T-hairpin structure found in the RNA element involved in piRNA biogenesis

PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In Drosophila, the Traffic jam (Tj) mRNA is consumed to produce piRNA in its 3′ UTR. A cis element located within the 3′-UTR, Tj-cis, is necessary for piRNA biogenesis. In this study, we analyzed the structure of the Tj-cis RNA, a 100 nt RNA corresponding to the Tj-cis element, by the SHAPE and NMR analyses and found that a stable hairpin structure formed in the 5′ half of the Tj-cis RNA. The tertiary structure of the 16 nt stable hairpin was analyzed by NMR, and a novel stem-loop structure, the T-hairpin, was found. In the T-hairpin, four uridine residues are exposed to the solvent, suggesting that this stem loop is the target of Yb protein, a Tudor domain-containing piRNA biogenesis factor. The piRNA biogenesis assay showed that both the T-hairpin and the 3′ half are required for the function of the Tj-cis element, suggesting that both the T-hairpin and the 3′ half are recognized by Yb protein.

Structural Requirements in the Hemagglutinin Cleavage Site-Coding RNA Region for the Generation of Highly Pathogenic Avian Influenza Virus

Highly pathogenic avian influenza viruses (HPAIVs) with H5 and H7 hemagglutinin (HA) subtypes are derived from their low pathogenic counterparts following the acquisition of multiple basic amino acids in their HA cleavage site. It has been suggested that consecutive adenine residues and a stem-loop structure in the viral RNA region that encodes the cleavage site are essential for the acquisition of the polybasic cleavage site. By using a reporter assay to detect non-templated nucleotide insertions, we found that insertions more frequently occurred in the RNA region (29 nucleotide-length) encoding the cleavage site of an H5 HA gene that was predicted to have a stem-loop structure containing consecutive adenines than in a mutated corresponding RNA region that had a disrupted loop structure with fewer adenines. In virus particles generated by using reverse genetics, nucleotide insertions that created additional codons for basic amino acids were found in the RNA region encoding the cleavage site of an H5 HA gene but not in the mutated RNA region. We confirmed the presence of virus clones with the ability to replicate without trypsin in a plaque assay and to cause lethal infection in chicks. These results demonstrate that the stem-loop structure containing consecutive adenines in HA genes is a key molecular determinant for the emergence of H5 HPAIVs.

One-loop structure of parton distribution for the gluon condensate and “zero modes”

We present results for one-loop corrections to the recently introduced “gluon condensate” PDF F(x). In particular, we give expression for the gg-part of its evolution kernel. To enforce strict compliance with the gauge invariance requirements, we have used on-shell states for external gluons, and have obtained identical results both in Feynman and light-cone gauges. No “zero mode” δ(x) terms were found for the twist-4 gluon PDF F(x). However a q2δ(x) term was found for the ξ = 0 GPD F(x, q2) at nonzero momentum transfer q. Overall, our results do not agree with the original attempt of one-loop calculations of F(x) for gluon states, which sets alarm warning for calculations that use matrix elements with virtual external gluons and for lattice renormalization procedures based on their results.

A Conserved Histophilus somni 23S Intervening Sequence Yields Functional, Fragmented 23S rRNA

The genome biology underlying H. somni virulence, pathogenicity, environmental adaptability, and broad tissue tropism is understood poorly. We identified a novel H. somni 109-nt IVS stem-loop structure, of which the central portion is excised from the 23S rRNA transcript, resulting in the fragmentation of this rRNA in the H. somni isolate USDA-ARS-USMARC-63250 and the release of a 94-nt structured RNA of unknown function.

Single chain models illustrate the 3D RNA folding shape during translation

The three-dimensional conformation of RNA is important in the function and fate of the molecule. The common conformation of mRNA is formed based on the closed-loop structure and internal base pairings with the activity of the ribosome movements. However, recent reports suggest that the closed-loop structure might not be formed in many mRNAs. This implies that mRNA can be considered as a single polymer in the cell. We developed TRIP; Three-dimensional RNA Illustration Program, to model the three-dimensional RNA folding shape based on single-chain models. We identified the angle restriction of each bead component from previously reported single-molecule FISH experimental data. This simulation method was able to recapitulate the mRNA conformation change of the translation activity and three-dimensional positional interaction between organelle and its localized mRNAs. Within the analyzed cases base-pairing interactions only have minor effects on the three-dimensional mRNA conformation, and instead single-chain polymer characteristics have a more significant impact on the conformation. This method will be used to predict the potential aggregation force for mRNA and long noncoding RNA conformation in specific cellular conditions such as nucleolus and phase-separated granules.

Error Uncertainty Analysis in Planar Closed-Loop Structure with Joint Clearances

For planar closed-loop structures with clearances, the angular and positional error uncertainties are studied. By using the vector translation method and geometric method, the boundaries of the errors are analyzed. The joint clearance is considered as being distributed uniformly in a circle area. A virtual link projection method is proposed to deal with the clearance affected length error probability density function (PDF) for open-loop links. The error relationship between open loop and closed loop is established. The open-loop length PDF and the closed-loop angular error PDF both approach being Gaussian distribution if there are many clearances. The angular propagation error of multi-loop structures is also investigated by using convolution. The positional errors of single and multiple loops are both discussed as joint distribution functions. Monte Carlo simulations are conducted to verify the proposed methods.

Diverse Roles and Therapeutic Potentials of Circular RNAs in Urological Cancers

Circular RNAs (circRNAs) are a novel class of noncoding RNAs, which are mainly formed as a loop structure at the exons caused by noncanonical splicing; they are much more stable than linear transcripts; recent reports have suggested that the dysregulation of circRNAs is associated with the occurrence and development of diseases, especially various human malignancies. Emerging evidence demonstrated that a large number of circRNAs play a vital role in a series of biological processes such as tumor cell proliferation, migration, drug resistance, and immune escape. Additionally, circRNAs were also reported to be potential prognostic and diagnostic biomarkers in cancers. In this work, we systematically summarize the biogenesis and characteristics of circRNAs, paying special attention to potential mechanisms and clinical applications of circRNAs in urological cancers, which may help develop potential therapy targets for urological cancers in the future.