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Muscle miRNAome shows suppression of chronic inflammatory miRNAs with both prednisone and vamorolone.

Corticosteroids are highly prescribed and effective anti-inflammatory drugs but the burden of side effects with chronic use significantly detracts from patient quality of life, particularly in children. Developing safer steroids amenable to long-term use is an important goal for treatment of chronic inflammatory diseases such as Duchenne muscular dystrophy (DMD). We have developed vamorolone (VBP15), a first-in-class dissociative glucocorticoid receptor (GR) ligand that shows the anti-inflammatory efficacy of corticosteroids without key steroid side effects in animal models. miRNAs are increasingly recognized as key regulators of inflammatory responses. To define effects of prednisolone and vamorolone on the muscle miRNAome, we performed a preclinical discovery study in the mdx mouse model of DMD. miRNAs associated with inflammation were highly elevated in mdx muscle. Both vamorolone and prednisolone returned these toward wild-type levels (miR-142-5p, miR-142-3p, miR-146a, miR-301a, miR-324-3p, miR-455-5p, miR-455-3p, miR-497, miR-652). Effects of vamorolone were largely limited to reduction of proinflammatory miRNAs. In contrast, prednisolone activated a separate group of miRNAs associated with steroid side effects and a noncoding RNA cluster homologous to human chromosome 14q32. Effects were validated for inflammatory miRNAs in a second, independent preclinical study. For the anti-inflammatory miRNA signature, bioinformatic analyses showed all of these miRNAs are directly regulated by, or in turn activate, the inflammatory transcription factor NF-κB. Moving forward miR-146a and miR-142 are of particular interest as biomarkers or novel drug targets. These data validate NF-κB signaling as a target of dissociative GR-ligand efficacy in vivo and provide new insight into miRNA signaling in chronic inflammation.

Animals↗

Molecular cloning and sequencing of cDNAs encoding the entire rat fatty acid synthase.

Overlapping cloned cDNAs representing the entire sequence of the rat fatty acid synthase mRNA have been isolated from a cDNA library and sequenced. Authenticity of the cDNA clones was supported by hybridization to fatty acid synthase mRNA and by amino-terminal sequencing of 39 fatty acid synthase CNBr fragments. The full-length fatty acid synthase mRNA is 9156 nucleotides long and includes an 84-nucleotide 5' noncoding region, a 7515-nucleotide coding sequence, and a 1537-nucleotide 3' noncoding region; a second mRNA species containing a shortened 3' noncoding sequence is also transcribed in the rat. The encoded fatty acid synthase subunit contains 2505 amino acids and has a molecular weight of 272,340. Active sites and substrate binding sites were located within the sequence, thus establishing the order of domains on the multifunctional animal fatty acid synthase as condensing enzyme-transferase-dehydrase-enoyl reductase-ketoreductase-acyl carrier protein-thioesterase.

Amino Acid Sequence↗

Genomic organization and chromosomal localization of the gene encoding human P-selectin glycoprotein ligand.

The gene for P-selectin glycoprotein ligand (PSGL-1) has been cloned from a human placenta genomic DNA library. A single intron of approximately 9 kilobases was found in the 5'-untranslated region and the complete coding region resides in exon 2. The genomic clone differs from the cDNA clone isolated from HL-60 cells in that it encodes an extra copy of the decameric repeat located in the extracellular domain of PSGL-1. Further analysis indicated that the PSGL-1 genes of HL-60 and U-937 cells contain 15 repeats, whereas the PSGL-1 genes of polymorphonuclear leukocytes, monocytes, and several other cell lines contain 16 repeats. Transfection experiments did not indicate a functional difference between these two variants of PSGL-1. The two previously observed PSGL-1 mRNA species of 2.5 and 4 kilobases most likely arise from differential utilization of polyadenylation signal sequences. The organization of the PSGL-1 gene closely resembles those of CD43 and human platelet glycoprotein GPIb alpha, both of which have an intron in the 5'-noncoding region, a long second exon containing the complete coding region, and TATA-less promoters. The gene for human PSGL-1, which has been designated SELPLG by the Human Gene Nomenclature Committee, was mapped to chromosome 12q24 using Southern blot analysis of DNA from a set of human-mouse cell hybrids, and fluorescent in situ hybridization on metaphase chromosome spreads.

