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PubMed2025

Improving RNA Secondary Structure Prediction Through Expanded Training Data.

In recent years, deep learning has revolutionized protein structure prediction, achieving remarkable speed and accuracy. RNA structure prediction, however, has lagged behind. Although several methods have shown some success in predicting RNA secondary and tertiary structures, none have reached the accuracy observed with contemporary protein models. The lack of success of these RNA structure prediction models has been proposed to be due to limited high-quality structural information that can be used as training data. To probe this proposed limitation, we developed a large and diverse dataset comprising paired RNA sequences and their corresponding secondary structures. We assess the utility of this enhanced dataset by retraining on a deep learning model, SincFold. We find that SincFold exhibited improved generalization to some previously unseen RNA families, enhancing its capability to predict accurate de novo RNA secondary structures. The RNASSTR dataset provides a substantial advance for RNA structure modeling, laying a strong foundation for the development of future RNA secondary structure prediction algorithms.

Journal Article↗
PubMed1979

Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species.

Secondary structure models of 54 5S RNA species are constructed based on the comparative analyses of their primary structure. All 5S RNAs examined have essentially the same secondary structure. However, there are revealing characteristic differences between eukaryotic and prokaryotic types. The prokaryotic 5S RNAs may be further classified into two types, one having 120 nucleotides (120-N type) and another having 116 (116-N type). A possible mechanism for the conversion of the prokaryotic 116-N type to the 120-N type 5S RNAs (or vice versa) is discussed on the basis of their nucleotide alignments. Finally, by comparing the nucleotide alignments, we propose a phylogenic tree of the 54 5S RNA species.

Animals↗
PubMedDate not supplied

[Influence of ionic strength on RNA-polymerase structure].

Chromatography of RNA polymerase holoenzyme preincubated under different ionic strength conditions on the DNA agarose column was studied. Ratio of two peaks identified to be core and holoenzyme was analysed. In the range of 0.15 to 0.05 M KCl the relative content of the holoenzyme peak gradually decreased from 100 to 50%. At the same time a peak of free sigma-subunit appeared as detected by the chromatography on DNA agarose gel A-1.5 m. The dissociation of half of the sigma-subunit amount occured within the enzyme dimer-monomer transition range. The results suggest that the dimerization follows the equation: E sigma + E sigma in equilibrium with E2 sigma. Reconstitution of the RNA polymerase holoenzyme from purified core enzyme and sigma-subunit was also studied by the same method. Reconstitution did not occur at a low ionic strength (0--0.1 M KCl), but takes place at ionic strength of 0.2 M or higher. Possible function of the dimerisation of the enzyme in search of promoter site and regulation of RNA synthesis is discussed.

DNA↗
PubMed2025

Structure of coxsackievirus cloverleaf RNA and 3Cpro dimer establishes the RNA-binding mechanism of enterovirus protease 3Cpro.

In positive-strand RNA viruses, the genome serves as a template for both protein translation and negative-strand RNA synthesis. Enteroviruses use the cloverleaf RNA structure at the 5' end of the genome to balance these two processes. Cloverleaf acts as a promoter for RNA synthesis and forms a complex with viral 3CD protein, the precursor to 3Cpro protease, and 3Dpol polymerase. The interaction between cloverleaf and 3CD is mediated by the 3Cpro domain, yet how 3Cpro promotes specific RNA-binding is not clear. We report the structure of coxsackievirus cloverleaf RNA-3Cpro complex, wherein two 3Cpro molecules interact with cloverleaf stem-loop D. 3Cpro dimer mainly recognizes the shape of the dsRNA helix through symmetric interactions, suggesting that 3Cpro is a previously undiscovered type of RNA binding protein. We show that 3CD protein also dimerizes on cloverleaf RNA and binds the RNA with higher affinity than 3Cpro. The structure provides insight into the RNA-binding mechanism of 3Cpro or 3CD with other cis-acting replication elements.

RNA, Viral↗
PubMed1979

Quantitative conservation of chromatin-bound RNA polymerases I and II in mitosis. Implications for chromosome structure.

RNA synthesis almost ceases in mitosis. It is ambiguous whether this temporal, negative control of RNA synthesis is solely because of the nature of chromosomes per se, (i.e., their condensed state), or to a physical loss of RNA polymerases along with other nuclear proteins which have been shown to pass into the cytoplasm in mitosis, or to their combined feature. Aside from such regulatory considerations, a question has also been raised as to whether RNA polymerases are constituents of metaphase chromosomes. To clarify these aspects of RNA polymerase-chromatin interaction in mitosis, the enzymes in chromosomes were quantitated and their levels compared to those in interphase nuclei and cells at various phases of the cell cycle. The results show that the amounts of form I, form II, and probably form III enzymes bound to a genome-equivalent of chromatin stay constant during the cell cycle. Thus, the mechanism for the negative control of RNA synthesis in mitosis appears to exist in the chromosomes per se, but not to be directly related to the RNA polymerase levels. This quantitative conservation of chromatin-bound RNA polymerases implies that they may persist as structural components of the chromosomes in mitosis.

