C9orf72 Poly(PR) Dipeptide Repeats Disturb Biomolecular Phase Separation and Disrupt Nucleolar Function.

Repeat expansion in the C9orf72 gene is the most common cause of the neurodegenerative disorder amyotrophic lateral sclerosis (C9-ALS) and is linked to the unconventional translation of five dipeptide-repeat polypeptides (DPRs). The two enriched in arginine, poly(GR) and poly(PR), infiltrate liquid-like nucleoli, co-localize with the nucleolar protein nucleophosmin (NPM1), and alter the phase separation behavior of NPM1 in vitro. Here, we show that poly(PR) DPRs bind tightly to a long acidic tract within the intrinsically disordered region of NPM1, altering its phase separation with nucleolar partners to the extreme of forming large, soluble complexes that cause droplet dissolution in vitro. In cells, poly(PR) DPRs disperse NPM1 from nucleoli and entrap rRNA in static condensates in a DPR-length-dependent manner. We propose that R-rich DPR toxicity involves disrupting the role of phase separation by NPM1 in organizing ribosomal proteins and RNAs within the nucleolus.

Designing immunostimulatory double stranded messenger RNA with maintained translational activity through hybridization with poly A sequences for effective vaccination.

Messenger (m)RNA vaccines require a safe and potent immunostimulatory adjuvant. In this study, we introduced immunostimulatory properties directly into mRNA molecules by hybridizing them with complementary RNA to create highly immunogenic double stranded (ds)RNAs. These dsRNA formulations, comprised entirely of RNA, are expected to be safe and highly efficient due to antigen expression and immunostimulation occurring simultaneously in the same antigen presenting cells. In this strategy, design of dsRNA is important. Indeed, hybridization using full-length antisense (as)RNA drastically reduced translational efficiency. In contrast, by limiting the hybridized portion to the mRNA poly A region, efficient translation and intense immunostimulation was simultaneously obtained. The immune response to the poly U-hybridized mRNAs (mRNA:pU) was mediated through Toll-like receptor (TLR)-3 and retinoic acid-inducible gene (RIG)-I. We also demonstrated that mRNA:pU activation of mouse and human dendritic cells was significantly more effective than activation using single stranded mRNA. In vivo mouse immunization experiments using ovalbumin showed that mRNA:pU significantly enhanced the intensity of specific cellular and humoral immune responses, compared to single stranded mRNA. Our novel mRNA:pU formulation can be delivered using a variety of mRNA carriers depending on the purpose and delivery route, providing a versatile platform for improving mRNA vaccine efficiency.

Identification of internal poly(A) tracts (IPATs) of variable lengths in a novel tobacco rattle virus RNA2 in potatoes.

The nucleotide (nt) sequences of two closely related isolates (CeWF-2 and CeWGH-2) of a novel tobacco rattle virus (TRV) RNA2 were determined. The sequences of their RNA2-specific regions were almost identical and contained four open reading frames (ORFs) in an arrangement similar to that found in the previously described TRV TpO1 RNA2. Their predicted ORF 1 gene products shared 97 % amino acid sequence identity with the TpO1 coat protein, but the ORF 2 and ORF 3 gene products shared only 82 % sequence identity, and no appreciable sequence similarity was found between the CeWF-2/CeWGH-2 and TpO1 ORF 4 gene products. In the CeWGH-2 sequence, the RNA2-specific and RNA1-related regions were separated by seven adenine (A) residues. In CeWF-2, however, an internal poly(A) tract (IPAT) of variable size consisting of ca. 20 to 30 (A) residues was found. This is the first report of an IPAT occurring in a tobravirus RNA2.

Isolation and partial characterization of a novel pollen-specific cDNA with multiple polyadenylation sites from wheat.

