal DNA damage.


Subject(s)
Autophagy , DNA Damage , Lamin Type B , Neurons , Spinal Cord Injuries , Sumoylation , Ubiquitin-Conjugating Enzymes , Animals , Mice , Cell Nucleus/metabolism , Lamin Type B/metabolism , Lamin Type B/genetics , Neurons/metabolism , Neurons/pathology , Spinal Cord Injuries/metabolism , Spinal Cord Injuries/genetics , Spinal Cord Injuries/pathology , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Conjugating Enzymes/genetics , Mice, Inbred C57BL , Cell Line, Tumor
17.
Mol Hum Reprod ; 30(7)2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38870534

ABSTRACT

Acephalic spermatozoa syndrome (ASS) is a severe teratospermia with decaudated, decapitated, and malformed sperm, resulting in male infertility. Nuclear envelope protein SUN5 localizes to the junction between the sperm head and tail. Mutations in the SUN5 gene have been identified most frequently (33-47%) in ASS cases, and its molecular mechanism of action is yet to be explored. In the present study, we generated Sun5 knockout mice, which presented the phenotype of ASS. Nuclear membrane protein LaminB1 and cytoskeletal GTPases Septin12 and Septin2 were identified as potential partners for interacting with SUN5 by immunoprecipitation-mass spectrometry in mouse testis. Further studies demonstrated that SUN5 connected the nucleus by interacting with LaminB1 and connected the proximal centriole by interacting with Septin12. The binding between SUN5 and Septin12 promoted their aggregation together in the sperm neck. The disruption of the LaminB1/SUN5/Septin12 complex by Sun5 deficiency caused separation of the Septin12-proximal centriole from the nucleus, leading to the breakage of the head-to-tail junction. Collectively, these data provide new insights into the pathogenesis of ASS caused by SUN5 deficiency.


Subject(s)
Membrane Proteins , Mice, Knockout , Nuclear Envelope , Septins , Sperm Head , Sperm Tail , Male , Septins/metabolism , Septins/genetics , Animals , Mice , Sperm Head/metabolism , Sperm Head/pathology , Nuclear Envelope/metabolism , Sperm Tail/metabolism , Membrane Proteins/metabolism , Membrane Proteins/genetics , Lamin Type B/metabolism , Lamin Type B/genetics , Teratozoospermia/metabolism , Teratozoospermia/genetics , Infertility, Male/metabolism , Infertility, Male/genetics , Spermatozoa/metabolism , Humans
18.
Arch Virol ; 169(2): 36, 2024 Jan 24.
Article in English | MEDLINE | ID: mdl-38265511

ABSTRACT

Current therapies for hepatitis B virus (HBV) infection can slow disease progression but cannot cure the infection, as it is difficult to eliminate or permanently silence HBV covalently closed circular DNA (cccDNA). The interaction between host factors and cccDNA is essential for their formation, stability, and transcriptional activity. Here, we focused on the regulatory role of the host factor ENPP1 and its interacting transcription factor LMNB1 in HBV replication and transcription to better understand the network of host factors that regulate HBV, which may facilitate the development of new antiviral drugs. Overexpression of ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) in Huh7 cells decreased HBV pregenomic RNA (pgRNA) and hepatitis B core antigen (HBcAg) expression levels, whereas knockdown of ENPP1 increased them. A series of HBV promoter and mutant plasmids were constructed, and a luciferase reporter assay showed that overexpression of ENPP1 caused inhibition of the HBV promoter and its mutants. A DNA pull-down assay showed that lamin B1 (LMNB1), but not ENPP1, interacts directly with the HBV enhancer II/ basic core promoter (EnhII/BCP). ZDOCK and PyMOL software were used to predict the interaction of ENPP1 with LMNB1. Overexpression of LMNB1 inhibited the activity of the HBV promoter and its mutant. The acetylation levels at the amino acids 111K, 261K, and 483K of LMNB1 were reduced compared to the control, and an LMNB1 acetylation mutant containing 111R, 261Q, 261R, 483Q, and 483R showed increased promoter activity. In summary, ENPP1 together with LMNB1 increased the acetylation level at 111K and 261K, and LMNB1 inhibited the activity of HBV promoter and downregulated the expression of pregenomic RNA and HBcAg. Our follow-up studies will investigate the expression, clinical significance, and relevance of ENPP1 and LMNB1 in HBV patient tissues, explore the effect of LMNB1 on post-transcriptional progression, and examine whether ENPP1 can reduce cccDNA levels in the nucleus.