Animals↗
PubMed1975

Stable polypeptides associated with the 250S mengovirus-induced RNA polymerase structure.

One host polypeptide (40,000 daltons) synthesized prior to infection is associated with the 250S RNA polymerase structure partially purified by a combination of velocity sedimentation and isopycnic separation. A series of pulse-chase experiments have shown that a 56,000 dalton polypeptide made during the eclipse phase of infection is inserted into the 250S viral RNA polymerase structure. This 56,000 dalton polypeptide is bound in a stable manner since labeled 56,000 dalton polypeptide is not removed from the 250S polymerase structure by a 2-hour chase (3 to 5 hours after infection) and it is the major labeled polypeptide species remaining. However, the 56,000 dalton polypeptide (viral-specific polypeptide E) made at 4 hours after infection is not present in the 250S polymerase structure following a 50 minue chase. Levels of cycloheximide which inhibit protein synthesis 95 per cent in the infected cell have no effect on the amount of viral-specific RNA polymerase activity (in vitro) when the inhibitor is added for 30 minutes at the time of maximum rate of viral RNA synthesis in whole cells. These inhibitor studies support the hypothesis that the viral-specific RNA polymerase polypeptide may be a stable polypeptide that is not rapidly turning over in the infected cell. In view of these results the stable 56,000 dalton polypeptide (polypeptide E) made early in infection may be a candidate for the viral-specific polymerase polypeptide.

Amino Acids↗
PubMedDate not supplied

[Secondary structure of RNA of influenza virus in free form and in ribonucleoprotein].

Large amounts of RNA and RNP isolated from influenza virus were obtained. This has allowed us to undertake detailed physical studies of the secondary structure of RNA of influenza virus in free form and in RNP. Analysis of CD spectrum and the hypochromic effect after thermal denaturation of RNA indicated that RNA in free form contains 58--62% double-stranded regions. By comparative studies of the secondary structure of RNA in RNP, it was estimated that 12--14% of the RNA exists in double-stranded form.

Hot Temperature↗
PubMed1977

Secondary structure of RNA from bacteriophages f2 Qbeta, and PP7.

Electron microscopy of RNA-protein monolayers prepared under partial denaturing conditions has been used to compare the secondary structure of coliphage f2 and Qbeta and Pseudomonas aeruginosa phage PP7 RNAs. The secondary structure map of f2 RNA contains a central open loop and four symmetrically placed hairpins, which is similar to the pattern reported by Jacobson (A. B. Jacobson, Proc. Natl. Acad. Sci. U.S.A. 73:307-311, 1976) for the closely related phage MS2. With the same denaturing conditions, Qbeta RNA, which is 20% larger than f2 or PP7 RNA, has a central open loop and a smaller terminal loop. PP7 RNA has two large, closed secondary structures, one of which is nearly central. The base composition of PP7 RNA was determined and is similar to that of the group I coliphage RNAs. Thus, the greater amount of large base-paired structure is not related to an increased guanine-plus-cytosine content of PP7 RNA. With increased denaturing conditions, the central, closed structure of PP7 RNA is converted into an open loop. The central structures of all three phages include about 700 nucleotides. The relevance of these findings to the genetic maps of the coliphage RNAs is discussed.

Bacteriophages↗
PubMed1979

Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region.

The secondary structure of the terminated trp leader transcript from Escherichia coli was analyzed by RNase T1 partial digestion. Base-paired regions were recovered by nondenaturing gel electrophoresis and identified by denaturing gel electrophoresis and fingerprinting. The tandem tryptophan codons in the leader peptide coding region were found to be base paired with a more distal region of the transcript. This and other secondary structures that the trp leader RNA can form help explain the physiological response of the operon as well as the behavior of regulatory mutants.

Codon↗
PubMed2025

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.

Pre-mRNA splicing is kinetically coupled to transcription as shown by the widespread effects of transcription speed on alternative splicing (AS) outcomes. The molecular basis for such kinetic coupling is incompletely understood, but one potential mechanism is through elongation rate-dependent alternative folding pathways of the nascent pre-messenger RNA (pre-mRNA). To search for RNA structures in nascent pre-mRNA, we modified Sequencing of Psoralen Crosslinked, Ligated And Selected Hybrids (SPLASH) [J. G. Ashley Aw et al., Mol. Cell 62, 603-617 (2016)] for use with Chromatin Associated RNA. We applied this method called Chromatin Associated RNA (CAR)-SPLASH to cells expressing wild-type and slow mutant RNA polymerase II and identified >3,000 intramolecular RNA duplexes of which >400 are proximal to splice sites. Antisense oligonucleotide (ASO) disruption of several such duplexes that sequester splice sites has a major impact on AS outcomes, even though the ASOs do not directly disrupt splice sites. ASO disruption of these regulatory elements that we designate "RNA kinetic switches" modified AS of NISCH Exon 18, GAK Exon 7, and MEGF8 Exon 14 in a way that depends on the rate of transcription elongation. We propose that these switches mediate kinetic coupling via the effects of transcription speed on folding of nascent RNA structures that modulate AS and that many nascent RNA structures can thereby serve as targets for splice-modifying ASOs.