A novel pollen-specific full-length cDNA clone PSG076 was isolated using suppression subtractive hybridization and 5'/3' RACE techniques. PSG076 was shown to exhibit multi-site polyadenylation by sequencing the 3' ends of the cDNAs. At least six transcripts with different length were produced from the single gene based on different poly(A) tail attachment sites. However, polyadenylation consensus sequence AAUAAA was not seen at the 3'-untranslated sequence. PSG076 contained a 299 bp 5' untranslated region and an open reading frame of 663 bp encoding a 221 amino acid peptide with pI of 4.31. A blast search revealed that this sequence did not show a significant similarity to any genes deposited in the public database. Southern blot indicated that PSG076 was a single copy gene. Northern blot and RT-PCR analysis indicated that PSG076 transcripts showed specific expression in mature pollen, and weak or undetectable signals in uninucleate microspore, immature seed, stem, young leave, root and ovary. Further analysis of the expression pattern in gametophyte showed that PSG076 transcripts were undetectable in uninucleate, binucleate microspore and pollen at early stage, and were first detectable and increased rapidly at middle and late stages of pollen development with the maximum level in mature pollen and also expressed in germinating pollen in vivo, suggesting that PSG076 might play a role in pollen germination and pollen tube growth in addition to its function in maturation. The evidences gathered in this work indicated that the six different transcripts from the single gene were differentially expressed during pollen development.

Gene structure and evolution of Tieg3, a new member of the Tieg family of proteins.

TGF beta-inducible immediate early gene, Tieg, belongs to the superfamily of Sp1-like transcription factors containing three C(2)H(2)-zinc finger DNA binding motifs close to the C-terminus. So far, Tieg1 and Tieg2 have been identified in human and mouse. We identified Tieg3, a new member of the Tieg protein family by screening a mouse cDNA library. Tieg3 has almost all the known features of the Tieg protein family: it shares a highly conserved C(2)H(2) zinc finger DNA binding domain and is 96% identical to Tieg2 and 86% to Tieg1, respectively. In addition, the three repression domains at the N-terminus, R1, R2 and R3 are conserved in all the Tiegs. Similar to Tieg1 and Tieg2, Tieg3 mRNA is up-regulated in response to TGF beta 1 treatment and can perform the Sp1 sites mediated repression of transcription. A 4 kilobase (kb) long transcript of mouse Tieg3 can be detected using Northern-blot analysis. The gene of mouse Tieg3 contains four exons. Due to the amino acid sequence similarity, mouse Tieg2 is regarded as an orthologue of human Tieg2. However, the mouse Tieg3 gene is localized in a conserved segment on mouse chromosome 12 corresponding to human Tieg2 on chromosome 2 with the same gene order. An interesting explanation for this apparent contradiction might be a homologous recombination leading to loci exchange between the mouse Tieg3 and Tieg2.

Drosophila lola encodes a family of BTB-transcription regulators with highly variable C-terminal domains containing zinc finger motifs.

Alternative splicing is an important mechanism contributing to the increased proteome diversity in higher eukaryotes. We have explored the alternative splicing events in the Drosophila longitudinals lacking (lola) gene by means of 5' RACE, 3' RACE, genome sequence searches, and EST sequencing. We demonstrated that the lola locus is comprised of 32 exons spanning over 60 kb, and encodes a total of 80 alternatively spliced variants consisting of 5' and 3' variable sequences and constitutive common exons. All the variants shared a common sequence (exons 5-8) encoding the N-terminal region containing the BTB domain, but both the 5' and 3' ends were variable. There were four promoters responsible for the variation in the 5' end (exons 1-4). Alternative splicing was involved in the variation in the 3' end corresponding to the C-terminal variable region, which was encoded by one or two exons that were selected from 20 groups of exons in a mutually exclusive manner (exons 9-32). Seventeen of the 20 isoforms contained C(2)H(2)-like zinc finger motifs in the C-terminal variable region. Analyses of the 3' variant-specific cDNA pools revealed that all combinations of 5' and 3' variable sequences were expressed in both the embryonic and third instar larval stages. Since the BTB domain mediates dimerization, lola encodes a family of transcription regulators with a large variety of DNA- or protein-binding specificities, and could be involved in various developmental processes, including the embryonic neural pathfindings. We also showed that the structures of Lola isoforms were highly conserved in Drosophila pseudoobscura.