Amino Acid Sequence↗

Mitochondrial diversity of early-branching metazoa is revealed by the complete mt genome of a haplosclerid demosponge.

The first mitochondrial (mt) genomes of demosponges have recently been sequenced and appear to be markedly different from published eumetazoan mt genomes. Here we show that the mt genome of the haplosclerid demosponge Amphimedon queenslandica has features that it shares with both demosponges and eumetazoans. Although the A. queenslandica mt genome has typical demosponge features, including size, long noncoding regions, and bacterialike rRNA genes, it lacks atp9, which is found in the other demosponges sequenced to date. We found strong evidence of a recent transposon-mediated transfer of atp9 to the nuclear genome. In addition, A. queenslandica bears an incomplete tRNA set, unusual amino acid deletion patterns, and a putative control region. Furthermore, the arrangement of mt rRNA genes differs from that of other demosponges. These genes evolve at significantly higher rates than observed in other demosponges, similar to previously observed nuclear rRNA gene rates in other haplosclerid demosponges.

Animals↗

Structure of the promoter of the Dictyostelium discoideum prespore EB4 gene.

EB4 is one of several cloned cDNAs that is expressed as mRNA only after the aggregation stage of Dictyostelium discoideum differentiation and exclusively in prespore and spore cells (E. Barklis and H. F. Lodish, Cell 32:1139-1148, 1983). We have isolated the unique genome fragment corresponding to the 5' portion of the EB4 message and the EB4 promoter. The EB4 transcript has an unusually long, G + C-rich, 5' noncoding region, but initiates at several start sites within a region of DNA that is 96% A + T. The sequence GTGGTGG, along with slight variations, occurs several times in the promoter. We have used the EB4 promoter to drive the transcription of an EB4/beta-galactosidase fusion transcript in yeast cells. Although the cap sites of the fused transcript in yeast cells are located in the region where multiple EB4 transcripts are initiated in Dictyostelium, the unregulated expression of the fusion transcript in yeast does not mimic the normal regulated pattern of EB4 mRNA expression in D. discoideum.

Base Sequence↗

Sequence data and chromosomal localization of human type I and type II hair keratin genes.

A cDNA library constructed with poly(A)+ RNA from human scalp was screened with selected fragments of both murine type I and type II hair keratin cDNAs. Two keratin clones, one type I, phKI-2, and one type II, phKII-1, were isolated and sequenced. In Northern blots, cDNA probes containing the 3'-noncoding sequences of the clones specifically hybridized to scalp mRNA species. Based on sequence homology comparisons with the four known murine type I hair keratins mHa1-4, the phKI-2 encoded keratin could be identified as human hair keratin hHa2. Similarly, sequence comparison with the four type II sheep wool keratins K2.9-12 revealed an orthologous relationship between the largest member of the type II wool keratin subfamily, K2.9 (i.e., sHb1) and the phKII-1 encoded human hair keratin (hHb1). The specific 3'-noncoding sequences of hHa2 and hHb1 were also used to isolate genomic fragments for both keratins from human genomic libraries which were than used for fluorescence in situ hybridization to human metaphase chromosomes. The hHa2 gene could be mapped to the long arm of chromosome 17, whereas the hHb1 gene was found on the long arm of chromosome 12. DAPI banding of the chromosomes allowed sublocalization of the hHa2 gene to 17q12-q21 and the hHb1 gene to 12q13, i.e., gene loci that have also been previously determined for human type I and type II epithelial keratins.

Amino Acid Sequence↗

Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli.

Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of approximately 60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30-65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5'- and 3'-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3'-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3'-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5' or 3' ends of the mRNAs with perfect complementarity.

3' Untranslated Regions↗

Endogenous avian retroviruses contain deficient promoter and leader sequences.

