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Zebrafish have come into focus to model cerebellar diseases such as spinocerebellar ataxias (SCAs), which is caused by an expansion of translated CAG repeats in several unrelated genes. In spinocerebellar ataxia type 1 (SCA1), gain-of-function in the mutant ATXN1 contributes to SCA1’s neuropathy. Human ATXN1 and its paralog ATXN1L are chromatin-binding factors, act as transcriptional repressors, and have similar expression patterns. However, little is known about atxn1 genes in zebrafish. Recently, two family members, atxn1a and atxn1b, were identified as duplicate orthologs of ATXN1, as was atxn1l, the ortholog of ATXN1L. In this study, we analyzed the phylogenetic relationship of the atxn1 family members in zebrafish, compared their genetic structures, and verified the predicted transcripts by both RT-PCR and whole-mount in situ hybridization. All three genes, atxn1a, atxn1b, and atxn1l, show overlapping, but also distinct, expression domains during embryonic and larval development. While atxn1a and atxn1l display similar spatiotemporal embryonic expression, atxn1b expression is initiated during the onset of brain development and is predominantly expressed in the cerebellum throughout zebrafish development. These results provide new insights into atxn1 genes and their expression patterns in zebrafish during embryonic and late-larval development and may contribute importantly to future experiments in disease modeling of SCAs.

The Arp2/3 complex generates branched actin filament networks operating in cell edge protrusion and vesicle trafficking. Here we employ a conditional knockout mouse model permitting tissue- or cell-type specific deletion of the murine Actr3 gene (encoding Arp3). A functional Actr3 gene appeared essential for fibroblast viability and growth. Thus, we developed cell lines for exploring the consequences of acute, tamoxifen-induced Actr3 deletion causing near-complete loss of functional Arp2/3 complex expression as well as abolished lamellipodia formation and membrane ruffling, as expected. Interestingly, Arp3-depleted cells displayed enhanced rather than reduced cell spreading, employing numerous filopodia, and showed little defects in the rates of random cell migration. However, both exploration of new space by individual cells and collective migration were clearly compromised by the incapability to efficiently maintain directionality of migration, while the principal ability to chemotax was only moderately affected. Examination of actin remodeling at the cell periphery revealed reduced actin turnover rates in Arp2/3-deficient cells, clearly deviating from previous sequestration approaches. Most surprisingly, induced removal of Arp2/3 complexes reproducibly increased FMNL formin expression, which correlated with the explosive induction of filopodia formation. Our results thus highlight both direct and indirect effects of acute Arp2/3 complex removal on actin cytoskeleton regulation.

The Arp2/3 complex generates branched actin filament networks operating in cell edge protrusion and vesicle trafficking. Here we employ a novel, conditional knockout mouse model permitting tissue- or cell-type specific deletion of the murine Actr3 gene (encoding Arp3). A functional Actr3 gene appeared essential for fibroblast viability and growth. Thus, we developed cell lines for exploring the consequences of acute, tamoxifen-induced Actr3 deletion causing near-complete loss of Arp/3 complex function as well as abolished lamellipodia formation and membrane ruffling, as expected. However, Arp3-depleted cells displayed enhanced rather than reduced cell spreading, employing numerous filopodia, and showed little defects in individual cell migration. Reduction of collective cell migration as observed for instance in wound healing assays likely derived from defects in maintaining directionality during migration, while the principal ability to chemotax was only moderately affected. Analyses of actin turnover at the cell periphery revealed reduced actin turnover rates in Arp2/3-deficient cells, clearly deviating from previous sequestration approaches. Most surprisingly, induced removal of Arp2/3 complexes reproducibly increased FMNL formin expression, which correlated with the explosive induction of filopodia formation. Our results thus highlight both direct and indirect effects of acute Arp2/3 complex removal on actin cytoskeleton regulation.

