Digoxigenin-labeled RNA Probes Research Articles

Distribution of goblet cells and MUC5AC mRNA in the canine nictitating membrane

This study evaluated the distribution of goblet cells and the expression of MUC5AC mRNA in the canine nictitating membrane. The distribution of goblet cells in the nictitating membrane and temporal bulbar conjunctiva of beagle dogs was examined by histochemical analysis of impression cytology specimens and frozen sections. MUC5AC mRNA was detected by the reverse transcription polymerase chain reaction (RT-PCR). The distribution of MUC5AC mRNA was also examined by in situ hybridization using digoxigenin-labeled antisense and sense RNA probes. Histochemical analysis showed that the canine nictitating membrane epithelium contained many more periodic acid-Schiff positive goblet cells, particularly on the palpebral side, compared with the temporal bulbar conjunctiva. RT-PCR revealed that MUC5AC was expressed in both the nictitating membrane and in conjunctival tissue. When the distribution of MUC5AC mRNA was assessed by in situ hybridization, its expression was high on the palpebral side of the nictitating membrane and low in the temporal bulbar conjunctiva. MUC5AC mRNA expression corresponded with the distribution of goblet cells by histochemical examination. In conclusion, there were numerous goblet cells in the canine nictitating membrane epithelium, particularly on the palpebral side, and MUC5AC mRNA was expressed in the nictitating membrane epithelium at locations corresponding to the goblet cells.

Traf2- and Nck-interacting Kinase Is Essential for Canonical Wnt Signaling in Xenopus Axis Formation

Wnt signaling pathways play important roles in various stages of developmental events and several aspects of adult homeostasis. Aberrant activation of Wnt signaling has also been associated with several types of cancer. We have recently identified Traf2- and Nck-interacting kinase (TNIK) as a novel activator of Wnt signaling through a comprehensive proteomic approach in human colorectal cancer cell lines. TNIK is an activating kinase for T-cell factor-4 (TCF4) and essential for the beta-catenin-TCF4 transactivation and colorectal cancer growth. Here, we report the essential role of TNIK in Wnt signaling during Xenopus development. We found that Xenopus TNIK (XTNIK) was expressed maternally and that the functional knockdown of XTNIK by catalytically inactive XTNIK (K54R) or antisense morpholino oligonucleotides resulted in significant malformations with a complete loss of head and axis structures. XTNIK enhanced beta-catenin-induced axis duplication and the expression of beta-catenin-TCF target genes, whereas knockdown of XTNIK inhibited it. XTNIK was recruited to the promoter region of beta-catenin-TCF target genes in a beta-catenin-dependent manner. These results demonstrate that XTNIK is an essential factor for the transcriptional activity of the beta-catenin-TCF complex and dorsal axis determination in Xenopus embryos.

Embryonic Expression of Cyclooxygenase-2 Causes Malformations in Axial Skeleton

Cyclooxygenases (COXs) have important functions in various physiological and pathological processes. COX-2 expression is highly induced by a variety of stimuli and is observed during certain periods of embryonic development. In this report, the direct effect of COX-2 expression on embryonic development is examined in a novel COX-2 transgenic mouse model that ubiquitously expresses human COX-2 from the early stages of embryonic development. COX-2 transgenic fetuses exhibit severe skeletal malformations and die shortly after birth. Skeletal malformations are localized along the entire vertebral column and rib cage and are linked to defective formation of cartilage anlagen. The cartilage anlagen of axial skeleton fail to properly develop in transgenic embryos because of impaired precartilaginous sclerotomal condensation, which results from the reduction of cell number in the sclerotome. Despite the ubiquitous expression of COX-2, the number of apoptotic cells is highly increased in the sclerotome of transgenic embryos but not in other tissues, suggesting that it is a tissue-specific response. Therefore, the loss of sclerotomal cells due to an increased apoptosis is probably responsible for axial skeletal malformations in transgenic fetuses. In addition, the sclerotomal accumulation of p53 protein is observed in transgenic embryos, suggesting that COX-2 may induce apoptosis via the up-regulation of p53. Our results demonstrate that the aberrant COX-2 signaling during embryonic development is teratogenic and suggest a possible association of COX-2 with fetal malformations of unknown etiology.

