In vitro assembly of mutant U5 snRNAs.
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Autoantigens↗
Biomedical subjects
J R Patton
Publications and source records attributed to J R Patton.
U2 small nuclear RNP assembly in vitro.
Incubation of a SP6-transcribed human U2 RNA precursor molecule in a HeLa cell S100 fraction resulted in the formation of ribonucleoprotein complexes. In the presence of ATP, the particles that assembled had several properties of native U2 snRNP, including resistance to dissociation in Cs2SO4 gradients, their buoyant density, and pattern of digestion by micrococcal nuclease. These particles also reacted with Sm monoclonal antibody and a human autoantibody with specificity for the U2 snRNP-specific proteins A' and B", but not with antibodies for U1 snRNP-specific proteins. In contrast, the particles that formed in the absence of ATP did not have these properties. ATP analogs with non-hydrolyzable beta-gamma bonds did not substitute for ATP in U2 snRNP assembly. Additional experiments with a mutant U2 RNA confirmed that nucleotides 154-167 of U2 RNA are required for binding of the U2 snRNP-specific proteins but not of the "Sm" core proteins. Pseudouridine formation, a major post-transcriptional modification of U2 RNA, was enhanced under assembly permissive conditions.
Adenosine Triphosphate↗
U1 small nuclear ribonucleoprotein particle-specific proteins interact with the first and second stem-loops of U1 RNA, with the A protein binding directly to the RNA independently of the 70K and Sm proteins.
The U1 small nuclear ribonucleoprotein particle (U1 snRNP), a cofactor in pre-mRNA splicing, contains three proteins, termed 70K, A, and C, that are not present in the other spliceosome-associated snRNPs. We studied the binding of the A and C proteins to U1 RNA, using a U1 snRNP reconstitution system and an antibody-induced nuclease protection technique. Antibodies that reacted with the A and C proteins induced nuclease protection of the first two stem-loops of U1 RNA in reconstituted U1 snRNP. Detailed analysis of the antibody-induced nuclease protection patterns indicated the existence of relatively long-range protein-protein interactions in the U1 snRNP, with the 5' end of U1 RNA and its associated specific proteins interacting with proteins bound to the Sm domain near the 3' end. UV cross-linking experiments in conjunction with an A-protein-specific antibody demonstrated that the A protein bound directly to the U1 RNA rather than assembling in the U1 snRNP exclusively via protein-protein interactions. This conclusion was supported by additional experiments revealing that the A protein could bind to U1 RNA in the absence of bound 70K and Sm core proteins.
Autoantibodies↗
The Mr 70,000 protein of the U1 small nuclear ribonucleoprotein particle binds to the 5' stem-loop of U1 RNA and interacts with Sm domain proteins.
The U1 small nuclear ribonucleoprotein (snRNP) particle, a cofactor in mRNA splicing, contains nine proteins, six of which are also present in other U snRNPs and three of which are specific to the U1 snRNP. Here we have used a reconstituted human U1 snRNP together with snRNP monoclonal antibodies to define the RNA binding sites of one of the U1 snRNP-specific proteins. When Sm monoclonal antibody (specific for the B', B, and D proteins of U snRNPs) was bound to U1 snRNPs prior to micrococcal nuclease digestion, the same approximately equal to 24 nucleotide fragment of U1 RNA (corresponding to nucleotides 120-143 and termed the "Sm domain") was protected as when no antibody was bound prior to digestion. In contrast, when RNP monoclonal antibody, which reacts with the U1 snRNP-specific Mr 70,000 protein, was bound, additional U1 RNA regions were protected against nuclease digestion. This phenomenon, which we term "antibody-mediated nuclease protection," was exploited to map the position of the Mr 70,000 protein to stem-loop I of U1 RNA. However, there were also sites of Mr 70,000 protein interaction with more 3'-ward regions of U1 RNA, particularly the Sm domain. This indicates that in the three-dimensional structure of the U1 snRNP, the RNP and Sm antigens are in contact with each other. The proximity of the Mr 70,000 protein's RNA binding site (stem-loop I) to the functionally important 5' end of U1 RNA suggests that this protein may be involved in the recognition of, or stabilization of base pairing with, pre-mRNA 5' splice sites.
Antibodies, Monoclonal↗
Reconstitution of the U1 small nuclear ribonucleoprotein particle.