RNA modifications are dynamic chemical entities that regulate RNA fate, and an avenue for environmental response in neuronal function. However, which RNA modifications may be playing a role in neuronal plasticity and environmental responses is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m 2,2 G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNA Ala (AGC) isoacceptors at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.

Lovastatin was used to study the role of isoprenylated proteins on stimulus-induced increase of cytosolic Ca2+ in retinoic acid-differentiated U937 and HL-60 cells. Preincubation of the cells with lovastatin for 11-24 h reduced the Ca(2+)-influx induced by PAF of FMLP. The maximal decrease was 60% in U937 cells and 40% in HL-60 cells. The ID50s of lovastatin in U937 and HL-60 cells were 5 microM and 15 microM, respectively. Lovastatin did not inhibit Ca(2+)-discharge from intracellular stores. Addition of mevalonate to lovastatin-treated cells completely reversed the inhibition of PAF- and FMLP-stimulated Ca(2+)-mobilization. Immunoreactivity of ras-like proteins was decreased in membranes and increased in the cytosol of U937 cells by 1 day treatment with lovastatin. We conclude that isoprenylated proteins are involved in the regulation of receptor-stimulated Ca(2+)-entry of differentiated HL-60 and U937 cells.

In a search for a model cell system that might allow studies of the function of the Rho-related GTPase CDC42Hs in human cells, we measured the content and distribution of CDC42Hs in monocytes that were differentiating into macrophages. The total content of this protein increased 5- to 6-fold in phorbol ester-treated human monocytic THP-1 and U-937 cells and increased 13-fold in normal human blood monocytes. Moreover, membrane-associated CDC42Hs in these cells increased 13-fold and 30-fold, respectively, while cytosolic CDC42Hs increased only 3- and 6-fold. Measurements made specifically in U-937 cells showed that the increase in membrane CDC42Hs correlated closely with an increase in cell spreading. The changes in CDC42Hs in U-937 cells probably depended on increased mRNA translation and/or decreased protein degradation, since no change in CDC42Hs mRNA could be detected. Finally, the changes in CDC42Hs were relatively specific, since contents of the CDC42Hs-binding protein Rho-GDI and the Rho-related protein Rac2 were unaffected and no change in CDC42Hs occurred when the cells were stimulated by agonists that induce monocytes to differentiate into nonadherent cells. These findings show that marked changes in content and distribution of CDC42Hs occur when monocytes differentiate into macrophages, suggesting that membrane CDC42Hs may play a role in cell spreading.

The molecular mechanisms maintaining glomerular filtration barrier are under intensive study. This study describes a mutant Nphs1 mouse line generated by gene-trapping. Nephrin, encoded by Nphs1 , is a structural protein of interpodocyte filtration slits crucial for formation of primary urine. Nephrin trap/trap mutants show characteristic features of proteinuric disease and die soon after birth. Morphologically, fibrotic glomeruli with distorted structures and cystic tubular lesions were observed, but no prominent changes in the branching morphogenesis of the developing collecting ducts could be found. Western blotting and immunohistochemical analyses confirmed the absence of nephrin in nephrin trap/trap glomeruli. The immunohistochemical staining showed also that the interaction partner of nephrin, CD2-associated protein (CD2AP), and the slit-diaphragm-associated protein, ZO-1α − , appeared unchanged, whereas the major anionic apical membrane protein of podocytes, podocalyxin, somewhat punctate as compared with the wild-type (wt) and nephrin wt/trap stainings. Electron microscopy revealed that >90% of the podocyte foot processes were fused. The remaining interpodocyte junctions lacked slit diaphragms and, instead, showed tight adhering areas. In the heterozygote glomeruli, approximately one third of the foot processes were fused and real-time RT-PCR showed >60% decrease of nephrin-specific transcripts. These results show an effective nephrin gene elimination, resulting in a phenotype that resembles human congenital nephrotic syndrome. Although the nephrin trap/trap mice can be used to study the pathophysiology of the disease, the heterozygous mice may provide a useful model to study the gene dose effect of this crucial protein of the glomerular filtration barrier.