The TRPV6 gene, cDNA and protein.

The mouse TRPV6 gene is localized on chromosome 6 and extends over 15.66kb. The encoded protein comprises 727 amino acid residues with a calculated relative molecular mass of 83,210Da. TRPV6 is glycosylated and both variants, the glycosylated and the de-glycosylated proteins, are recognized by various polyclonal and monoclonal antibodies, which were raised against TRPV6. Like human TRPV6, mouse TRPV6 binds calmodulin in the presence, but not in the absence of Ca2+. TRPV6 is abundantly expressed in mouse pancreas and placenta, and to a much lesser extend in mouse stomach and kidney. No transcript expression was detected in poly(A)+RNA isolated from heart, brain, intestine, esophagus or aortic endothelial cells.

Identification of a novel human zinc finger protein gene ZNF313.

A novel human zinc finger protein gene that contains both ring finger and C(2)H(2) domain was first isolated by mRNA differential display between the testes of fertile adults and azoospermic patients followed by rapid amplification of cDNA ends (RACE). Total 6 exons of the human gene span a 17,484 bp genomic DNA sequence that was mapped to chromosome 20q13 by fluorescence in situ hybridization. The mature processed mRNA encodes a 228-amino acid protein with a C(3)HC(4) ring finger and three C(2)H(2) domains. Genomic analysis of the human gene identified two polyadenylation signals in exon 6 resulting in alternative 3'-untranslated regions. Results of Northern blot and RT-PCR of RNAs extracted from multiple tissues revealed that the gene has two transcripts of which the shorter transcript was expressed abundantly in fertile adult testes, but much less in testes of azoospermic patient, fetus as well as other human tissues. These data suggest that the gene may play a role in human spermatogenesis and male fertility.

Mouse epididymal Spam1 (pH-20) is released in the luminal fluid with its lipid anchor.

Previously we demonstrated that the murine sperm adhesion molecule 1 (Spam1 or PH-20) is synthesized by the epididymal epithelium, preferentially in the distal region, and is released into the luminal fluid. We also showed that whereas testicular and epididymal Spam1 have hyaluronidase activity at neutral pH, they are under different transcriptional regulation. The aim of this study was to further compare characteristics of the two forms of this glycosyl-phosphatidylinositol-linked protein and their transcripts, and to determine whether secreted epididymal Spam1 is released with its lipid anchor. With GeneRacer amplification of the 3' end of the complementary DNA we show that the poly(A) tails are significantly (P <.05) shorter in the epididymis than in the testis. Two-dimensional polyacrylamide gel electrophoresis with immunoblotting reveals one to three isoforms for epididymal Spam1 with the isoelectric point (pl) ranging from 7.3 to 9.0, and four isoforms ranging from 6.6 to 9.0 pl for testicular Spam1. Two isoforms with a pl ranging from 7.6 to 9.0 were observed for caudal sperm. Lectin blotting analysis shows that Phaseolus vulgaris erythroagglutinin, Lycopersicon esculentum lectin (LEL), and Solanum tuberosum lectin, which all bind to N-linked chains, recognize a 67 kd band in the epididymis and caudal sperm, but not in the testis. Treatment of the protein extracts with anti-Spam1 serum prior to blotting with LEL led to the disappearance of the banding, indicating Spam1 specificity of the staining. The lectin peanut agglutinin, which preferentially binds to O-linked side chains, recognizes a 67 kd band in all three cell types. Enzymatic deglycosylation studies confirmed the presence of an O-linked glycan in all three cell types. Ultracentrifugation of the luminal fluid reveals that epididymal Spam1 is secreted predominantly as insoluble particles, which when treated with phosphatidylinositol-specific phospholipase C or Triton X-100, reveal that the majority of epididymal Spam1 is released with its lipid anchor, a form in which it can bind to sperm.

Strength evaluation of transcriptional regulatory elements for transgene expression by adenovirus vector.