A sensitive and quantitative biological assay has been utilized to measure the ability of the exogenous and endogenous avian retroviral long terminal repeats (LTR) to promote gene expression in avian cells. This assay has revealed that the exogenous virus RAV-2 LTR is approximately equal to 10-fold more active than the LTRs of endogenous viruses RAV-0, ev-1, and ev-2. The endogenous viral LTRs show approximately equal activity. Upstream flanking cellular or viral sequences have no significant modulating effect on gene expression in our assay. Unexpectedly, we have detected and localized an additional defect outside of the LTR in the 5' noncoding leader sequence of ev-1 that further decreases gene expression relative to RAV-0 by approximately equal to 10-fold.

Animals↗

RNA-RNA interaction prediction and antisense RNA target search.

Recent studies demonstrating the existence of special noncoding "antisense" RNAs used in post transcriptional gene regulation have received considerable attention. These RNAs are synthesized naturally to control gene expression in C. elegans, Drosophila, and other organisms; they are known to regulate plasmid copy numbers in E. coli as well. Small RNAs have also been artificially constructed to knock out genes of interest in humans and other organisms for the purpose of finding out more about their functions. Although there are a number of algorithms for predicting the secondary structure of a single RNA molecule, no such algorithm exists for reliably predicting the joint secondary structure of two interacting RNA molecules or measuring the stability of such a joint structure. In this paper, we describe the RNA-RNA interaction prediction (RIP) problem between an antisense RNA and its target mRNA and develop efficient algorithms to solve it. Our algorithms minimize the joint free energy between the two RNA molecules under a number of energy models with growing complexity. Because the computational resources needed by our most accurate approach is prohibitive for long RNA molecules, we also describe how to speed up our techniques through a number of heuristic approaches while experimentally maintaining the original accuracy. Equipped with this fast approach, we apply our method to discover targets for any given antisense RNA in the associated genome sequence.

Adenosine Triphosphatases↗

Effects of long 5' leader sequences on initiation by eukaryotic ribosomes in vitro.

Lengthening the 5' noncoding sequence on SP6-derived transcripts can increase their translational efficiency by an order of magnitude under some conditions of translation in reticulocyte lysates. This effect was observed upon reiterating three different synthetic oligonucleotides, the sequences of which were designed simply to preclude secondary structure. It seems unlikely that such arbitrarily designed sequences are recognized by sequence-specific translational enhancer proteins. Rather, long 5' leader sequences appear to accumulate extra 40S ribosomal subunits, which may account for their translational advantage. The buildup of 40S subunits on long, unstructured leader sequences is predicted by the scanning model for initiation. Leader sequences such as these may be ideal for in vitro expression vectors.

Base Sequence↗

Rapid degradation of AU-rich element (ARE) mRNAs is activated by ribosome transit and blocked by secondary structure at any position 5' to the ARE.

The 3' noncoding region (NCR) AU-rich element (ARE) selectively confers rapid degradation on many mRNAs via a process requiring translation of the message. The role of cotranslation in destabilization of ARE mRNAs was examined by insertion of translation-blocking stable secondary structure at different sites in test mRNAs containing either the granulocyte-macrophage colony-stimulating factor (GM-CSF) ARE or a control sequence. A strong (-80 kcal/mol [1 kcal = 4.184 kJ]) but not a moderate (-30 kcal/mol) secondary structure prevented destabilization of mRNAs when inserted at any position upstream of the ARE, including in the 3' NCR. Surprisingly, a strong secondary structure did not block rapid mRNA decay when placed immediately downstream of the ARE. Studies are also presented showing that the turnover of mRNAs containing control or ARE sequences is not altered by insertion of long (1,000-nucleotide) intervening segments between the stop codon and the ARE or between the ARE and poly(A) tail. Characterization of ARE-containing mRNAs in polyadenylated and whole cytoplasmic RNA fractions failed to find evidence for decay intermediates degraded to the site of strong secondary structure from either the 5' or 3' end. From these and other data presented, this study demonstrates that complete translation of the coding region is essential for activation of rapid mRNA decay controlled by the GM-CSF ARE and that the structure of the 3' NCR can strongly influence activation. The results are consistent with activation of ARE-mediated decay by possible entry of translation-linked decay factors into the 3' NCR or translation-coupled changes in 3' NCR ribonucleoprotein structure or composition.

Base Composition↗

Isolation and characterization of the human apolipoprotein A-I gene.