Localization of avian bornavirus RNA by in situ hybridization in tissues of psittacine birds with proventricular dilatation disease

Proventricular dilatation disease (PDD) of psittacine birds is caused by a number of different genotypes of a novel viral species, avian bornavirus (ABV). Here we present an in situ hybridization (ISH) procedure using digoxigenin-labeled RNA probes for localizing viral genomic and mRNA of ABV-2 and ABV-4 in tissues of affected birds. Out of eleven immunohistochemically positive birds ISH signals were only found in seven. Partial sequencing of the viral genome had shown that four of them were infected with ABV-2, two with ABV-4 and one had a mixed infection with ABV-2 and ABV-4. ISH signals were present in the brain, in the vegetative nerve system, glandular epithelia and smooth muscle cells of the intestinal tract and in cardiomyocytes. Hybridization signals for viral genome were more abundant than signals for mRNA. As the probes were not strictly genotype-specific, four of the birds had hybridization signals with both, the ABV-2 and ABV-4 probes. The signals achieved with the homologous probes were more intense and more abundant than those resulting from heterologous probes. Taken together, the results of this study show that ISH can be used as a tool for localizing ABV sequences in tissues of birds with PDD and confirm the causative role of ABVs by showing viral replication in affected tissues.

2. Histocytochemistry Series In Situ Hybridization Using Non-radioisotope labeled RNA Probes (4)

In situ hybridization is a powerful method directed toward obtaining spatial and temporal information concerning the expression and distribution of RNA molecules (e.g., messenger RNA and microRNA) in vivo. In this technical note, we describe procedures for in situ hybridization with non-radioisotope labeled RNA probes, especially a digoxigenin-labeled RNA probe.

Dendritic mRNA Targeting of Jacob and N-Methyl-d-aspartate-induced Nuclear Translocation after Calpain-mediated Proteolysis

Jacob is a recently identified plasticity-related protein that couples N-methyl-d-aspartate receptor activity to nuclear gene expression. An expression analysis by Northern blot and in situ hybridization shows that Jacob is almost exclusively present in brain, in particular in the cortex and the limbic system. Alternative splicing gives rise to multiple mRNA variants, all of which exhibit a prominent dendritic localization in the hippocampus. Functional analysis in primary hippocampal neurons revealed that a predominant cis-acting dendritic targeting element in the 3'-untranslated region of Jacob mRNAs is responsible for dendritic mRNA localization. In the mouse brain, Jacob transcripts are associated with both the fragile X mental retardation protein, a well described trans-acting factor regulating dendritic mRNA targeting and translation, and the kinesin family member 5C motor complex, which is known to mediate dendritic mRNA transport. Jacob is susceptible to rapid protein degradation in a Ca(2+)- and Calpain-dependent manner, and Calpain-mediated clipping of the myristoylated N terminus of Jacob is required for its nuclear translocation after N-methyl-d-aspartate receptor activation. Our data suggest that local synthesis in dendrites may be necessary to replenish dendritic Jacob pools after truncation of the N-terminal membrane anchor and concomitant translocation of Jacob to the nucleus.

P.1.a.002 Association study of −1727 A/T and −50C/T GSK-3 beta gene polymorphism with suicidal behaviour in depressed patients

Glycogen synthase kinase-3α and -3β (GSK-3α and -3β) are multi-substrate, serine/threonine-specific kinases that can phosphorylate microtubule-associated protein tau and other neuronal proteins. In this study, the expression level and mRNA distribution of two GSK-3 isoforms, GSK-3α and -3β in mice were investigated. Northern blot analyses indicated that GSK-3α mRNA is encoded by a 2.5-kb transcript in adult tissues, whereas a 4.1-kb transcript was found in neonatal tissues. The GSK-3β mRNA is encoded by a 1.6-kb transcript in the testis and a 7.6-kb transcript in the brain, and in many other adult tissues, but not neonatal tissues. Western blot analyses demonstrated that GSK-3β protein was mainly expressed in the brain and heart, whereas GSK-3α was highly expressed in the brain, heart, and testis. A non-radioactive in situ hybridization study using specific digoxigenin-labeled RNA probes showed that GSK-3α and -3β mRNAs were found in many brain regions, and were especially abundant in the hippocampus, cerebral cortex, and the Purkinje cells of the cerebellum. This implies the importance of GSK-3α and -3β for brain function. The differential expression of GSK-3α and -3β mRNAs as well as proteins in other tissues indicate that they play different roles in cellular functions and the developmental process.

