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Exon skipping is a disease-modifying therapy in which oligonucleotide analogues mask specific exons, eliminating them from the mature mRNA, and also the cognate protein. That is one possible therapeutic aim, but it can also be used to restore the reading frame for diseases caused by frameshift mutations, which is the case for Duchenne muscular dystrophy (DMD). DMD most commonly arises as a result of large exonic deletions that create a frameshift and abolish protein expression. Loss of dystrophin protein leads to the pathology of the disease, which is severe, causing death generally in the second or third decade of life. Here, the primary aim of exon skipping is restoration of protein expression by reading frame correction. However, the therapeutically expressed protein is missing both the region of the underlying genetic defect and the therapeutically skipped exon. How removing some region from the middle of a protein affects its structure and function is unclear. Many different underlying deletions are known, and exon skipping can be applied in many ways, in some cases in different ways to the same defect. These vary in how severely perturbative they are, with possible clinical consequences. In this study, we examine a systematic, comprehensive panel of exon edits in a region of dystrophin and identify for the first time exon edits that are minimally perturbed and appear to keep the structural stability similar to that of wild-type protein. We also identify factors that appear to be correlated with how perturbative an edit is.

The DEAH protein Prp22 is important for the second transesterification step of pre-mRNA splicing, and it is essential for releasing mature mRNA from the spliceosome. Recombinant Prp22 has RNA-stimulated ATPase and ATP-dependent unwinding activities, which are crucial for the mRNA release step. In this study, we characterize the RNA-binding, NTP hydrolysis, and RNA unwinding functions of Prp22. Using nitrocellulose filter binding assays, we determined that the apparent affinity of Prp22 is approximately 20-fold greater for single-stranded RNA than for single-stranded DNA or duplex nucleic acids. Inclusion of hydrolyzable ATP in binding reactions increased the apparent K(D) for RNA by 3-4-fold. The Prp22-RNA interaction is influenced by the length of the RNA chain, and the apparent K(D) values for poly(A)(40) and poly(A)(10) are 17 and 140 nM, respectively. RNA-stimulated ATP hydrolysis is similarly affected by chain length, and optimal activity requires RNA oligomers of >or=20 nt. We show that Prp22 can hydrolyze all common NTPs and dNTPs with comparable efficiencies and that Prp22 unwinds RNA duplexes with 3' to 5' directionality.

In an RNA transcript, the 2'-OH group at the 3'-terminal nucleotide is unique as it is the only 2'-OH group that is adjacent to a 3'-OH group instead of a phosphate backbone. The 2'-OH group at the 3'-terminal nucleotide of certain RNAs is methylated in vivo, which is acheived by a methyltransferase named Hen1 that is mechanistically distinct from other known RNA 2'-O-methyltransferases. In eukaryotic organisms, 3'-terminal 2'-O-methylation of small RNAs stabilizes these small RNAs for RNA interference (RNAi). In bacteria, the same methylation during RNA repair results in repaired RNA resisting future damage at the site of repair. Although the chemistry performed by the eukaryotic and bacterial Hen1 is the same, the mechanisms of how RNA is stabilized as a result of the 3'-terminal 2'-O-methylation are different between the eukaryotic RNAi and the bacterial RNA repair. In this review, I will discuss the distribution of Hen1 in living organisms, the classification of Hen1 into four subfamilies, the structure and mechanism of Hen1 that allows it to conduct RNA 3'-terminal 2'-O-methylation, and the possible evolutionary origin of Hen1 present in bacterial and eukaryotic organisms.

A method was developed for the extraction of RNA from chick embryo calvaria which should be generally applicable to other connective tissues. Total RNA prepared by this method was translated by a mRNA-dependent reticulocyte lysate into discrete pro alpha chains. Several criteria were used to identify these translation products, including (1) preferential labeling with [3H]proline, (2) appropriate migration on sodium dodecyl sulfate-polyacrylamide gels, (3) selective sensitivity to collagenase digestion, and (4) specific precipitability by two different antisera against procollagen. Data from the immunoprecipitation experiments indicated that the majority of the pro alpha chains contained the carboxy-terminal antigenic determinants. These results demonstrate that this translation system can be used as an assay for intact procollagen mRNAs and as a source of in vitro synthesized pro alpha chains for future structural analysis.

Cytoplasmic nonpolysomal mRNAs have been isolated in the form of 16-40S ribonucleoprotein particles from the postribosomal supernatant of 14-day-old chick embryonic muscles. An 8-20S RNA fraction isolated from these particles directs the synthesis of actin in a wheat germ embryo S-30 system, as judged by copurification of the products with chicken muscle actin by repeated cycles of G- to F-actin transformation; mobilities of the purified product on sodium dodecyl sulfate-polyacrylamide gels and urea gels; and analysis of the CNBr-cleaved peptides. The 16-40S particles have a buoyant density of 1.4 g/cm3 which corresponds to an RNA/protein ratio of 1:3. They do not contain detectable levels of ribosomal subunits, as judged by the absence of typical ribosomal proteins in the range of 15,000-30,000. They contain at least eight distinct polypeptide species in the molecular weight range of 44,000-100,000, including a prominent 44,000 species. The presence of these particles suggests that they may have a role in the regulation of translation in developing muscles.