Subject(s)
Hepatitis B virus , Lamin Type B , Phosphoric Diester Hydrolases , Pyrophosphatases , Humans , Acetylation , Hepatitis B , Hepatitis B Core Antigens , Hepatitis B virus/genetics , Lamin Type B/genetics , Phosphoric Diester Hydrolases/genetics , Pyrophosphatases/genetics , RNA
19.
Exp Cell Res ; 426(2): 113573, 2023 05 15.
Article in English | MEDLINE | ID: mdl-37003558

ABSTRACT

Ovarian cancer (OC) is a common malignant tumor in gynecology. LMNB1 is an important component of the nuclear skeleton. The expression of LMNB1 in ovarian cancer is significantly higher than that in normal tissues, but its role in tumor still needs comprehensive investigation. In this study, we overexpressed and knocked down LMNB1 in ovarian cancer cells and explore the effect of LMNB1 on the cell proliferation, migration and the underlying mechanism. We analyzed the expression levels of LMNB1 in ovarian cancer and their clinical relevance by using bioinformatics methods, qRT-PCR, Western blot and immunohistochemistry. To state the effect and mechanism of LMNB1 on OC in vitro and in vivo, we performed mouse xenograft studies, CCK8, cloning formation, Edu incorporation, wound healing, transwell and flow cytometry assay in stable LMNB1 knockdown OC cells, following by RNA-seq. Overexpression of LMNB1 indicates the progression of OC. LMNB1 knockdown inhibited the proliferation and migration of OC cells by suppressing the FGF1-mediated PI3K-Akt signaling pathway. Our study shows LMNB1 as a novel prognostic factor and therapeutic target in OC.


Subject(s)
Lamin Type B , Ovarian Neoplasms , Proto-Oncogene Proteins c-akt , Animals , Female , Humans , Mice , Cell Line, Tumor , Cell Movement/genetics , Cell Proliferation/genetics , Ovarian Neoplasms/pathology , Phosphatidylinositol 3-Kinases/genetics , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins c-akt/genetics , Proto-Oncogene Proteins c-akt/metabolism , Lamin Type B/genetics , Gene Deletion
20.
Proc Natl Acad Sci U S A ; 118(25)2021 06 22.
Article in English | MEDLINE | ID: mdl-34161290

ABSTRACT

Defects or deficiencies in nuclear lamins cause pathology in many cell types, and recent studies have implicated nuclear membrane (NM) ruptures as a cause of cell toxicity. We previously observed NM ruptures and progressive cell death in the developing brain of lamin B1-deficient mouse embryos. We also observed frequent NM ruptures and DNA damage in nuclear lamin-deficient fibroblasts. Factors modulating susceptibility to NM ruptures remain unclear, but we noted low levels of LAP2ß, a chromatin-binding inner NM protein, in fibroblasts with NM ruptures. Here, we explored the apparent link between LAP2ß and NM ruptures in nuclear lamin-deficient neurons and fibroblasts, and we tested whether manipulating LAP2ß expression levels would alter NM rupture frequency. In cortical plate neurons of lamin B1-deficient embryos, we observed a strong correlation between low LAP2ß levels and NM ruptures. We also found low LAP2ß levels and frequent NM ruptures in neurons of cultured Lmnb1-/- neurospheres. Reducing LAP2ß expression in Lmnb1-/- neurons with an siRNA markedly increased the NM rupture frequency (without affecting NM rupture duration), whereas increased LAP2ß expression eliminated NM ruptures and reduced DNA damage. Consistent findings were observed in nuclear lamin-deficient fibroblasts. Reduced LAP2ß expression increased NM ruptures, whereas increased LAP2ß expression virtually abolished NM ruptures. Increased LAP2ß expression nearly abolished NM ruptures in cells subjected to mechanical stress (an intervention that increases NM ruptures). Our studies showed that increasing LAP2ß expression bolsters NM integrity in nuclear lamin-deficient cells and markedly reduces NM rupture frequency.


Subject(s)
DNA-Binding Proteins/metabolism , Fibroblasts/metabolism , Lamin Type B/deficiency , Membrane Proteins/metabolism , Neurons/metabolism , Nuclear Envelope/metabolism , Animals , Cell Death , Cell Differentiation , Cerebral Cortex/pathology , DNA Damage , Embryo, Mammalian/metabolism , Lamin Type A/deficiency , Lamin Type A/metabolism , Lamin Type B/metabolism , Mice, Knockout , Organ Specificity
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