In Situ Hybridization on Ant Ovaries and Embryos

The detection of transcript distribution throughout a fixed tissue is a major step in studying the transcriptional activity of target genes and their function. In situ hybridization specifically detects the spatial distribution of RNA transcripts using an antisense RNA probe. This protocol describes the preparation of digoxigenin-labeled antisense RNA probes and their hybridization to complementary mRNA sequences; expression can then be localized using an antibody against digoxigenin conjugated to a chromogenic enzyme. In ants, this method can be applied to visualize cell populations of interest among other populations in a tissue, such as insect ovaries, or in the whole organism, such as insect embryos. Specific markers (e.g., genes known to be expressed in particular clusters of cells) can be cloned and used as probes to study the distribution and development of germline cells (e.g., nanos, vasa), neurons (repo), or limb structures (e.g., distal-less). Various markers might also allow the study of oogenesis (nanos, par-1, oskar), segmentation in the embryo (e.g., engrailed, wingless), or other developmental processes.

Distribution of vasoactive intestinal peptide and substance P messenger ribonucleic acid in intestinal nerve of Remak of chicken

The intestinal nerve of Remak (INR) is unique to birds. The exact distributions and secretions of the peptide transmitters in the INR that innervate the intestine, and the patterns of their projections to the nerve plexus of the intestinal wall, are still unclear. In the present study, the distributions of chicken vasoactive intestinal peptide (VIP) mRNA and substance P (SP) mRNA in the chicken INR were demonstrated by means of in situ hybridization histochemistry, using sense and antisense digoxigenin-labeled RNA probes. The in situ hybridization histochemistry results suggested that VIP mRNA-positive neurons were mainly distributed in ganglions, whereas some of the INR fibers were weakly positive. The proportion of VIP mRNA-positive cells among total neurons was 75% in the juxta-jejunoileum portion and 87% in the juxta-rectal portion of the INR. Most SP mRNA-positive cells were sporadically distributed in layers or small groups within the ganglions, as well as in nerve trunks between ganglions. Moreover, the proportion of positive cells among total neurons was 83% in the juxta-jejunoileum portion and 98% in the juxta-rectal portion of the INR, which suggests that both VIP and SP mRNA are coexpressed in the chicken INR. Our results provide an approach to further study of the locations of VIP and SP in nerve tissue.

The Expression Patterns of Cdc25A, Cdc25B, Sox2 and Mnb in Central Nervous System in Early Chicken Embryos

The sense and antisense digoxigenin-labeled RNA probes of four genes, Cdc25A, Cdc25B, Sox2 and Mnb, were produced by using SP6 and T7 RNA polymerases, respectively, and in vitro transcription. Expression patterns of the four genes were detected by in situ hybridization in HH (Hamburger and Hamilton) stage 10 chick embryos. In general, expression patterns of the four genes were similar. mRNA of the four genes was mostly restricted to the entire CNS (central nervous system). All were confined to an identical region, neural tube, neural groove and caudal neural plate, corresponding to the notochord or spinal cord, but there was some distinction in specific region or in concentration, for example in somites. The overlap in expression at the same developmental stage in the CNS suggests that the four genes may be functional similar or related in CNS development. Expression patterns of the four genes support specific roles of these regulators in the developing CNS.

