The reversible action of alpha-amanitin on nuclear structure and molecular composition

Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study

Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study, we tested whether NS exhibit any stable association with chromatin and show that limited DNAse-1 nicking of chromatin leads to the collapse of NS into isotropic distribution or aggregates of constituent proteins without affecting other nuclear structures. Further biochemical probing revealed that NS proteins were tightly associated with chromatin, extractable only by high-salt treatment just like histone proteins. NS were also co-released with solubilised mono-dinucleosomal chromatin fraction following the MNase digestion of chromatin. We propose a model that NS-chromatin constitutes a “putative stable association” whose coupling might be subject to the combined regulation from both chromatin and NS changes.

Abbreviations: NS: Nuclear speckles; DSB: double strand breaks; PTM: posttranslational modifications; DDR: DNA damage repair; RBP-RNA binding proteins; TAD: topologically associated domains; LCR: low complexity regions; IDR: intrinsically disordered regions.

Nuclear speckle specific hnRNP D-like prevents age- and AD-related cognitive decline by modulating RNA splicing

BACKGROUND

Aberrant alternative splicing plays critical role in aging and age-related diseases. Heterogeneous nuclear ribonucleoproteins (hnRNPs) reportedly regulate RNA splicing process. Whether and how hnRNPs contribute to age-related neurodegenerative diseases, especially Alzheimer's disease (AD), remain elusive.

METHODS

Immunoblotting and immunostaining were performed to determine expression patterns and cellular/subcellular localization of the long isoform of hnRNP D-like (L-DL), which is a hnRNP family member, in mouse hippocampus. Downregulation of L-DL in WT mice was achieved by AAV-mediated shRNA delivery, followed by memory-related behavioural tests. L-DL interactome was analysed by affinity-precipitation and mass spectrometry. Alternative RNA splicing was measured by RNA-seq and analyzed by bioinformatics-based approaches. Downregulation and upregulation of L-DL in APP/PS1 mice were performed using AAV-mediated transduction.

RESULTS

We show that L-DL is specifically localized to nuclear speckles. L-DL levels are decreased in the hippocampus of aged mouse brains and downregulation of L-DL impairs cognition in mice. L-DL serves as a structural component to recruit other speckle proteins, and regulates cytoskeleton- and synapse-related gene expression by altering RNA splicing. Mechanistically, these splicing changes are modulated via L-DL-mediated interaction of SF3B3, a core component of U2 snRNP, and U2AF65, a U2 spliceosome protein that guides U2 snRNP's binding to RNA. In addition, L-DL levels are decreased in APP/PS1 mouse brains. While downregulation of L-DL deteriorates memory deficits and overexpression of L-DL improves cognitive function in AD mice, by regulating the alternative splicing and expression of synaptic gene CAMKV.

CONCLUSIONS

Our findings define a molecular mechanism by which hnRNP L-DL regulates alternative RNA splicing, and establish a direct role for L-DL in AD-related synaptic dysfunction and memory decline.

Nuclear speckles: molecular organization, biological function and role in disease

The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.

Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells

PRPF3 is an element of the splicing machinery ubiquitously expressed, yet mutations in this gene are associated with a tissue-specific phenotype: autosomal dominant retinitis pigmentosa (RP). Here, we studied the subcellular localization of endogenous- and mutant-transfected PRPF3. We found that (i) subcellular distribution of the endogenous wild-type protein co-localizes with small nuclear ribonucleoproteins, partially with a nucleolar marker and accumulates in speckles labeled by SC35; (ii) in human retinas, PRPF3 does not show a distinctive abundance in photoreceptors, the cells affected in RP and (iii) the RP causing mutant PRPF3, differently from the wild-type protein, forms abnormally big aggregates in transfected photoreceptor cells. Aggregation of T494M mutant PRPF3 inside the nucleus triggers apoptosis only in photoreceptor cells. On the basis of the observation that mutant PRPF3 accumulates in the nucleolus and that transcriptional, translational and proteasome inhibition can induce this phenomenon in non-photoreceptor cells, we hypothesize that mutation affects splicing factor recycling. Noteworthy, accumulation of the mutant protein in big aggregates also affects distribution of some other splicing factors. Our data suggest that the mutant protein has a cell-specific dominant effect in rod photoreceptors while appears not to be harmful to epithelial and fibroblast cells.

