Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple ...protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function—the sperm-to-oocyte cell fate switch. Y479A’s effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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•A conserved PUF-partner interface modulates the in vivo PUF-RNA binding landscape•Partners can increase or reduce FBF-2 occupancy of specific sites in RNA targets•Partnerships can separate FBF-2 biological functions•FBF-2 partnerships drive a spatially patterned switch from repression to activation
Carrick et al. demonstrate that a conserved PUF/PUM partner-binding interface on FBF-2 defines its RNA binding landscape (transcriptome-wide sites of FBF-2 occupancy) and regulation of cell fate. Moreover, they show that the FBF-2 partner-binding interface can drive a spatially patterned switch from RNA repression to activation.
This paper proposes an efficient localized meshless technique for approximating the viscoelastic wave model. This model is a significant methodology to explain wave propagation in solids modeled with ...a wide collection of viscoelastic laws. In the first method, a difference scheme with the second-order accuracy is implemented to obtain a semi-discrete scheme. Then, a localized radial basis function partition of unity scheme is adopted to get a full-discrete scheme. This localization technique consists of decomposing the initial domain into several sub-domains and constructing a local radial basis function approximation over every sub-domain. A well-conditioned resulting linear system and a low computational burden are the main merits of this technique compared to global collocation methods. Further, the stability and convergence analysis of the temporal discretization scheme are deduced using discrete energy method. Numerical results are shown to validate the accuracy and effectiveness of the proposed method.
RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the ...sequence, structure, and context preferences of these proteins in vitro by deep sequencing of bound RNAs. These data enable construction of “RNA maps” of RBP activity without requiring crosslinking-based assays. We found an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity toward a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, however, we observed extensive preferences for contextual features distinct from short linear RNA motifs, including spaced “bipartite” motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. Our results emphasize the importance of contextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif.
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•In vitro specificity of 78 human RNA binding proteins determined by deep sequencing•RBP motifs have low diversity, compositional complexity, and RNA structure potential•RBPs that bind similar motifs often differ in their sequence context preferences•Many favor specific “bipartite” motifs, flanking base composition, or RNA structures
Dominguez et al. describe in vitro binding specificities of 78 human RNA binding proteins (RBPs) to RNA sequences and structures. They find that many RBPs bind similar RNA motifs but differ in affinity for spaced “bipartite” motifs, flanking composition, and RNA structure, supporting the model that distinct motif occurrences are often discriminated based on sequence context.
•The Sobolev equation is the mathematical model of the vertical non stationary groundwater flow with dynamic capillary-pressure effect in a porous medium.•A new hybrid scheme based LRBF-PUM is ...formulated to approximate the Sobolev equation.•The theoretical convergence and unconditional stability of the proposed semi-discrete approach are both analyzed and confirmed numerically.•The LRBF-PUM method useful for complex domains with acceptable accuracy was proposed.
This paper develops a numerical approach for finding the approximate solution of the Sobolev model. This model describes many natural processes, such as thermal conduction for different media and fluid evolution in soils and rocks. The proposed method approximates the unknown solution with the help of two main stages. At a first stage, the time discretization is performed by means of a second-order finite difference procedure. At a second stage, the space discretization is accomplished using the local radial basis function partition of unity collocation method based on the finite difference (LRBF-PUM-FD). The major disadvantage of global techniques is the high computational burden of solving large linear systems. The LRBF-PUM-FD significantly sparsifies the linear system and reduces the computational burden, while simultaneously maintaining a high accuracy level. The time-discrete formulation is studied in terms of the stability and convergence analysis via the energy method. Three examples are illustrated to verify the efficiency and accuracy of the method.
Pseudouridimycin (PUM) is a selective nucleoside-analog inhibitor of bacterial RNA polymerase with activity against Gram-positive and Gram-negative bacteria. PUM, produced by Streptomyces sp. ...ID38640, consists of a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 5′-aminopseudouridine. We report the characterization of the PUM gene cluster. Bioinformatic analysis and mutational knockouts of pum genes with analysis of accumulated intermediates, define the PUM biosynthetic pathway. The work provides the first biosynthetic pathway of a C-nucleoside antibiotic and reveals three unexpected features: production of free pseudouridine by the dedicated pseudouridine synthase, PumJ; nucleoside activation by specialized oxidoreductases and aminotransferases; and peptide-bond formation by amide ligases. A central role in the PUM biosynthetic pathway is played by the PumJ, which represents a divergent branch within the TruD family of pseudouridine synthases. PumJ-like sequences are associated with diverse gene clusters likely to govern the biosynthesis of different classes of C-nucleoside antibiotics.
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•Pseudouridimycin as a C-nucleoside antibiotic inhibiting bacterial RNA polymerase•First biosynthetic pathway for a C-nucleoside antibiotic elucidated•Free pseudouridine as a pathway intermediate•Dedicated pseudouridine synthase, oxidoreductases, aminotransferases, amide ligases
Sosio et al. describe the biosynthetic pathway for the C-nucleoside antibiotic pseudouridimycin. Biosynthesis proceeds through formation of pseudouridine by the pseudouridine synthase PumJ, with specialized oxidoreductase, aminotransferase, and amide ligases leading to the final compound. Microbial genomes harbor diverse gene clusters encoding PumJ-related sequences.
We construct cubature methods on scattered data via resampling on the support of known algebraic cubature formulas, by different kinds of adaptive interpolation (polynomial, RBF, PUM). This approach ...gives a promising alternative to other recent methods, such as direct meshless cubature by RBF or least-squares cubature formulas.
This paper develops an efficient local meshless collocation algorithm for approximating the time fractional evolution model that is applied for the modeling of heat flow in materials with memory. The ...model is based on the Riemann-Liouville fractional integral. The proposed method discretizes the unknown solution using two main parts. First, the temporal direction is approximated through the second-order finite difference scheme. Second, the spatial direction of the governing problem is discretized via the local radial basis function partition of unity technique. The major drawback of global collocation techniques is the computational cost associated with arisen dense algebraic system. This localized method is based on partitioning the original domain to several subdomains by means of the kernel approximation on each local domain and allows one to significantly sparsify the algebraic system having small condition number in addition to lowering the computational cost. The stability and convergence of the time difference formulation are discussed in detail with respect to the H1-norm. Numerical results and comparisons are illustrated in order to confirm theoretical analysis and the accuracy of the method.
Pumilio RNA-binding family member 1 (PUM1) has been implicated in both the progression of colorectal cancer and the regulation of inflammation. The role of PUM1 in the polarization of ...tumor-associated macrophages (TAMs) into the M2 phenotype has not yet been reported in hepatocellular carcinoma. Using the PUM1-knockout mice model, flow cytometry, and IHC, we validated the role of PUM1 in hepatocellular carcinoma (HCC) TAMs. One-way analysis of variance (ANOVA) or student's t-tests was used to compare the experimental groups. We found that PUM1 inhibited anti-tumor immunity in HCC through TAM-mediated inhibition of CD8+ T cells. We also showed that PUM1 promotes the transformation of TAMs into pro-tumorigenic M2-like phenotypes by activating cAMP signaling pathway. This study emphasized the potential of PUM1 as a target for immunotherapy in HCC through TAMs. The present study revealed the molecular mechanism underlying the pro-tumor role of PUM1 in HCC.
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