Detection, Distribution, and Genetic Variability of European mountain ash ringspot-associated virus

European mountain ash ringspot-associated virus (EMARAV) was recently characterized from mountain ash (rowan) (Sorbus aucuparia) in Germany. The virus belongs tentatively to family Bunyaviridae but is not closely related to any classified virus. How commonly EMARAV occurs in ringspot disease (EMARSD) affected mountain ash trees was not reported and was investigated here. Virus-specific detection tools such as reverse transcription-polymerase chain reaction and dot blot hybridization using digoxigenin-labeled RNA probes were developed to test 73 mountain ash trees including 16 trees with no virus-like symptoms from 16 districts in Finland and Viipuri, Russia. All trees were infected with EMARAV. Hence, EMARAV is associated with EMARSD and can also cause latent infections in mountain ash. Symptom expression and the variable relative concentrations of viral RNA detected in leaves showed no correlation. Infectious EMARAV was detected also in dormant branches of trees in winter. Subsequently, genetic variability, geographical differentiation, and evolutionary selection pressures were investigated by analyzing RNA3 sequences from 17 isolates. The putative nucleocapsid (NP) gene sequence (944 nucleotides) showed little variability (identities 97 to 99%) and was under strong purifying selection. Amino acid substitutions were detected in two positions at the N terminus and one position at the C terminus of NP in four isolates. The 3' untranslated region (442 nucleotides) was more variable (identities 94 to 99%). Six isolates from a single sampling site exhibited as wide a genetic variability as isolates from sites that were hundreds of kilometers apart and no spatial differentiation of populations of EMARAV was observed.

SAP18 Promotes Krüppel-dependent Transcriptional Repression by Enhancer-specific Histone Deacetylation

Body pattern formation during early embryogenesis of Drosophila melanogaster relies on a zygotic cascade of spatially restricted transcription factor activities. The gap gene Krüppel ranks at the top level of this cascade. It encodes a C2H2 zinc finger protein that interacts directly with cis-acting stripe enhancer elements of pair rule genes, such as even skipped and hairy, at the next level of the gene hierarchy. Krüppel mediates their transcriptional repression by direct association with the corepressor Drosophila C terminus-binding protein (dCtBP). However, for some Krüppel target genes, deletion of the dCtBP-binding sites does not abolish repression, implying a dCtBP-independent mode of repression. We identified Krüppel-binding proteins by mass spectrometry and found that SAP18 can both associate with Krüppel and support Krüppel-dependent repression. Genetic interaction studies combined with pharmacological and biochemical approaches suggest a site-specific mechanism of Krüppel-dependent gene silencing. The results suggest that Krüppel tethers the SAP18 bound histone deacetylase complex 1 at distinct enhancer elements, which causes repression via histone H3 deacetylation.

Whole-Mount In Situ Hybridization in Amphimedon

INTRODUCTIONDevelopmental gene expression is analyzed predominantly via whole-mount in situ hybridization using digoxigenin-labeled RNA probes. This protocol describes how to perform this procedure in Amphimedon queenslandica, including fixation, hybridization, and sectioning of embryonic, larval, and post-larval juvenile stages.

An Oncogenic Role for the Phosphorylated h-Subunit of Human Translation Initiation Factor eIF3

Dysregulation of protein synthesis has been implicated in oncogenesis through a mechanism whereby "weak" mRNAs encoding proteins involved in cell proliferation are strongly translated when the protein synthesis apparatus is activated. Previous work has determined that many cancer cells contain high levels of eIF3h, a protein subunit of translation initiation factor eIF3, and overexpression of eIF3h malignantly transforms immortal NIH-3T3 cells. This is a general feature of eIF3h, as high levels also affect translation, proliferation, and a number of malignant phenotypes of CHO-K1 and HeLa cells and, most significantly, of a primary prostate cell line. Furthermore, overexpressed eIF3h inhibits Myc-dependent induction of apoptosis of primary prostate cells. eIF3h appears to function through translation, as the initial appearance of overexpressed eIF3h in rapidly induced NIH-3T3 cells correlates tightly with the stimulation of protein synthesis and the generation of malignant phenotypes. This oncogenic potential of eIF3h is enhanced by phosphorylation at Ser(183). Finally, reduction of eIF3h levels in breast and prostate cancer cell lines by short interfering RNA methods reduces their rates of proliferation and anchorage-independent growth in soft agar. The results provide compelling evidence that high eIF3h levels directly stimulate protein synthesis, resulting in the establishment and maintenance of the malignant state in cells.

