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Computational Biology and Chemistry Feb 2015Polyadenylation is the process of addition of poly(A) tail to mRNA 3' ends. Identification of motifs controlling polyadenylation plays an essential role in improving...
Polyadenylation is the process of addition of poly(A) tail to mRNA 3' ends. Identification of motifs controlling polyadenylation plays an essential role in improving genome annotation accuracy and better understanding of the mechanisms governing gene regulation. The bioinformatics methods used for poly(A) motifs recognition have demonstrated that information extracted from sequences surrounding the candidate motifs can differentiate true motifs from the false ones greatly. However, these methods depend on either domain features or string kernels. To date, methods combining information from different sources have not been found yet. Here, we proposed an improved poly(A) motifs recognition method by combing different sources based on decision level fusion. First of all, two novel prediction methods was proposed based on support vector machine (SVM): one method is achieved by using the domain-specific features and principle component analysis (PCA) method to eliminate the redundancy (PCA-SVM); the other method is based on Oligo string kernel (Oligo-SVM). Then we proposed a novel machine-learning method for poly(A) motif prediction by marrying four poly(A) motifs recognition methods, including two state-of-the-art methods (Random Forest (RF) and HMM-SVM), and two novel proposed methods (PCA-SVM and Oligo-SVM). A decision level information fusion method was employed to combine the decision values of different classifiers by applying the DS evidence theory. We evaluated our method on a comprehensive poly(A) dataset that consists of 14,740 samples on 12 variants of poly(A) motifs and 2750 samples containing none of these motifs. Our method has achieved accuracy up to 86.13%. Compared with the four classifiers, our evidence theory based method reduces the average error rate by about 30%, 27%, 26% and 16%, respectively. The experimental results suggest that the proposed method is more effective for poly(A) motif recognition.
Topics: Computational Biology; Molecular Sequence Data; Nucleotide Motifs; Poly A; Polyadenylation; Principal Component Analysis; RNA, Messenger; Support Vector Machine
PubMed: 25594576
DOI: 10.1016/j.compbiolchem.2014.12.001 -
Journal of Biomolecular Structure &... Apr 1993CD spectra were used to compare the acid-induced structural transitions of poly[d(A)] and poly[d(C)] with those of poly[r(A)] and poly[r(C)], respectively. The types of... (Comparative Study)
Comparative Study
CD spectra were used to compare the acid-induced structural transitions of poly[d(A)] and poly[d(C)] with those of poly[r(A)] and poly[r(C)], respectively. The types of base pairing were probably the same in the acid self-complexes of both A-containing polymers and in the acid self-complexes of both C-containing polymers. Similar base pairings were indicated by similarities in the difference CD spectra showing the changes during the first major acid-induced transitions of the polymers. Information from the CD spectra and pKa values of the transitions suggested that the transitions for the RNA polymers involved similar structural changes. The two DNA polymers were markedly different. Single-stranded poly[d(A)] was in the most stacked structure and had the lowest pKa for forming an acid self-complex. Single-stranded poly[d(C)] was in the least stacked structure and had the highest pKa for forming a protonated duplex.
Topics: Base Composition; Circular Dichroism; Hydrogen-Ion Concentration; Poly A; Poly C
PubMed: 8318162
DOI: 10.1080/07391102.1993.10508677 -
The Journal of Biological Chemistry Aug 2009Poly(A) tails of mRNAs are synthesized in the cell nucleus with a defined length, approximately 250 nucleotides in mammalian cells. The same type of length control is...
Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor.
Poly(A) tails of mRNAs are synthesized in the cell nucleus with a defined length, approximately 250 nucleotides in mammalian cells. The same type of length control is seen in an in vitro polyadenylation system reconstituted from three proteins: poly(A) polymerase, cleavage and polyadenylation specificity factor (CPSF), and the nuclear poly(A)-binding protein (PABPN1). CPSF, binding the polyadenylation signal AAUAAA, and PABPN1, binding the growing poly(A) tail, cooperatively stimulate poly(A) polymerase such that a complete poly(A) tail is synthesized in one processive event, which terminates at a length of approximately 250 nucleotides. We report that PABPN1 is required to restrict CPSF binding to the AAUAAA sequence and to permit the stimulation of poly(A) polymerase by AAUAAA-bound CPSF to be maintained throughout the elongation reaction. The stimulation by CPSF is disrupted when the poly(A) tail has reached a length of approximately 250 nucleotides, and this terminates processive elongation. PABPN1 measures the length of the tail and is responsible for disrupting the CPSF-poly(A) polymerase interaction.
Topics: Animals; Cattle; Cleavage And Polyadenylation Specificity Factor; Electrophoretic Mobility Shift Assay; Poly A; Poly(A)-Binding Protein I; Polynucleotide Adenylyltransferase; Protein Binding; RNA 3' Polyadenylation Signals
PubMed: 19509282
DOI: 10.1074/jbc.M109.018226 -
Journal of Biological Inorganic... Aug 2019Two ruthenium(II) polypyridyl complexes containing different ancillary ligands, [Ru(bpy)(dppz-Br)] (Ru1; bpy = 2,2'-bipyridine...