Phosphatidylinositol 3-kinase c2alpha contains a nuclear localization sequence and associates with nuclear speckles

Phosphoinositide 3-kinase C2alpha (PI3K-C2alpha) belongs to the class II phosphatidylinositol 3-kinases, which are defined by their in vitro usage of phosphatidylinositol and phosphatidylinositol 4-phosphate as substrates. All type II phosphatidylinositol 3-kinases contain at their C terminus a C2-like domain. Here we demonstrate that Homo sapiens phosphoinositide 3-kinase C2alpha (HsPI3K-C2alpha) has dual cellular localization present in the cytoplasm and in the nucleus. A distinct nuclear localization signal sequence was identified by expressing HsPI3K-C2alpha-green fluorescent protein fusion proteins in HeLa cells. The nuclear localization signal was mapped to a stretch of 11 amino acids (KRKTKISRKTR) located within C2-like domain of the kinase. In the cytoplasm and the nucleus HsPI3K-C2alpha associates with macromolecular complexes that are resistant to detergent extraction. Indirect immunofluorescence reveals that in the nucleus HsPI3K-C2alpha is enriched at distinct subnuclear domains known as nuclear speckles, which contain pre-mRNA processing factors and are functionally connected to RNA metabolism. Phosphorylation of HsPI3K-C2alpha is induced by inhibition of RNA polymerase II-dependent transcription and coincides with enlargement and rounding up of the nuclear speckles. The results suggest that phosphorylation of HsPI3K-C2alpha is inversely linked to mRNA transcription and supports the importance of phosphoinositides for nuclear activity.

The concept of self-organization in cellular architecture

In vivo microscopy has recently revealed the dynamic nature of many cellular organelles. The dynamic properties of several cellular structures are consistent with a role for self-organization in their formation, maintenance, and function; therefore, self-organization might be a general principle in cellular organization.

Functional architecture in the cell nucleus

The major functions of the cell nucleus, including transcription, pre-mRNA splicing and ribosome assembly, have been studied extensively by biochemical, genetic and molecular methods. An overwhelming amount of information about their molecular mechanisms is available. In stark contrast, very little is known about how these processes are integrated into the structural framework of the cell nucleus and how they are spatially and temporally co-ordinated within the three-dimensional confines of the nucleus. It is also largely unknown how nuclear architecture affects gene expression. In order to understand how genomes are organized, and how they function, the basic principles that govern nuclear architecture and function must be uncovered. Recent work combining molecular, biochemical and cell biological methods is beginning to shed light on how the nucleus functions and how genes are expressed in vivo. It has become clear that the nucleus contains distinct compartments and that many nuclear components are highly dynamic. Here we describe the major structural compartments of the cell nucleus and discuss their established and proposed functions. We summarize recent observations regarding the dynamic properties of chromatin, mRNA and nuclear proteins, and we consider the implications these findings have for the organization of nuclear processes and gene expression. Finally, we speculate that self-organization might play a substantial role in establishing and maintaining nuclear organization.

Protein dynamics: implications for nuclear architecture and gene expression

Studies of nuclear architecture reveal that the dynamic properties of proteins in the nucleus are critical for their function. The high mobility of proteins ensures their availability throughout the nucleus; their dynamic interplay generates an ever-changing, but overall stable, architectural framework, within which nuclear processes take place. As a consequence, overall nuclear morphology is determined by the functional interactions of nuclear components. The observed dynamic properties of nuclear proteins are consistent with a central role for stochastic mechanisms in gene expression and nuclear architecture.

Prespliceosomal assembly on microinjected precursor mRNA takes place in nuclear speckles