Epithelial Distribution and Replication of Foot-and-Mouth Disease Virus RNA in Infected Pigs

Although the pathogenesis of foot-and-mouth disease (FMD) has been extensively investigated, relatively few studies have addressed the localization of FMD virus (FMDV) and in particular its replication in relation to the typical in-vivo sites of FMD lesions. In the present study, pigs were infected experimentally with FMDV serotype O UKG 34/2001 and tissue samples were collected from 1 to 4 days post-infection. Samples were stored at -70 degrees C and frozen sections were prepared for in-situ hybridization (ISH). A digoxigenin-labelled RNA probe complementary to a coding part of the RNA-dependent RNA polymerase (3D) genomic region was prepared. The FMDV positive strand RNA was prominent in the basal layers of the epithelium. A diffuse positive signal was also noted in the cytoplasm of cells of the stratum spinosum of lesional epithelium, but there was no signal in the stratum corneum. Detection of FMDV negative strand RNA was observed in basal cells above the basement membrane and along the dermal papillae. The basal cells therefore demonstrate the highest signal for detection of the FMDV positive and negative strand RNAs in both tongue and foot epithelium. These novel results suggest that the epithelial basal cells could be an early replication site of FMDV in vivo.

Eena Promotes Myeloid Proliferation through Stimulating ERK1/2 Phosphorylation in Zebrafish

The EEN (extra eleven nineteen) gene is one of the fusion partners of mixed-lineage leukemia, located on chromosome 19p13. Here we cloned two een genes (designated as eena and eenb) in zebrafish, which are assigned to linkage groups 8 and 2, respectively. Whole-mount in situ hybridization assay showed that eena and eenb have overlapping but distinct expression patterns during embryogenesis. Ubiquitous or targeted overexpression of eena, but not eenb, into wild-type or transgenic embryos (green fluorescent protein-labeled myeloid progenitors) induced a significant proliferation and ectopic distribution of myeloid progenitors in the yolk sac. Using a morpholino antisense gene knockdown approach, we showed that the number of myeloid progenitors and their downstream mature myelomonocytic cells was significantly decreased in the eena- deficient embryos. Mechanistically, overexpression of eena selectively stimulated ERK phosphorylation and increased the level of transcription factor c-Fos in vitro and in vivo, whereas eena lacking the Src homology 3 domain completely abolished these effects. Furthermore, a MAPK/ERK kinase (MEK) inhibitor, PD98059, blocked the eena-induced cell proliferation and activation of ERK signaling. The results suggest that eena plays an important role in the development of the myeloid cell through activation of the ERK pathway and may provide a valuable reference for future studies of the role of EEN in leukemogenesis.

Genome-wide Analysis Identifies Interleukin-10 mRNA as Target of Tristetraprolin

Tristetraprolin (TTP) is an RNA-binding protein required for the rapid degradation of mRNAs containing AU-rich elements. Targets regulated by TTP include the mRNAs encoding tumor necrosis factor-alpha, granulocyte-macrophage colony-stimulating factor, interleukin-2 (IL-2), and immediate early response 3. To identify novel target mRNAs of TTP in macrophages, we used a genome-wide approach that combines RNA immunoprecipitation and microarray analysis. A list was compiled of 137 mRNAs that are associated with TTP with an estimated accuracy on the order of 90%. Sequence analysis revealed a highly significant enrichment of AU-rich element motifs, with AUUUA pentamers present in 96% and UUAUUUAUU nonamers present in 44% of TTP-associated mRNAs. We further show that IL-10 is a novel target regulated by TTP. IL-10 mRNA levels were found to be elevated because of a reduced decay rate in primary macrophages from TTP(-/-) mice. Our study demonstrates the importance of experimental approaches for identifying targets of RNA-binding proteins.