In studies of both gene function and gene therapy, transgene expression may be assisted considerably through the use of transcriptional regulatory elements with high activity. In this study, we evaluated the strength of various transcriptional regulatory elements both in vitro (six types of cell line) and in vivo (mouse heart, lung, kidney, spleen, and liver) by adenovirus-mediated gene transfer. In the case of the promoter/enhancer (P/E), the activity of CMV P/E (from the human cytomegalovirus immediate-early 1 gene) and hybrid CA P/E (composed of the CMV enhancer and chicken beta-actin promoter) were investigated, both of which are known to be strong and widely used. While hybrid CA P/E showed a higher transgene expression activity than CMV P/E, the addition of the intron A sequence (the largest intron of CMV) to CMV P/E increased the activity of CMV P/E to the same or higher level than that of hybrid CA P/E. Concerning the polyadenylation signal (P(A)) sequence, one from the bovine growth hormone (BGH) gene was about two times more efficient than that from the Simian virus 40 (SV40) late gene, both in vitro and in vivo. In the context of the CMV P/E containing the intron A sequence, a further increase in transgene expression was obtained by the addition of a SV40 enhancer downstream from the P(A) sequence. The combination of the SV40 P(A) and a SV40 enhancer showed almost comparable activity to BGH P(A). This information would be helpful for the construction of adenovirus vectors for studies regarding both gene function and gene therapy.

Potassium channel mRNAs with AU-rich elements and brain-specific expression.

GIRK2 (G protein-gated inwardly rectifying K(+) channel 2) located on the Down syndrome region 21q22.2 in humans has been reported to have several alternative transcripts and transcripts longer than 4 kb that do not have the poly-A tail. We sequenced GIRK2 transcripts with a long 3'-untranslated region (3'-UTR) containing multiple adenylate uridylate-rich elements (AREs) with the poly-A tail. In a 16-kb transcript, 28 AUUUA pentanucleotides, 9 AUUUUA hexanucleotides, 5 AUUUUUA heptanucleotides, and 3 UUAUUUA[U/A][U/A] nonanucleotides were found. Northern blot and in situ hybridization revealed abundant expression of the 16-kb transcripts in the rat brain despite no detectable signals in other tissues examined. The AREs have been reported to mediate the turnover of mRNAs encoding proteins regulating cellular proliferation/differentiation and body response to inflammatory and environmental stimuli. This is the first study indicating that ion channel transcripts have multiple AREs.

NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines.

We describe the isolation and characterization of NSD3, the third member of a gene family including Nsd1 and NSD2. Murine Nsd1 was isolated in a search for proteins that interact with the ligand-binding domain of retinoic acid receptor alpha. NSD2 (also known as WHSC1 and MMSET) is located in the Wolf-Hirschhorn syndrome (WHS) critical region on 4p16.3 and is involved in multiple myeloma with t(4;14) translocations. The proteins Nsd1, NSD2, and NSD3 are highly similar within a block of about 700 amino acids. This block contains several conserved domains, such as the SET domain and the PHD finger, present in proteins involved in development and/or chromatin reorganization. The NSD3 gene consists of an 8.5-kb transcript composed of 23 coding exons and spans >90 kb of genomic DNA. NSD3 maps to chromosome band 8p12 and is amplified in several tumor cell lines and primary breast carcinomas.

Molecular analysis of genetic differences among inbred mouse strains controlling tissue expression pattern of alcohol dehydrogenase 4.