Nuclear speckles (speckles) represent a distinct nuclear compartment within the interchromatin space and are enriched in splicing factors. They have been shown to serve neighboring active genes as a reservoir of these factors. In this study, we show that, in HeLa cells, the (pre)spliceosomal assembly on precursor mRNA (pre-mRNA) is associated with the speckles. For this purpose, we used microinjection of splicing competent and mutant adenovirus pre-mRNAs with differential splicing factor binding, which form different (pre)spliceosomal complexes and followed their sites of accumulation. Splicing competent pre-mRNAs are rapidly targeted into the speckles, but the targeting is temperature-dependent. The polypyrimidine tract sequence is required for targeting, but, in itself, is not sufficient. The downstream flanking sequences are particularly important for the targeting of the mutant pre-mRNAs into the speckles. In supportive experiments, the behavior of the speckles was followed after the microinjection of antisense deoxyoligoribonucleotides complementary to the specific domains of snRNAs. Under these latter conditions prespliceosomal complexes are formed on endogenous pre-mRNAs. We conclude that the (pre)spliceosomal complexes on microinjected pre-mRNA are formed inside the speckles. Their targeting into and accumulation in the speckles is a result of the cumulative loading of splicing factors to the pre-mRNA and the complexes formed give rise to the speckled pattern observed.

Cell biology of transcription and pre-mRNA splicing: nuclear architecture meets nuclear function

Gene expression is a fundamental cellular process. The basic mechanisms involved in expression of genes have been characterized at the molecular level. A major challenge is now to uncover how transcription, RNA processing and RNA export are organized within the cell nucleus, how these processes are coordinated with each other and how nuclear architecture influences gene expression and regulation. A significant contribution has come from cell biological approaches, which combine molecular techniques with microscopy methods. These studies have revealed that the mammalian cell nucleus is a complex but highly organized organelle, which contains numerous subcompartments. I discuss here how two essential nuclear processes - transcription and pre-mRNA splicing - are spatially organized and coordinated in vivo, and how this organization might contribute to the control of gene expression. The dynamic nature of nuclear proteins and compartments indicates a high degree of plasticity in the cellular organization of nuclear functions. The cellular organization of transcription and splicing suggest that the morphology of nuclear compartments is largely determined by the activities of the nucleus.

Serine/threonine phosphatase 1 modulates the subnuclear distribution of pre-mRNA splicing factors

HeLa cell nuclei were permeabilized and reconstituted with nuclear extract to identify soluble nuclear factors which play a role in the organization of pre-mRNA splicing factors in the mammalian cell nucleus. Permeabilized nuclei reconstituted with nuclear extract were active in transcription and DNA replication and nuclear speckles containing pre-mRNA splicing factors were maintained over several hours independent of soluble nuclear components. The characteristic rounding up of nuclear speckles in response to inhibition of RNA polymerase II seen in vivo was reproduced in permeabilized cells and was strictly dependent on a catalytic activity present in the nuclear extract. By inhibitor titration experiments and sensitivity to inhibitor 2, this activity was identified as a member of the serine/threonine protein phosphatase 1 family (PP1). Interference with PP1 activity affected the distribution of pre-mRNA splicing factors in transcriptionally active, permeabilized cells, and excess PP1 activity caused increased dephosphorylation of SR proteins in nuclear speckles. These data show that the dynamic reorganization of the mammalian cell nucleus can be studied in permeabilized cells and that PP1 is involved in the rounding up of speckles as well as the overall organization of pre-mRNA splicing factors in the mammalian cell nucleus.

The roles of nucleolar structure and function in the subcellular location of the HIV-1 Rev protein

The human immunodeficiency virus 1 (HIV-1) Rev transactivator protein plays a critical role in the regulation of expression of structural proteins by controlling the pathway of mRNA transport. The Rev protein is located predominantly in the nucleoli of HIV-1 infected or Rev-expressing cells. Previous studies demonstrated that the Rev protein forms a specific complex in vitro with protein B23 which is suggested to be a nucleolar receptor and/or carrier for the Rev protein. To study the role of the nucleolus and nucleolar proteins in Rev function, transfected COS-7 or transformed CMT3 cells expressing the Rev protein were examined for subcellular locations of Rev and other proteins using indirect immunofluorescence and immunoelectron microscopy. One day after transfection the Rev protein was found in most cells only in the nucleolar dense fibrillar and granular components where it colocalized with protein B23. These were designated class 1 cells. In a second class of cells Rev and B23 accumulated in the nucleoplasm as well as in nucleoli. Treatment of class 1 cells with actinomycin D (AMD) under conditions that blocked only RNA polymerase I transcription caused Rev to completely redistribute from nucleoli to the cytoplasm. Simultaneously, protein B23 was partially released from nucleoli, mostly into the nucleoplasm, with detectable amounts in the cytoplasm. In cells recovering from AMD treatment in the presence of cycloheximide Rev and B23 showed coincident relocation to nucleoli. Class 2 cells were resistant to AMD-induced Rev redistribution. Selective inhibition of RNA polymerase II transcription by alpha-amanitin or by DRB did not cause Rev to be released into the cytoplasm suggesting that active preribosomal RNA transcription is required for the nucleolar location of Rev. However, treatment with either of the latter two drugs at higher doses and for longer times caused partial disruption of nucleoli accompanied by translocation of the Rev protein to the cytoplasm. These results suggest that the nucleolar location of Rev depends on continuous preribosomal RNA transcription and a substantially intact nucleolar structure.