Although the U1 small nuclear ribonucleoprotein particle (snRNP) was the first mRNA-splicing cofactor to be identified, the manner in which it functions in splicing is not precisely understood. Among the information required to understand how U1 snRNP participates in splicing, it will be necessary to know its structure. Here we describe the in vitro reconstitution of a particle that possesses the properties of native U1 snRNP. 32P-labeled U1 RNA was transcribed from an SP6 promoter-human U1 gene clone and incubated in a HeLa S100 fraction. A U1 particle formed which displayed the same sedimentation coefficient (approximately 10S) and buoyant density (1.40 g/cm3) as native U1 snRNP. The latter value reflects the ability to withstand isopycnic banding in Cs2SO4 without prior fixation, a property shared by native U1 snRNP. The reconstituted U1 particle reacted with both the Sm and RNP monoclonal antibodies, showing that these two classes of snRNP proteins were present. Moreover, the reconstituted U1 snRNP particle was found to display the characteristic Mg2+ switch of nuclease sensitivity previously described for native U1 snRNP: an open, nuclease-sensitive conformation at a low Mg2+ concentration (3 mM) and a more compact, nuclease-resistant organization at a higher concentration (15 mM). The majority of the U1 RNA in the reconstituted particle did not contain hypermethylated caps, pseudouridine, or ribose 2-O-methylation, showing that these enigmatic posttranscriptional modifications are not essential for reconstitution of the U1 snRNP particle. The extreme 3' end (18 nucleotides) of U1 RNA was required for reconstitution, but loop II (nucleotides 64 to 77) was not. Interestingly, the 5' end (15 nucleotides) of U1 RNA that recognizes pre-mRNA 5' splice sites was not required for U1 snRNP reconstruction.
Humans↗
Specific regions of the intervening sequences of beta-globin RNA are resistant to nuclease in 50S heterogeneous nuclear RNA-protein complexes.
The specific assembly of heterogeneous nuclear RNA-protein complexes (hnRNPs) containing precursor beta-globin RNA was investigated by using the 50S hnRNP released from chicken reticulocyte nuclei by endogenous nuclease. The nuclease-resistant regions were mapped on adult beta-globin intervening sequences (IVS) at the resolution of nucleotides with an RNA mapping method [Patton, J. R. and Chae, C.-B. (1983) J. Biol. Chem. 258, 3991-3995]. We found that there is one 28-nucleotide-long nuclease-resistant region in the first IVS and there are four nuclease-resistant regions in the second IVS. Of particular interest is the presence in 50S hnRNP of a nuclease-resistant region (24-28 nucleotides long) in both IVS immediately upstream from the putative lariat branch site in an RNA splicing intermediate. Our results demonstrate that hnRNPs containing precursor beta-globin RNA are, like those containing mature beta-globin RNA, assembled in a site-specific manner.
Animals↗
Specific regions of beta-globin RNA are resistant to nuclease digestion in RNA-protein complexes in chicken reticulocyte nuclei.
The interaction between beta-globin RNA and proteins in chicken reticulocyte nuclei was studied by determining the sequence of nuclease-resistant beta-globin RNA. Two types of nuclease-resistant RNAs were isolated for this study: endogenous nuclease-resistant RNA from 50S heterogeneous nuclear RNA-protein complexes and micrococcal nuclease-resistant nuclear RNA from whole nuclei. The nuclease-resistant regions were identified with the use of a RNA mapping method we recently developed (J.R. Patton and C.-B. Chae, J. Biol. Chem. 258:3991-3995, 1983). We found that beta-globin RNA is assembled into heterogeneous nuclear RNA-protein complexes in a specific manner. There are several regions of nuclease resistance in the first and third exons interrupted at regular intervals by sensitive regions. The second exon has only one nuclease-resistant region. The resistant regions range in size from 20 to 50 nucleotides. This organization may reflect a specific mode of assembly for heterogeneous nuclear RNA-protein complexes.
Animals↗
Chicken reticulocyte polysomal messenger RNA-protein complex: absence of bound proteins in most of the coding region of beta globin mRNA.
The 15s globin mRNA-protein complex (mRNP) was isolated from chicken reticulocyte polyribosomes dissociated in EDTA. To determine protein binding sites, the mRNP was treated with micrococcal nuclease and the nuclease resistant RNA was mapped to the beta globin gene at the nucleotide level. As far as we can determine there is no bound protein from the Cap site to the poly A addition site of beta globin mRNA in the mRNP except for a short area in the coding region near the translation initiation site.