Specific regional distribution of gec1 mRNAs in adult rat central nervous system

GEC1 protein shares high identity with GABARAP (GABA A Receptor-Associated Protein), interacts with tubulin and GABA A receptors and is potentially involved in intracellular transport processes. Recently, using quantitative real time PCR, we have reported the gec1 mRNA expression in different rat brain areas. In the present study, we investigated the cell types expressing gec1 in rat brain. Sense and anti-sense gec1 RNA probes, corresponding to the 3′-untranslated region, were generated. In northern blotting experiments, the anti-sense probe revealed only the 1.75 kb gec1 mRNAs. On the other hand, in immunohistochemistry experiments, GEC1 polyclonal antibodies did not discriminate between GEC1 and GABARAP proteins. Therefore, we used digoxigenin-labeled RNA probes for in situ hybridization (ISH) experiments to map the gec1 expression. Using the anti-sense probe, we detected the gec1 mRNAs specifically in neurons throughout the rostrocaudal extent of the brain as well as in the spinal cord. Although a majority of neurons expressed the gec1 mRNAs, different intensities of labeling were observed depending on the areas: the strongest labeling was observed in the isocortex, hippocampus, basal telencephalon, some thalamic and most of hypothalamic nuclei, cerebellum, and numerous brainstem nuclei. Furthermore, the gec1 mRNAs were intensely expressed in neurons involved in somatomotor and neuroendocrine functions and weakly expressed in sensory and reticular structures. These results corroborate the putative role of the GEC1 protein in the trafficking of receptor GABA A.

High-resolution in situ hybridization to whole-mount zebrafish embryos

The in situ hybridization (ISH) technique allows the sites of expression of particular genes to be detected. This protocol describes ISH of digoxigenin-labeled antisense RNA probes to whole-mount zebrafish embryos. In our method, PCR-amplified sequence of a gene of interest is used as a template for the synthesis of an antisense RNA probe, which is labeled with digoxigenin-linked nucleotides. Embryos are fixed and permeabilized before being soaked in the digoxigenin-labeled probe. We use conditions that favor specific hybridization to complementary mRNA sequences in the tissue(s) expressing the corresponding gene. After washing away excess probe, hybrids are detected by immunohistochemistry using an alkaline phosphatase-conjugated antibody against digoxigenin and a chromogenic substrate. The whole procedure takes only 3 days and, because ISH conditions are the same for each probe tested, allows high throughput analysis of zebrafish gene expression during embryogenesis.

Expression and Regulation of the Osteoarthritis-associated Protein Asporin

Asporin (ASPN) is a small leucine-rich proteoglycan that is involved in pathological processes of osteoarthritis. Previously, we showed that asporin can inhibit transforming growth factor-beta1 (TGF-beta1)-mediated expression of cartilage matrix genes and chondrogenesis in vitro (Kizawa, H., Kou, I., Iida, A., Sudo, A., Miyamoto, Y., Fukuda, A., Mabuchi, A., Kotani, A., Kawakami, A., Yamamoto, S., Uchida, A., Nakamura, K., Notoya, K., Nakamura, Y., and Ikegawa, S. (2005) Nat. Genet. 37, 138-144). However, details about regulation of asporin itself are not yet known. Here, we examined ASPN expression in skeletal tissue and potential regulation of ASPN by TGF-beta. In situ hybridization revealed the presence of ASPN mRNA in the perichondrium/periosteum of long bones, but its absence in articular cartilage and growth plates. Immunohistochemical analysis also showed ASPN protein expression predominantly in the perichondrium/periosteum. TGF-beta1 induced endogenous ASPN mRNA expression over time in vitro, and this induction was suppressed by the TGF-beta type I receptor kinase inhibitor SB431542. Inhibition of Smad3 significantly reduced TGF-beta1-induced ASPN expression, whereas overexpression of Smad3 augmented the induction. Characterization of the human ASPN promoter region revealed a region from -126 to -82 that is sufficient for full promoter activity; however, TGF-beta1 failed to increase activity through the ASPN promoter. Our findings indicate that TGF-beta1 induces ASPN through Smad3 but that this induction is indirect.