The ADH gene family in vertebrates is composed of at least seven distinct classes based upon sequence comparisons and enzyme properties. The Adh4 gene product may play an important role in differentiation and development because of its capacity to metabolize retinol to retinoic acid. Allelic gene differences exist among inbred mouse strains which control structure and tissue-specific regulation of Adh4. C57BL/6 mice are unique and have no detectable ADH4 enzyme activity in epididymis and low levels in seminal vesicle, ovary and uterus compared to other strains. C57BL/6 mice express Adh4 in stomach at levels similar to other strains. The goal of this research was to investigate this genetic variation at the molecular level. Northern analysis revealed that the content of ADH4 mRNA in tissues correlate with the enzyme expression pattern. Interestingly, C57BL/6 mice express an ADH4 mRNA in stomach which is smaller than expressed in C3H and other mice. An analysis of the 5'- and 3'-ends of the mRNA using RACE analysis determined that the ADH4 mRNA in C57BL/6 mice is truncated in the 3'-untranslated region. Sequence analysis of RACE products showed that the truncation is due to a single nucleotide mutation which produces an early polyadenylation signal. Additional RACE and Northern analysis revealed that at least five different polyadenylation sites are used in the Adh4 gene. Using 3'-end polymorphisms found between C57BL/6 and C3H strains and RT-PCR, it was shown that the lack of expression in epididymis in C57BL/6 mice is cis-acting in F(1) hybrid animals. The DNA sequence of the proximal promoter (-600/+42 nt) was determined in several mouse strains differing in tissue-specific expression patterns and did not reveal any nucleotide substitutions correlating with expression pattern suggesting further upstream or downstream sequences may be involved.

Sink- and vascular-associated sucrose synthase functions are encoded by different gene classes in potato.

Two differentially regulated classes of sucrose synthase genes, Sus3 and Sus4, were identified in potato. They cannot be classified as Sus1 and Sus2 types based on sequence homology and appear to have evolved after the divergence of the major families of dicotyledonous plants but before the divergence of tomato and potato. The potato sucrose synthase clones Sus3-65 and Sus4-16 share an 87% nucleotide identity in the coding regions, and both are interrupted by 13 introns, including a long leader intron. Potato Sus3 genes are expressed at the highest levels in stems and roots and appear to provide the vascular function of sucrose synthase. In contrast, Sus4 genes are expressed primarily in the storage and vascular tissue of tubers and appear to facilitate sink function. The genes are differentially regulated in root tips, with Sus3 expressed at high levels in the cell division zone and Sus4 expressed at high levels in the meristem and cap.

Human CuZn superoxide dismutase enzymatic activity in cells is regulated by the length of the mRNA.

Single functional human CuZnSOD gene encodes two species of mRNA differing in size by 200 nucleotides in the 3'-untranslated region (UTR). We studied the expression of the CuZnSOD cDNA with different 3'- and 5'-UTR. Deletion in the 5'-end does not affect the expression of the enzyme, however, deletion in the 3'-UTR decreases the level of expression of CuZnSOD. The plasmids containing the long CuZnSOD cDNA with all polyadenylation signal sequences utilize primarily the last polyadenylation site and give a long mRNA, which produces three times more enzyme than the short mRNA lacking the last polyadenylation site and the AU-rich region.

Expression of acinar and ductal products in Capan-1 cells growing in synthetic serum and serum-free media.

BACKGROUND: Capan-1 is a human pancreatic adenocarcinoma cell line of presumed ductal origin. This is based on the histologic appearance of the tumor from which it arose. Yet considerable controversy exists regarding the actual cell of origin for these exocrine carcinomas. Two acinar antigens, ribonuclease and trypsin, were analyzed in cells growing in synthetic serum. METHODS: Capan-1 cells were adapted to grow in basal medium supplemented with synthetic serum, because fetal bovine serum (FBS) normally used to culture cells contains bovine ribonuclease, which can interfere with measurements of the ribonuclease secretion. These cells were also adapted to grow in different serum-free media, allowing us to determine its minimal growth requirements. The presence of ribonuclease in Capan-1 and PANC-1 conditioned media was monitored by activity. Other acinar and ductal markers were monitored using Northern blot analysis. RESULTS: Capan-1, PANC-1, IBF-CP3, and MDAAmp-7 cell lines were successfully adapted to grow in synthetic serum by means of the adaptation protocol reported here. The adaptation of Capan-1 to serum-free media showed that the cells are capable of growing in a medium containing insulin, transferrin, selenium, a nonprotein carrier, and lipoic and linoleic acids. Northern blot analysis showed the expression of carbonic anhydrase II, cytokeratin 18, ribonuclease, and trypsin in Capan-1 cells growing in FBS and synthetic serum. No changes in morphology, karyotype, or gene expression were observed in these cells as a result of the adaptation process. CONCLUSION: The cell line Capan-1 is expressing some ductal as well as acinar products despite its supposed ductal origin. The expression of trypsin at the mRNA level and ribonuclease at mRNA and protein levels is shown in Capan-1 cells. The protein expression will be further investigated as the cell line has been adapted to grow in synthetic serum and serum-free media with no apparent changes with respect to their growth in FBS.