Animals↗
A method for mapping RNA initiation, termination, splice, and protein binding sites. Ribosome binding sites on beta-globin messenger RNA.
A new method for mapping RNA initiation, termination, and splice sites was developed. The method involves: 1) hybridization of RNA to end-labeled single-stranded DNA; 2) mild digestion of the hybrid with a single strand specific nuclease; 3) high resolution gel electrophoresis and autoradiography. The regions of the labeled probe which are resistant to nuclease digestion are mapped by measuring the distance from the labeled end. The sequence can be determined by running the end-labeled probe sequenced according to the protocol of Maxam and Gilbert (Maxam, A.M., and Gilbert, W. (1980) Methods Enzymol. 65, 499-560) at the same time. The feasibility of this method was tested with adult chicken beta-globin mRNA, and we found that the transcription initiation, termination, and RNA splice sites can be determined to within a few bases of the known sites. Using this method we also found that ribosomes bind to beta-globin mRNA from 22 bases upstream from the translation start codon (AUG) to 15 bases past the stop codon (UAA).
Animals↗
A method for isolation of a large amount of a single-stranded DNA fragment.
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Animals↗
Integrated method for the gas chromatographic determination of antiepileptic drugs in human plasma.
The principles of three independent extraction methods were utilized to develop an integrated extraction scheme for use in routine therapeutic monitoring of seven antiepileptic agents. The final method, in which the three extraction methods were interfaced, permitted routine monitoring in a single 1 ml volume of human plasma of any one or combination of the following drugs: phenytoin (PHT), phenobarbital (PB), primidone (PD), 5-ethyl-5-phenylhydantoin (EPH), ethosuximide (ES), carbamazepine (CBZ), and valproic acid (VPA). An on-column methylation technique was used for simultaneous determination of PHT, PB, PD, EPH, and ES. CBZ and VPA were determined by independent methods as the underivatized compounds. Six appropriate internal standards were employed in the integrated method for quantitation of the drugs.
Anticonvulsants↗
Gas chromatographic method for the determination of valproic acid in human plasma.
A gas chromatographic method has been developed for the routine monitoring of valproic acid (VPA) in human plasma samples. Two compounds, 2-ethylpentanoic acid (EPA) and 2-propylhexanoic acid (PHA), were synthesized and evaluated as internal standards together with cyclohexane carboxylic acid (CHCA), a commonly employed internal standard. Crystalline barium salts of VPA, EPA, and PHA were prepared, which enabled preparation of standard solutions of high accuracy for use in calibration experiments and in daily intra-laboratory quality control tests. The extraction scheme was designed on the basis of the solvent partitioning properties of VPA. Solvent transfers are required in the extraction scheme, but solvent evaporations are not. Studies were made of the performances of EPA, PHA, and CHCA as internal standards in the VPA assay at different lifetimes of the 10% SP-1000 chromatography column. As judged by these studies, EPA or CHCA is a better choice than PHA as an internal standard, provided that certain guidelines are followed in the use of CHCA.
Chromatography, Gas↗
Learning disabilities: the challenges of adulthood.
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Adult↗
A life skills approach to mathematics instruction: preparing students with learning disabilities for the real-life math demands of adulthood.
Current mathematics instruction does not address the day-to-day needs of many students with learning disabilities. Although the vast majority of students with learning disabilities are not college bound, much of mathematics instruction provides college preparation. Too often, classes in mathematics ignore the skills needed in home and community and on the job. The present article examines the ways in which general mathematics instruction, focused on daily living skills, can easily be integrated into the classrooms of students with learning disabilities.
Activities of Daily Living↗
Mental retardation and learning disabilities: conceptual and applied issues.
The relationship between mental retardation and learning disabilities is clouded by conceptual issues and current practices in applied (i.e., educational and noneducational) settings. In this article, we initially discuss whether mental retardation can be considered a concomitant disability associated with learning disabilities or whether these two disabilities are mutually exclusive categories. Conceptual issues related to this question are then reviewed to provide a perspective for viewing these two traditional areas of exceptionality. Emerging areas of concern in term of definition, classification, etiology, and lifelong issues are addressed. Attention is then given to applied issues that have a direct effect on the lives of individuals with disabilities. Specific topics include educational curricula, instruction, inclusion, and adult services and supports.
Curriculum↗