RNA二级结构预测方法

RNA是一类具有重要生物学功能的生物大分子,它是遗传信息由DNA到蛋白质的中间传递体.RNA二级结构预测方法可以分为基于热力学的预测方法和基于系统发生学的预测方法两大类.本文就RNA二级结构预测的方法进行了综述,介绍了最低自由能预测法、配分函数预测法、协同变异预测法、随机上下文无关语法预测法等4种预测方法以及它们的优缺点.     

Splicing of messenger RNA precursors

A general mechanism for the splicing of nuclear messenger RNA precursors in eukaryotic cells has been widely accepted. This mechanism, which generates lariat RNAs possessing a branch site, seems related to the RNA-catalyzed reactions of self-splicing introns. The splicing of nuclear messenger RNA precursors involves the formation of a multicomponent complex, the spliceosome. This splicing body contains at least three different small nuclear ribonucleoprotein particles (snRNPs), U2, U5, and U4 + U6. A complex containing precursor RNA and the U2 snRNP particle is a likely intermediate in the formation of the spliceosome.     

RNA secondary structure repression of a muscle-specific exon in HeLa cell nuclear extracts

The chicken beta-tropomyosin pre-messenger RNA (pre-mRNA) is spliced in a tissue-specific manner to yield messenger RNA's (mRNA's) coding for different isoforms of this protein. Exons 6A and 6B are spliced in a mutually exclusive manner; exon 6B was included in skeletal muscle, whereas exon 6A was preferred in all other tissues. The distal portion of the intron upstream of exon 6B was shown to form stable double-stranded regions with part of the intron downstream of exon 6B and with sequences in exon 6B. This structure repressed splicing of exon 6B to exon 7 in a HeLa cell extract. Derepression of splicing occurred on disruption of this structure and repression followed when the structure was re-formed, even if the structure was formed between two different RNA molecules. Repression leads to inhibition of formation of spliceosomes. Disrupting either of the two double-stranded regions could lead to derepression, whereas re-forming the helices by suppressor mutations reestablished repression. These results support a simple model of tissue-specific splicing in this region of the pre-mRNA.     

Progesterone-dependent messenger RNA: heterospecific activity in vivo

The action of progesterone in mediating the synthesis of avidin by the chick oviduct can be simulated by the intraoviductal instillation of nitrocellulose-trapped RNA from hormonally prepared chick or pigeon oviduct. Similarly, the pigeon oviduct synthesizes avidin in response to chick oviduct RNA. Thus, a heterospecific transfer of hormonal stimulation, through the transfer of progesterone-induced RNA, is demonstrated. The biological activity is lost after digestion by pancreatic ribonuclease. The 50-fold purification achieved by nitrocellulose chromatography of the total RNA preparation suggests that the activity resides in a messenger RNA fraction.     

Requirement of microfilaments in sorting of actin messenger RNA

Specific messenger RNAs (mRNAs) can be sequestered within distinct cellular locations, but little is known about how this is accomplished. The participation of the three major cellular filaments in the localization of actin mRNA was studied in chicken embryo fibroblasts. Movement of actin mRNA to the cell periphery and maintenance of that regionalization required intact microfilaments (composed of actin) but not microtubules or intermediate filaments. The results presented here suggest that actin-binding proteins may participate in mRNA sorting.     

Short- and long-lived messenger RNA in embryonic chick lens

Cells of the embryonic chick lens pass through a definite sequence of macromolecular synthesis as they differentiate and migrate from one zone of the organ to another. Auto-radiographic studies of RNA synthesis and protein synthesis show that long-and short-lived messenger RNA's are both present in the lens.     

Localization of amyloid beta protein messenger RNA in brains from patients with Alzheimer's disease

The distribution of cells containing messenger RNA that encodes amyloid beta protein was determined in hippocampi and in various cortical regions from cynomolgus monkeys, normal humans, and patients with Alzheimer's disease by in situ hybridization. Both 35S-labeled RNA antisense and sense probes to amyloid beta protein messenger RNA were used to ensure specific hybridization. Messenger RNA for amyloid beta protein was expressed in a subset of neurons in the prefrontal cortex from monkeys, normal humans, and patients with Alzheimer's disease. This messenger RNA was also present in the neurons of all the hippocampal fields from monkeys, normal humans and, although to a lesser extent in cornu ammonis 1, patients with Alzheimer's disease. The distribution of amyloid beta protein messenger RNA was similar to that of the neurofibrillary tangles of Alzheimer's disease in some regions, but the messenger RNA was also expressed in other neurons that are not usually involved in the pathology of Alzheimer's disease.     