Relocalization of small ribonucleoprotein particles (snRNPs) during the first cell cycle of mouse embryo development is independent of RNA synthesis, DNA synthesis and cytokinesis

The process of localization of small nuclear ribonucleoprotein particles (snRNPs) during the first cell cycle of mouse embryo development was investigated following treatment of fertilized eggs with cytochalasin D, aphidicolin and alpha-amanitin. The pattern of accumulation of snRNPs in nuclei of treated embryos as assessed by indirect immunofluorescence was unaffected by the inhibitors. The results demonstrate that the localization of snRNPs during the first cell cycle does not require ongoing cytokinesis, DNA replication or transcription of RNA polymerase II genes. These findings suggest that maternally derived snRNPs become localized to the nucleus of the fertilized ovum prior to the reinitiation of transcription from the zygote genome and are required for processing of messenger RNA precursors when genetic activity of the embryonic genome is activated at the early 2-cell stage.

Changes of SCE frequency and chromatin molecular composition in rat progeny whose mothers were treated with oral contraceptives in early pregnancy

Wistar female rats were fed with oral contraceptives (OC, containing ethinylestradiolum and methylnorethrindronum) in early pregnancy. The dosage used for rats was 6.6 times more than the clinical dosage for humans in weight per kilogram. The SCE frequencies of liver and ovary cells and the changes of chromatin molecular composition in progeny of the rats fed with OC were observed. The results showed that the liver and ovary cells of newborns 12 h after birth exhibited increased SCEs value (liver: p less than 0.03; ovary: p less than 0.0004). These elevated SCE frequencies declined to the normal level about the 15th day after birth. The results for the quantity of nonhistone (NHP) and chromatin RNA in mother rats and their progenies also exhibited a significant increase, and declined to the normal level at the same period mentioned above. The results suggested that the high level of NHP and chromatin RNA may be induced by OC fed in early pregnancy and be maintained for some time after withdrawal of the OC pills. The changes of the chromatin molecular composition are perhaps somehow related to the increased SCE frequencies in the rat-liver cells. We suggest that the external steroids and their metabolites may activate more genes which were originally inactive and result in increased junctions between euchromatin and heterochromatin, resulting in more SCEs in quickly dividing embryo cells. The report here suggests that during early pregnancy the pills taken by women following OC failures may have a potential mutagenic effect on their progeny for some time after the pills have been stopped.

Effect of alpha-amanitin on liver non-histone chromatin proteins of starved hens

A diminution of RNA content in hen liver nuclei was observed after either prolonged starvation or short-term exposure to alpha-amanitin. Using polyacrylamide gel electrophoresis, it has been revealed a limited number of altered polypeptide bands in the gel patterns of 0.35 M NaCl- and 5 M urea-soluble non-histone proteins from liver chromatin of starved or alpha-amanitin-treated birds. The low-molecular-weight polypeptides were found to increase in the protein fractions from liver chromatin of alpha-amanitin-injected hens. Only two protein bands (48 and 79 kDa) in the gel patterns of 5 M urea-soluble chromatin fraction altered in similar manner both in starved and alpha-amanitin-treated animals. The amount of the 48-kDa protein decreased and that of the 79-kDa protein increased under these conditions. alpha-Amanitin seems to affect differently the non-histone chromatin proteins from starved and fed animals. The level of the 48-kDa urea-soluble protein was lower and that of the 64-kDa protein was higher in liver chromatin of starved animals receiving alpha-amanitin in comparison with the corresponding proteins from fed animals treated with this drug.