Very reliable methods have been developed to extract RNA from different tissues and cell lines (1, 2, 3). RNA preparation, however, is still cumbersome and time consuming, especially when extracting a large number of cells (>107) and cell samples. The isolation of RNA from leucocytic cells is particularly difficult for three reasons: a) high levels of endogenous RNase; b) low amount of RNA (RNA/DNA ratio of 0.08 in granulocytes compared to 4.0 in cultured fibroblasts) (3); c) contamination of the RNA isolate with DNA and protein. To overcome these problems, we developed a simple and efficient RNA isolation procedure by modifying the method described by Chomczynski and Sacchi (2). Our modified protocol has the following advantages: a) it is simple to perform and needs no major equipment; b) it reduces drastically the volume of costly and hazardous solvents; c) both, small scale (5 x 106 cells: RNA yield 30-50 jig) and large scale (1 x 108 cells: RNA yield 300-600 ILg) RNA extractions can be performed using exactly the same protocol in small 1.5 ml microfuge tubes with many cell samples (up to 20) in parallel in a short time (5 hours); d) the protocol produces extremely pure total RNA at high yield. We used the method mainly to measure quantitavely low level gene expression by Northern blot. The following detailed stepby-step protocol was tested using various undifferentiated and differentiated leucocytic cell lines (U937, HL60, HEL, MM6), but should be applicable to any cell type growing in suspension. Pellet leucocytic cells from a 50 ml culture flask (1x105-2x106 cells/ml) in a 50 ml Falcon tube. Pour off medium, turn Falcon tube upside down and put it on a kimwipe to drain the pellet. While vortexing the pellet, splash 600 1l solution D (4M guanidinium thiocyanate; 25 mM sodium citrate, pH 7; 0.5% sarcosyl; 0.1% 2-mercaptoethanol; 0.1% antifoam A) to the cells. Vortex until reaching a clear very viscous lysate. Pour the suspension directly into a 1.5 ml Eppendorf cup. Aspirate the lysate into a 2 ml syringe fitted with a 23G-needle and expel it into the tube applying high pressure. Repeat this step 10 times. (Antifoam A prevents foaming while shearing DNA). Add 600 y1 8 M LiCl, mix by turning the cup until the clear suspension becomes cloudy (do not vortex). Cool on ice for at least 1 hour. Spin down precipitated RNA at 13000Xg for 20 min. at 4°C. Remove completely supernatant. Take up RNA pellet in 650 ,I DEPC-treated water and transfer suspension to another tube. Then add 700 itl acidic phenol (pH 4.3) and vortex vigorously. Add 140 td chloroform/isoamyl-alcohol (24:1) and vortex vigorously. Spin tube (13000 g, 10 min., 4°C) and transfer 650 $1 from the aqueous upper phase into another tube and vortex vigorously with 650 Al chloroform/isoamyl alcohol (24:1). Spin again (13000 g, 10 min, 40C) and carefully recover 500 1d from the aqueous supernatant and transfer it into a new tube. Add 50 11 8 M LiCl, mix, add 500 A1 precooled (-200C) isopropanol and mix well (do not vortex). Precipitate RNA for 30 min. at -200C. Spin down RNA at 11000 xg, 10 min., 4C and remove supernatant completely. Rinse pellet with 1 ml 70% ethanol and spin again at 13000 xg, 5 min., 40C. Aspirate supernatant, dry the pellet only slightly and resuspend RNA in DEPC-treated water (100,ul). Measure O.D. and store RNA suspension at20°C. A wide range of cell numbers (5 x 106108 cells) was lysed in always the same volume of solution D (600 IAI), instead of adjusting the volume of solution D to the actual cell count (100 /d solution D per 106 cells) as indicated in (2). This procedure dramatically reduced the volume of solution D (up to 20-fold)