We have recently shown that an inherited polymorphism occurring in the human apolipoprotein A-I (apo A-I) gene is related to decreased high density lipoprotein and apo A-I levels in the plasma of two patients with severe premature atherosclerosis. Analysis of the molecular basis of this polymorphism and its possible effects on apo A-I gene expression requires direct comparison of both normal and polymorphic apo A-I alleles. Here we report the isolation and characterization of the normal human apo A-I gene and we show that the gene is interrupted by three intervening sequences, IVS-1, IVS-2, and IVS-3, occurring in the 5' noncoding region of apo A-I mRNA, the mRNA sequence coding for the signal peptide of apo A-I, and the sequence coding for the mature protein, respectively. In addition, the nucleotide sequence analysis of the apo A-I gene allowed determination of the complete amino acid sequence of the primary translation product of apo A-I mRNA. This amino acid sequence consists of 267 residues including a 24-residue-long amino-terminal extension (preprosegment). Finally, we show that the apo A-I gene contains six 66-base-pair-long tandemly repeated DNA segments, which suggests that the gene may have evolved by intragenic duplication events.

Apolipoprotein A-I↗

Molecular cloning and sequence determination of DA strain of Theiler's murine encephalomyelitis viruses.

Theiler's murine encephalomyelitis viruses (TMEV) belong to the Picornaviridae, and are divided into two subgroups. TO subgroup strains produce a persistent demyelinating central nervous system infection in mice, while GDVII subgroup strains cause acute polioencephalomyelitis. We generated three overlapping clones of the genome of DA strain, a member of TO subgroup. Sequence analysis revealed that the genome is 8093 nucleotides long with a poly(A) tail. The 5' noncoding region stretches from nucleotides 1 to 1065 and lacks a poly(C) tract. The open reading frame stretches from 1066 to 7968 and encodes 2301 amino acids. DA strain sequence is more closely related to members of the Cardiovirus genus than to members of other Picornavirus genera. Comparison with sequence of BeAn strain, another TO subgroup strain, showed that the P1 area has the greatest number of differences, while the noncoding regions are more well-conserved. The three overlapping clones will be important in recombinant infectious cDNA studies between strains of both subgroups.

Amino Acid Sequence↗

cDNA-derived amino acid sequence of the gamma subunit of GTPase from bovine rod outer segments.

The sequence of the 74 amino acids in the gamma subunit of GTPase from bovine rod outer segments has been deduced from the cDNA sequence. Enriched GTPase mRNA was used to prepare a cDNA library in the expression vector lambda gt11. Clones encoding the gamma subunit were identified by screening the library with anti-GTPase antibodies and by cell-free translation of hybrid-selected mRNA. The longest cDNA (448 base pairs) contained the amino acid coding region for the entire gamma subunit as well as 5' and 3' noncoding regions of 67 and 159 base pairs, respectively. The 3' noncoding region contained the sequence, A-A-U-A-A-A, the presumed recognition sequence for polyadenylylation, and a 14-unit long poly(A) tract. The amino acid sequence derived for the gamma-subunit is mostly in agreement with that previously determined by McConnell and co-workers [McConnell, D. G., Kohnken, R. E. & Smith, A. J. (1984) Fed. Proc. Fed. Am. Soc. Exp. Biol. 43, 1585] and the partial sequence deduced by Van Dop and co-workers from cDNA [Van Dop, C., Medynski, D., Sullivan, K., Wu, A. M., Fung, B. K.-K. & Bourne, H. R. (1984) Biochem. Biophys. Res. Commun. 124, 250-255].

Amino Acid Sequence↗

The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes.