Mutations in rDNA : 3. Modulatory action of α-amanitin on aberration induction in nucleolus organizer regions

The action of α-amanitin, an inhibitor of RNA synthesis, on the induction by hydroxyurea (HU) of chromosomal aberrations in nucleolus organizer regions of barley was studied. The data obtained show that α-amanitin can effectively modify aberration induction in rDNA. Administered before mutagen treatment or in combination with the mutagen, the toxin significantly decreased the HU-induced aberration frequencies in NORs. The data obtained provide further evidence that α-amanitin is an effective modulator of aberration induction in NORs either by interfering with RNA synthesis or by modifying chromatin structure.

Effects of alpha-amanitin on the fine structure of adrenal fasciculata cells in the young rat

The administration of 0.2 micrograms/g/bw of alpha-amanitin to approximately 20 g rats provoked the following nuclear modifications in rat adrenal fasciculata cells at 60 min: chromatin condensation, nucleolar fragmentation, increase in the number of PCG and clumping of ICG in the center of the nucleus. At longer time intervals (2.5 and 4.5 hr) these alterations were more evident, but at 24 hr the nuclear structure was back to normal with the exception of a persistent increased number of PCG. After injection of 0.75 micrograms/g/bw and at 2.5 hr, there was pulverization of condensed chromatin, fragmentation and partial segregation of the nucleolus with increased density of the fibrillar component. Cytoplasmic alterations were severe including cap-shaped mitochondria with electron-dense matrix surrounding lipid droplets, reduced endoplasmic reticulum of vesicular type and clusters of microvesicles with dense content in the Golgi trans-area. At 24 hr, the nuclear and cytoplasmic morphology returned to normal. These findings are interpreted as the morphological counterpart of a disturbance of extranucleolar and nucleolar RNA synthesis, as well as of lipid and lipoprotein metabolism, brought about by the drug.

Changes in structure and composition of lymphocyte nuclei during mitogenic stimulation

Nuclei of lymphocytes stimulated in vitro with concanavalin A (Con A) were classified into three morphotypes: I--unstimulated; II--partially stimulated; III--fully stimulated, lymphoblastic nuclei. During the Con A-induced change from morphotype I to III nuclear volume increased up to sixfold, due to a near 10-fold increase in the interchromatinic region. At the same time, condensed chromatin rose in volume by only about 1.5-fold and became disaggregated in to small clumps. Regressive EDTA-uranyl staining demonstrated a large increase in interchromatinic fibrillar material in morphotypes II and III. Nuclear matrices isolated from stimulated murine lymphocytes showed structures comparable to the interchromatinic region of the morphotypes. The Con A-stimulated change in nuclear structure preceded onset of DNA replication and was unaffected by hydroxyurea or cytosine arabinoside. Cycloheximide blocked the structural change, even when given 20 hr after Con A. Autoradiography after [3H]leucine showed incorporation of label in the interchromatinic region of morphotype II and III nuclei, much of which remained stable during a 48-hr chase period. Nuclear structural activation was inhibited by alpha-amanitin but a significant stable nuclear RNA fraction was not detected. We conclude that an important event in lymphocyte activation is extensive synthesis of stable proteinaceous interchromatinic matrix which may be involved in chromatin remodeling and DNA replication and/or transcription.

The organization, composition and matrix of hepatocyte nuclei exposed to alpha-amanitin

Alterations in the structure and molecular composition of avian hepatocyte nuclei were compared following administration in vivo of lethal and sub-lethal doses of alpha-amanitin. This toxin interferes with extranucleolar transcription by direct inhibition of RNA polymerase II activity. the resultant effects include: extensive condensation of chromatin, displacement of nucleoplasmic contents and fragmentation of nucleoli. Changes in nuclear morphology were quantitated by stereometry and related to variations in RNA and residual, non-histone proteins (NHP). Gross alterations in nuclear structure and depletion of RNA and NHP levels were of similar magnitude with both doses of amanitin. The effects were fully reversible, however, with a minimal dose but terminal with a lethal dose. DNA and histone protein levels remained unchanged at all stages. These results imply that the process of transciption may itself keep and/or maintain chromatin in a dispersed state, and that in the absence of transcription chromatin naturally condenses. Modification of nuclear proteins may be necessary only to maintain chromatin compacted permanently or for extended periods of time. A model of nuclear organization is proposed to incorporate these considerations and to identify the probable location of the nuclear matrix in situ.