Two ruthenium(II) polypyridyl complexes containing different ancillary ligands, [Ru(bpy)(dppz-Br)] (Ru1; bpy = 2,2'-bipyridine dppz-Br = 7-Br-dipyrido[3,2-a,2',3'-c]-phenazine) and [Ru(dmb)(dppz-Br)] (Ru2; dmb = 4,4'-dimethyl-2,2'-bipyridine), have been synthesized and characterized. Binding properties of Ru1 and Ru2 with the RNA poly(U)•poly(A)*poly(U) triplex have been investigated by UV-Vis spectroscopy, fluorescence spectroscopy, viscosity measurements as well as circular dichroism and thermal denaturation. Spectrophotometric studies together with viscosity measurements suggest that both Ru1 and Ru2 bind with the triplex by intercalation mode, and the melting experiments demonstrate that the two complexes can effectively enhance the triplex stabilization. However, results indicate that Ru1 stabilizes the third-strand and Watson-Crick base-paired duplex of the triplex without obvious selectivity. In contrast, Ru2 prefers to bind with the third strand rather than the Watson-Crick base-paired duplex of the triplex to a some extent under the same conditions used in this study, thereby significantly stabilizing the third strand. The obtained results of this study suggest that slight differences in the ancillary ligands bpy and dmb should be the main factor affecting the binding interactions of the two complexes with the triplex.
Topics: Coordination Complexes; Intercalating Agents; Nucleic Acid Conformation; Poly A; RNA; Ruthenium
PubMed: 31312912
DOI: 10.1007/s00775-019-01685-y -
Journal of Virology Aug 1991A poly(A) tail was identified on the 3' end of the prototype tick-borne encephalitis (TBE) virus strain Neudoerfl. This is in contrast to the general lack of poly(A) in...
A poly(A) tail was identified on the 3' end of the prototype tick-borne encephalitis (TBE) virus strain Neudoerfl. This is in contrast to the general lack of poly(A) in the genomic RNAs of mosquito-borne flaviviruses analyzed so far. Analysis of several closely related strains of TBE virus, however, revealed the existence of two different types of 3' noncoding (NC) regions. One type (represented by strain Neudoerfl) is only 114 nucleotides long and carries a 3'-terminal poly(A) structure. This was also found in several TBE virus strains isolated from different geographic regions over a period of almost 30 years. The other type (represented by strain Hypr) is 461 nucleotides long and not polyadenylated. The sequence homology between the two types of TBE virus 3' NC regions terminates at a specific position 81 nucleotides after the stop codon. The second type of 3' NC region more closely resembles the common flavivirus pattern, including the potential for the formation of a 3'-terminal hairpin structure. However, it lacks primary sequence elements that are conserved among other flavivirus genomes.
Topics: Animals; Base Sequence; Cloning, Molecular; DNA, Viral; Encephalitis Viruses, Tick-Borne; Flavivirus; Molecular Sequence Data; Nucleic Acid Conformation; Poly A; Polymerase Chain Reaction; RNA; RNA, Messenger; RNA, Viral; Repetitive Sequences, Nucleic Acid; Transcription, Genetic
PubMed: 1712858
DOI: 10.1128/JVI.65.8.4070-4077.1991 -
Journal of Molecular Biology Mar 2000The mammalian nuclear poly(A) binding protein, PABP2, controls the length of the newly synthesized poly(A) tail on messenger RNAs. To gain a better understanding of the...
The mammalian nuclear poly(A) binding protein, PABP2, controls the length of the newly synthesized poly(A) tail on messenger RNAs. To gain a better understanding of the mechanism of length control, we have investigated the structure of the PABP2.poly(A) complex. Electron microscopy and scanning force microscopy studies reveal that PABP2, when bound to poly(A), forms both linear filaments and discrete-sized, compact, oligomeric particles. The maximum diameter of the filament is 7 nm; the maximum diameter of the particle is 21(+/-2) nm. Maximum particle size is realized when the PABP2. poly(A) complex is formed with poly(A) molecules 200-300 nt long, which corresponds to the average length of the newly synthesized poly(A) tail in vitro and in vivo. The equilibrium between filaments and particles is highly sensitive to ionic strength; filaments are favored at low ionic strength, while particles predominate at moderate to high ionic strength. Nitrocellulose filter binding and gel mobility shift assays indicate that the PABP2.poly(A) particle formed on A(300) is not significantly more stable than complexes formed with smaller species of poly(A). These results are discussed in the context of the proposed functions for PABP2.
Topics: Allosteric Regulation; Animals; Binding, Competitive; Biopolymers; Cattle; DNA-Binding Proteins; Hydrogen-Ion Concentration; Microscopy, Atomic Force; Microscopy, Electron; Molecular Weight; Osmolar Concentration; Poly A; Poly(A)-Binding Protein II; Poly(A)-Binding Proteins; Protein Binding; RNA; RNA-Binding Proteins; Thermodynamics
PubMed: 10731412
DOI: 10.1006/jmbi.2000.3572 -
Nucleic Acids Research Apr 2019Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length....
Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length. These mechanisms play crucial roles in the dynamics of cell polarization and embryonic development. Furthermore, mRNAs are emerging therapeutics and chemical alterations to increase their translational efficiency are highly sought after. We show that yeast poly(A) polymerase can be used to install multiple azido-modified adenosine nucleotides to luciferase and eGFP-mRNAs. These mRNAs can be efficiently reacted in a bioorthogonal click reaction with fluorescent reporters without degradation and without sequence alterations in their coding or untranslated regions. Importantly, the modifications in the poly(A) tail impact positively on the translational efficiency of reporter-mRNAs in vitro and in cells. Therefore, covalent fluorescent labeling at the poly(A) tail presents a new way to increase the amount of reporter protein from exogenous mRNA and to label genetically unaltered and translationally active mRNAs.
Topics: Adenosine Triphosphate; Cell Survival; Fluorescence; HeLa Cells; Humans; Poly A; Protein Biosynthesis; RNA, Messenger; Staining and Labeling
PubMed: 30726958
DOI: 10.1093/nar/gkz084 -
Nucleic Acids Symposium Series 1988Latex particles were covalently linked to the 5'-proximal region of oligo(dT)30. The resultant oligo(dT)30-Latex was tested for its hybridizability to poly(A) containing...
Latex particles were covalently linked to the 5'-proximal region of oligo(dT)30. The resultant oligo(dT)30-Latex was tested for its hybridizability to poly(A) containing mRNA. Several advantages were noted as compared to the conventional oligo(dT)30-cellulose column chromatography; (1) a highly efficient (approximately 95%) hybridization occurs in a short reaction period (10min), (2) more than 95% of poly(A) mRNA can be recovered from oligo(dT)30-Latex by a simple heating followed by brief centrifugation, (3) multiple samples can be handled simultaneously and moreover, (4) the poly(A)-mRNA on the oligo(dT)30-Latex can be directly transcribed by AMV reverse transcriptase to form the cDNA. These properties of oligo(dT)30-Latex promise an excellent reagent for nucleic acid technology.
Topics: Chromatography, Affinity; DNA, Viral; Indicators and Reagents; Latex; Oligodeoxyribonucleotides; Poly A; RNA, Messenger; Vaccinia virus
PubMed: 2906428
DOI: No ID Found -
Proceedings of the National Academy of... Mar 1980In general, poly(A)-mRNA appears to be derived from larger nuclear RNA precursors. The maturation of these precursors involves excision of sequences of variable length...
In general, poly(A)-mRNA appears to be derived from larger nuclear RNA precursors. The maturation of these precursors involves excision of sequences of variable length from within the molecule and splicing of the remaining structural and coding sequences. The mechanism by which this process occurs is not known. It does not appear to operate solely through the recognition of a defined primary sequence or through the formation of a consistent secondary structure. We propose an alternative model in which poly(A) facilitates the splicing event by promoting the formation of triple-stranded structures within the mRNA precursor.
Topics: Animals; Hydrogen Bonding; Hydrolysis; Models, Molecular; Nucleic Acid Conformation; Nucleic Acid Precursors; Poly A; RNA, Messenger; Structure-Activity Relationship
PubMed: 6929484
DOI: 10.1073/pnas.77.3.1278 -
Ciba Foundation Symposium 1983This paper concerns the structural characteristics of the poly(A) RNA stored in unfertilized amphibian and echinoderm eggs. Though located in the egg cytoplasm, at least...
This paper concerns the structural characteristics of the poly(A) RNA stored in unfertilized amphibian and echinoderm eggs. Though located in the egg cytoplasm, at least two-thirds of these maternal transcripts display an interspersed sequence organization similar to that of nuclear RNA. In Xenopus laevis interspersed poly(A) RNA molecules are synthesized and deposited in the oocyte cytoplasm throughout the main growth phase of oogenesis. Regions of the sea urchin genome that are represented by interspersed maternal transcripts have been recovered from recombinant clone libraries. In one case the same single-copy sequence is found both in an abundant message-sized 1.6 kilobase (kb) maternal transcript and in a 7.5 kb maternal transcript that structurally resembles a precursor form and is not found in embryonic polysomes. In a second example considered, a 9.5 kb transcript was identified in embryo nuclear RNA that may be identical in structure with an interspersed maternal poly(A) RNA derived from the same transcription unit. Transcription of this sequence appears to be constitutive in somatic cell nuclei, though no homologous cytoplasmic RNAs are found after early cleavage. This may be a widespread form of regulation for transcription units expressed in female germ cells, and represented in the maternal poly(A) RNA pools of unfertilized eggs.
Topics: Animals; Cell Compartmentation; Female; Gene Expression Regulation; Microscopy, Electron; Ovum; Poly A; RNA; RNA, Messenger; Sea Urchins; Transcription, Genetic; Xenopus laevis
PubMed: 6196164
DOI: 10.1002/9780470720790.ch2