Coordinate hormonal and synaptic regulation of vasopressin messenger RNA

Previous studies have shown that adrenalectomy augments arginine vasopressin (AVP) messenger RNA levels in the adult paraventricular nucleus. It is now demonstrated that unilateral lesions in the lateral septal nucleus enhance the adrenalectomy-induced expression of AVP mRNA. This effect was entirely ipsilateral to the lesion and most prominent in the rostral paraventricular nucleus and related nuclei. Moreover, AVP and AVP mRNA were found to be colocalized with oxytocin in a few neurons. These results indicate that mRNA expression is modulated by synaptic influences and raise the possibility that synaptically mediated selection of neuronal phenotypes is a dynamic feature of the mature central nervous system.     

Comparison of messenger RNA in photoperiodically induced and noninduced Xanthium buds

In response to the floral stimulus, Xanthium buds synthesize relatively more messenger RNA than do vegetative buds. This is demonstrated by fractionation, on methylated albumin-kieselguhr columns, of a mixture of nucleic acids from vegetative and induced buds, one being labeled with uridine-H(3) and the other with uridine-2-C(14). While floral induction stimulates a small increase in messenger RNA synthesis as revealed by labeling intact plants, this difference can be magnified by labeling excised buds in solution. From experiments with excised buds from Xanthium plants, it is concluded that buds from photoperiodically induced plants contain more messenger RNA than buds from noninduced ones do.     

Decapping and decay of messenger RNA occur in cytoplasmic processing bodies

A major pathway of eukaryotic messenger RNA (mRNA) turnover begins with deadenylation, followed by decapping and 5' to 3' exonucleolytic decay. We provide evidence that mRNA decapping and 5' to 3' degradation occur in discrete cytoplasmic foci in yeast, which we call processing bodies (P bodies). First, proteins that activate or catalyze decapping are concentrated in P bodies. Second, inhibiting mRNA turnover before decapping leads to loss of P bodies; however, inhibiting turnover at, or after, decapping, increases the abundance and size of P bodies. Finally, mRNA degradation intermediates are localized to P bodies. These results define the flux of mRNAs between polysomes and P bodies as a critical aspect of cytoplasmic mRNA metabolism and a possible site for regulation of mRNA degradation.     

Radioisotope uptake as a measure of synthesis of messenger RNA

Exogenously supplied radioactive uracil (or guanine) enters the intracellular pools of RNA precursors in Escherichia coli only as nucleotides are removed from these pools by net synthesis of RNA. Consequently uptake of uracil over a short period does not measure the sum of the synthesis of all forms of RNA, unstable and stable, as is often supposed. Uptake of uracil during changing conditions of growth may be influenced by changes in types of RNA's being made; under such conditions that no stable RNA is being made, the synthesis of unstable forms may be greatly underestimated.     

Induction of interleukin 2 messenger RNA inhibited by cyclosporin A

Cyclosporin A blocked production of the lymphokine interleukin 2 by activated T lymphocytes. In a human and a murine cell line this inhibition reflected an absence of interleukin 2 messenger RNA. Under conditions in which these cells are normally stimulated to secrete high levels of interleukin 2, they failed to do so in the presence of cyclosporin A. In both cell lines this failure was accompanied by an absence of interleukin 2 messenger accumulation.     

Xenopus oocytes injected with rat uterine RNA express very slowly activating potassium currents

Under the influence of estrogen, uterine smooth muscle becomes highly excitable, generating spontaneous and prolonged bursts of action potentials. In a study of the mechanisms by which this transition in excitability occurs, polyadenylated RNA from the uteri of estrogen-treated rats was injected into Xenopus oocytes. The injected oocytes expressed a novel voltage-dependent potassium current. This current was not observed in oocytes injected with RNA from several other excitable tissues, including rat brain and uterine smooth muscle from ovariectomized rats not treated with estrogen. The activation of this current on depolarization was exceptionally slow, particularly for depolarizations from relatively negative membrane potentials. Such a slowly activating channel may play an important role in the slow, repetitive bursts of action potentials in the myometrium.     

Breakdown of rat-liver ergosomes in vivo after actinomycin inhibition of messenger RNA synthesis

Ribosomes isolated from rat liver occur predominantly in the form of aggregates (ergosomes) corresponding to multiples of 73S particles held together by messenger RNA. After injecting rats with actinomycin, these aggregates gradually break down in vivo to 73S monomers and 113S dimers. We conclude that the observed breakdown results from the degradation of messenger RNA and the prevention by actinomycin of the synthesis of new messenger RNA.