We previously reported the sequence of a 9260-bp fragment of mitochondrial (mt) DNA of the cephalopod Loligo bleekeri [J. Sasuga et al. (1999) J. Mol. Evol. 48:692-702]. To clarify further the characteristics of Loligo mtDNA, we have sequenced an 8148-bp fragment to reveal the complete mt genome sequence. Loligo mtDNA is 17,211 bp long and possesses a standard set of metazoan mt genes. Its gene arrangement is not identical to any other metazoan mt gene arrangement reported so far. Three of the 19 noncoding regions longer than 10 bp are 515, 507, and 509 bp long, and their sequences are nearly identical, suggesting that multiplication of these noncoding regions occurred in an ancestral Loligo mt genome. Comparison of the gene arrangements of Loligo, Katharina tunicata, and Littorina saxatilis mt genomes revealed that 17 tRNA genes of the Loligo mt genome are adjacent to noncoding regions. A majority (15 tRNA genes) of their counterparts is found in two tRNA gene clusters of the Katharina mt genome. Therefore, the Loligo mt genome (17 tRNA genes) may have spread over the genome, and this may have been coupled with the multiplication of the noncoding regions. Maximum likelihood analysis of mt protein genes supports the clade Mollusca + Annelida + Brachiopoda but fails to infer the relationships among Katharina, Loligo, and three gastropod species.

Animals↗

Locus control region transcription plays an active role in long-range gene activation.

Activation of eukaryotic genes often relies on remote chromatin determinants. How these determinants function remains poorly understood. The hGH gene is activated by a 5'-remote locus control region (LCR). Pituitary-specific DNase I hypersensitive site I (HSI), the dominant hGH LCR element, is separated from the hGH-N promoter by a 14.5 kb span that encompasses the B-lymphocyte-specific CD79b gene. Here, we describe a domain of noncoding Pol II transcription in pituitary somatotropes that includes the hGH LCR and adjacent CD79b locus. This entire "LCR domain of transcription" is HSI [corrected] dependent and terminates 3' to CD79b, leaving a gap in transcription between this domain and the target hGH-N promoter. Insertion of a Pol II terminator within the LCR blocks CD79b transcription and represses hGH-N expression. These data document an essential role for LCR transcription in long-range control, link "bystander"CD79b transcription to this process, and support a unique model for locus activation.

Acetylation↗

Genome of coxsackievirus B3.

The entire nucleotide sequence of the coxsackievirus B3 strain Nancy (CB3) genome has been determined from cDNA. The genome is 7396 nucleotides long, and encodes a 2185 amino acid long polyprotein. It exhibits the same gene organization as other enterovirus genomes. A detailed comparison was carried out between the proteins encoded by the CB3 and poliovirus type 1 strain Mahoney (PV1) genomes. The genes encoding the VPg polypeptide and the viral polymerase are the most conserved regions. The structural polypeptides VP1, VP2, and VP3 are less well conserved although proline and tryptophan residues frequently are found in identical positions. The VP1 protein of CB3 shows a particularly limited homology in those regions which have been found to induce neutralizing antibodies against PV1. The 5' noncoding region of CB3 is closely related to that of PV1, with regard to both length and sequence organization, whereas the 3' noncoding region of CB3 exhibits some unique features.

Amino Acid Sequence↗

Molecular cloning and characterization of a cDNA encoding the human leucocyte vacuolar protein sorting (h1Vps45).

We have isolated a novel cDNA clone from human leucocyte cDNA library, encoding a Sec1p-like vacuolar protein sorting (h1Vps45) which is believed to be implicated in vesicular transportation. Although the deduced amino acid (AA) sequence of this cDNA has revealed 97% identity to other known mammalian vacuolar protein sorting, there is an extensive variation in nucleotide sequence in comparison to that of three previously reported human (hVps45), rat (rVps45) and mouse (mVps45) vacuolar protein sorting (Vps45) cDNAs [1-3]. At the nucleotide sequence level h1Vps45 demonstrated 90% homology to the hVps45 and rVps45 and 89% identity to mVps45 with no significant homology in their noncoding regions. The 2.4 Kb mRNA corresponding to the h1Vps45 clone is widely distributed in a variety of human tissues expressing highest levels in peripheral blood mononuclear cells (PBMC), neutrophils, heart, spleen, and testis. The chromosomal mapping studies have demonstrated that the h1Vps45 is localized to long arm of human chromosome 1 at q21-q22. Our data indicates that we have isolated, characterized and mapped a novel cDNA encoding h1Vps45, which may play an important role in protein trafficking as well as have clinical significance in the release of inflammatory mediators e.g. histamine, bradykinin and cytokine release.

Amino Acid Sequence↗