In this paper the sequence of a 5.2-kilobase (kb) cDNA covering the amino-terminal domain of human apolipoprotein B-100 (apoB-100) is reported. The cDNA-derived protein sequence provides the primary structure of 1748 amino acids. This segment of apoB-100 is more hydrophilic than hydrophobic and contains short stretches of predicted helical and beta structures that are interrupted by beta turns. Blotting analysis of RNA isolated from fetal human and adult monkey tissues and various human cell lines showed synthesis of apoB mRNA by liver and intestine and by cells of hepatic (HepG2) and intestinal (Caco-2) origin. The isolation and characterization of overlapping cDNA clones, which provide a nearly full-length copy of human apoB-100, are also reported. From the length of these clones the size of the cytoplasmic apoB mRNA is estimated to be 14.0 kb and codes for a protein of approximately 512,000 daltons.

It has been found that centrifugation of (ethylenediamine)tetraacetic acid dissociated L-cell polyribosomes at 25 degrees C through preformed CS2SO4 density gradients containing 15% dimethyl sulfoxide resolves them into two distinct classes of particles that contain ribosomal and messenger RNA, respectively. Ribosomal RNA bands at a higher density than mRNA, presumably because it is more extensively stripped of protein by the action of CS2SO4 than mRNA. Undergraded RNA can be recovered from the gradients by trapping the particles on nitrocellulose filters and then eluting at 60 degrees C with a solution containing formamide and sodium dodecyl sulfate. When cells were labeled with [3H]adenosine, either in the presence or absence of a dose of actinomycin D which selectively inhibits rRNA synthesis, and their polyribosomes centrifuged through CS2SO4 density gradients, a large amount of the radioactivity recovered from the messenger-ribonucleoprotein region of the gradient had the size distribution of mRNA, but lacked poly(adenylate) (poly (A)). This material constituted 29-31% of the total mRNA. Histone mRNA was the most prominent component of poly(A)-lacking mRNA. However, 50-65% of the poly(A)-lacking mRNA was of larger size than histone mRNA.

We describe a rapid and simple method for the purification of biologically active messenger RNAs. The method allows the isolation in a few hours of specific mRNAs from either whole cell or polysomal RNA even if the RNA represents less than 1% of the starting molecules. We used, as a model, cloned sea urchin (Strongylocentrotus purpuratus) histone gene fragments linked to cellulose by the method of B. E. Noyes & G. R. Stark (1975) Cell 5, 301--310) as hybridization probes to isolate specific histone mRNAs from whole cell and polysomal RNA extracts. RNAs isolated in this manner maintain their biological activity, serving as templates for histone proteins in a wheat-germ, cell-free protein translation system. In addition, radiolabeled histone-specific RNA purified from cleavage stage sea urchin embryos, pulse labeled for short periods of time and analyzed on denaturing polyacrylamide gels, was the same size as mature histone mRNA's.

A cell-free system for synthesizing protein from wheat germ was used to translate the messenger RNA extracted from 16-day embryonic chick calvaria. A part of the product had properties similar to collagenous peptides and served as a substrate for prolyl hydroxylase, an enzyme specific for collagen. The level of potassium was critical for the synthesis of high molecular weight products with properties similar to pro-alpha-chains. The potassium concentration for optimal protein synthesis, as judged by maximum incorporation of [3H]proline into acid precipitable material, was considerably lower than the concentration required for the synthesis of high molecular weight collagenous peptides.

Pre-proparathyroid hormone is the major protein synthesized in wheat-germ extracts in response to addition of an 8-15S fraction of parathyroid RNA. The accuracy of the translation of the mRNA from parathyroid tissue was examined by analysis of the carboxyl-terminal tryptic peptide and the amino-terminal amino acid of the protein, by analysis of the size distribution of the mRNA, and by translation of the mRNA in a second cell-free extract. When 8-15S RNA was fractionated on a sucrose gradient containing formamide, RNA that supported the synthesis of pre-proparathyroid hormone was present in a single symmetrical peak, suggesting that it was homogeneous. Analyses by paper chromatography and electrophoresis of the proline-containing tryptic peptides of pre-proparathyroid hormone indicate that they are identical with the corresponding proline-containing peptides of parathyroid hormone. Because the COOH-terminal tryptic peptide of parathyroid hormone contains proline, the data indicate that the COOH termini of pre-proparathyroid hormone and parathyroid hormone are identical. Methionine from initiator [35S]Met-tRNAfMet was rapidly incorporated into pre-proparathyroid hormone by the wheat-germ extract, and a single-step Edman degradation selectively removed almost all of the initiator [35S]methionine present in pre-proparathyroid hormone. Translation of the 8-15S RNA in a cell-free extract from Krebs-II ascites cells resulted in a protein that comigrated with pre-proparathyroid hormone on sodium dodecyl sulfate-acrylamide gel electrophoresis. These data support the conclusion that the wheat-germ system accurately translates the mRNA for parathyroid hormone, and they strengthen the contention that pre-proparathyroid hormone is the initial biosynthetic product.

The effect of various tRNAs on protein synthesis was investigated using a tRNA-dependent cell-free system from Ehrlich ascites cells. Ascites cell tRNA and rabbit liver tRNA were found to promote efficient translation of globin mRNA, oviduct mRNA, and encephalomycarditis (EMC) viral RNA. In contrast, reticulocyte tRNA participated efficiently only in the translation of globin mRNA; the translation of oviduct mRNA AND EMC viral RNA in the presence of reticulocyte tRNA resulted in the synthesis of relatively few large mature proteins and the accumulation of discrete, smaller polypeptides. These results suggest that isoaccepting tRNA species required for the synthesis of ovalbumin and EMC viral protein (but not hemoglobin) are probably functionally absent in reticulocyte tRNA, causing a premature, nonrandom termination of synthesis of these proteins. This provides preliminary evidence that variations in tRNA populations, frequently observed between different cell types, are large enough to define and perhaps regulate the proteins that the cell is capable of synthesizing.