RNA Precursors↗
PubMed1979

Analysis of RNA secondary structure by photochemical reversal of psoralen crosslinks.

Aminomethyltrioxsalen (AMT), a psoralen, is known to cause interstrand crosslinks in double stranded nucleic acids. We have demonstrated the photochemical reversal of this reaction, and have used this result to develop a method for identification of specific sequences which are adjacent because of RNA secondary structure formation. E. coli 5S rRNA is used as a model system. We isolated and characterized a product that is derived from the stem region of 5S RNA.

Base Composition↗
PubMedDate not supplied

Persistence of nucleolar RNA-rich structures and Ph1 duplication in the blastic crisis of chronic myeloid leukaemia.

Nucleolar persistence in metaphase plates is a feature observed in most of the cells in neoplastic processes. Pathological persistence or fragmentation of the nucleoli is thought to be the cause of some numerical chromosomal aberrations due to non-disjunction of the chromatids, with particular involvement of the satellite chromosomes. Thus, a combined selective staining of both the nucleoli (amido black 10B according to Mundkur and Brauer's cytochemical technique) and the chromosomes (neutral red) was applied to the metaphase plates of patients with chronic myeloid leukaemia in the blastic crisis. Duplicated Ph1 was associated with amido black-stained areas at a very high rate in some cases. Since the blastic crisis in chronic myeloid leukaemia is characterized by the appearance of an increased number of immature, highly nucleolated cells, these findings lend support to the hypothesis that the duplication of the Ph1 represents a feature possibly favoured by the pathological persistence of nucleolar RNA-rich structures in the metaphase.

Adult↗
PubMed1977

[Ribonucleoproteins containing heterogeneous nuclear and messenger cytoplasmic RNA. Characteristics, structure and relations (author's transl)].

Following the study of Spirin, many authors have shown that cytoplasmic messenger RNA and heterogeneous nuclear RNA are complexed with specific proteins to form ribonucleoprotein particles (RNP). These RNP are heterogeneous in size and present a high protein to RNA ratio. Different observations suggest a polymeric structure for nuclear ribonucleoproteins but their protein composition is more clearly complex than that of cytoplasmic ribonucleoproteins. If we accept the following processing: heterogeneous nuclear RNP leads to free cytoplasmic RNP leads to polysomic RNP, the question arises as to what extent proteins originally present in nuclear RNP are conserved. Proteins more or less tightly bound to RNA have different roles: packing and protection of RNA, regulation during gene expression processing.

Animals↗
PubMed1977

Heterogeneous nuclear RNA secondary structure: oligo (U) sequences base-paired with poly (A) and their possible role as binding sites for heterogeneous nuclear RNA-specific proteins.

HeLa cell heterogeneous nuclear RNA derived from high-molecular-weight nuclear ribonucleoprotein (RNP) particles contains oligo(U) sequences of 15-50 nucleotides base-paired with poly(A). These duplexes are resistant to pancreatic RNase at 0.5 M NaCl in native RNP, remain so after chemical deproteinization of the RNP digests, and then copurify with poly(A) on oligo(dT)-cellulose chromatography. Oligo(dT)-cellulose binding capacity of the oligo(U)-poly(A) duplexes is abolished by prior titration of the nonduplex poly(A) regions with excess poly(U). The oligo(dT)-purified fraction is 97.5 mole % A + U and the [3H]uridine-labeled component is resistant to redigestion by pancreatic RNase at 0.5 M NaCl but not at 0.01 M NaCl. After thermal denaturation, the [3H]uridine-labeled chains become RNase-sensitive at 0.5 M NaCl. Electrophoresis of [3H]adenosine- or [3H]uridine-labeled material in polyacrylamide gels containing 99% formamide confirms that the oligo(U) sequences are not covalently linked to poly(A). Controls establish that the A-U duplexes are not formed artifactually during isolation of heterogeneous nuclear RNP or subsequent fractionation. The oligo(U)-poly(A) duplexes appear to be associated with protein in native heterogeneous nuclear RNP, as reflected by the differential pancreatic RNase sensitivity of the duplexed oligo(U) in RNP (resistant) and RNA (sensitive), measured at physiological ionic strength.

Base Sequence↗
PubMed1977

Transcription termination at the trp operon attenuators of Escherichia coli and Salmonella typhimurium: RNA secondary structure and regulation of termination.

Transcription termination at the attenuators of the trp operons of Escherichia coli and Salmonella typhimurium was studied in vitro using DNA restriction fragments as templates. Readthrough transcription beyond the terminators occurred with 5 and 30% efficiency, respectively, in E. coli and S. typhimurium. This difference is correlated with the stability of proposed secondary structures of the respective trp leader transcripts. Secondary structure analyses of the two leader transcripts revealed a well-conserved pattern of RNA base paring. This and the possibility that trp leader RNA is translated suggest a model for regulation of transcription termination that is based on ribosome movement along the RNA and a shift between alternative RNA base-pairing configuration.

Escherichia coli↗