Hydrophilic and amphiphilic forms of Drosophila choline acetyltransferase are encoded by a single mRNA.

We have previously shown that the enzyme choline-O-acetyltransferase (ChAT) exists in a hydrophilic and an amphiphilic form in Drosophila head. A complementary DNA clone of 4.2 kb containing the entire coding region of ChAT was isolated from a cDNA library of Drosophila heads. The cDNA was subcloned in an expression vector and injected into the nucleus of Xenopus oocytes. Injected oocytes expressed high levels of ChAT activity. This activity was inhibited by bromoacetylcholine, a specific inhibitor of the enzyme. In the present study the non-ionic detergent Triton X-114 was used to analyse whether the expression of hydrophilic and amphiphilic ChAT was or was not directed by a single cDNA. The two forms of ChAT were found to be synthesized in injected oocytes. Approximately 9% of the recombinant enzyme partitioned as amphiphilic activity. This value was similar to that found for native amphiphilic ChAT in Drosophila heads. Sedimentation in sucrose gradients of amphiphilic enzyme was found to be influenced by the type of detergent present in the gradient whereas this was not the case for hydrophilic ChAT. Hydrophilic and amphiphilic enzyme activities differed in some of their biochemical properties. Amphiphilic ChAT was less sensitive to inhibition by the product acetylcholine than was hydrophilic ChAT. Moreover, amphiphilic ChAT was found to be more resistant than hydrophilic ChAT to heat inactivation at 45 degrees C. These properties were observed for the native as well as for recombinant ChAT. These results demonstrate that the hydrophilic and amphiphilic forms of ChAT are derived from one mRNA.

Expression of nuclear hormone receptors within the rat hippocampus: identification of novel orphan receptors.

Within the hippocampus, stimulus-transcriptional coupling plays an important role in post-seizure neuronal adaptation, post-ischemic cell death and the induction of long-term potentiation. To identify additional mediators of hippocampal transcriptional responses a targeted approach was developed and used to characterize the spectrum of nuclear hormone receptors expressed within this brain region. cDNAs encoding the DNA-binding domains of six different members of the nuclear hormone receptor superfamily were isolated. A majority were identical or closely related to receptors known to be expressed within the hippocampus. Two additional isolates, HZF-2 and HZF-3, encode the DNA-binding domain of novel members of the nuclear hormone receptor superfamily.

Differential expression of six glutamine synthetase genes in Zea mays.

The maize genome has been shown to contain six glutamine synthetase (GS) genes with at least four different expression patterns. Noncoding 3' gene-specific probes were constructed from all six GS cDNA clones and used to examine transcript levels in selected organs by RNA gel blot hybridization experiments. The transcript of the single putative chloroplastic GS2 gene was found to accumulate primarily in green tissues, whereas the transcripts of the five putative GS1 genes were shown to accumulate preferentially in roots. The specific patterns of transcript accumulation were quite distinct for the five GS1 genes, with the exception of two closely related genes.

Application of poly(A)+RNA patterns method for searching of differentially expressed genes.

Poly(A)+RNA composition differences for normal, fetal and cirrhotic human liver before and after retinoic acid-induced differentiation of the F9 embryonal carcinoma cell line were analyzed by a novel poly(A)+RNA patterns method. The method is based on the polyacrylamide gel electrophoretic analysis of short cDNA termination products, synthesized by reverse transcriptase using poly(A)+RNA as a template, a set of short 5'-end labeled primers, three natural and one terminator deoxyribonucleotide. A number of known differentially expressed genes and some unknown ones were then identified by direct sequencing of the differentially represented bands excised from a gel and searching a complementary mRNA target sites in Genbank database.