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Article
Structural insights into branch site proofreading by human spliceosome
Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying ...
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Article
A feedback control method for phase signal demodulation in fiber-optic hydrophones
In the realm of acoustic signal detection, the identification of weak signals, particularly in the presence of negative signal-to-noise ratios, poses a significant challenge. This challenge is further heighten...
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Article
Open AccessComputational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identi...
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Article
A paternal protein facilitates sperm RNA delivery to regulate zygotic development
Sperm contributes essential paternal factors, including the paternal genome, centrosome, and oocyte-activation signals, to sexual reproduction. However, it remains unresolved how sperm contributes its RNA mole...
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Article
Open AccessPervasive downstream RNA hairpins dynamically dictate start-codon selection
Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing al...
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Protocol
Prediction of Dynamic RBP–RNA Interactions Using PrismNet
A capacity to detect the binding profiles of RNA targets for an RNA-binding protein (RBP) under different cellular conditions is essential to understand the functions of the RBP in posttranscriptional regulati...
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Article
Open AccessEnhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0
RNA G-quadruplexes (rG4s) are non-canonical structural motifs that have diverse functional and regulatory roles, for instance in transcription termination, alternative splicing, mRNA localization and stabiliza...
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Article
Open AccessOnline single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
Computational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informativ...
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Article
Advances and opportunities in RNA structure experimental determination and computational modeling
Beyond transferring genetic information, RNAs are molecules with diverse functions that include catalyzing biochemical reactions and regulating gene expression. Most of these activities depend on RNAs’ specifi...
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Article
Context-dependent tumor-suppressive BMP signaling in diffuse intrinsic pontine glioma regulates stemness through epigenetic regulation of CXXC5
The most lethal subtype of diffuse intrinsic pontine glioma (DIPG) is H3K27M. Although ACVR1 mutations have been implicated in the pathogenesis of this currently incurable disease, the impacts of bone morphogenet...
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Article
Open AccessSingle-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation
The combined use of transcriptome and translatome as indicators of gene expression profiles is usually more accurate than the use of transcriptomes alone, especially in cell types governed by translational reg...
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Article
Open AccessDifferential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure
RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcrip...
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Article
Recent advances in RNA structurome
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel ...
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Article
Prediction of the sea buckthorn AQP gene structure and its spatiotemporal expression pattern under drought stress
Aquaporins (AQPs) are transmembrane proteins in the cell membrane that selectively transport water and other small molecules, which play important regulatory roles under drought stress. In this study, the full...
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Article
Hyperlipidemia patients carrying LDLR splicing mutation c.1187-2A>G respond favorably to rosuvastatin and PCSK9 inhibitor evolocumab
Mutations in the LDL receptor gene LDLR cause familial hypercholesterolemia (FH); however, the pharmacogenomics of specific LDLR mutations remains poorly understood. The goals of this study were to identify the g...
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Article
Open AccessComparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2
In contrast to the extensive research about viral protein–host protein interactions that has revealed major insights about how RNA viruses engage with host cells during infection, few studies have examined int...
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Article
A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments
Sequencing-based RNA structure probing can generate transcriptome-wide profiles of RNA secondary structures. Sufficient structural coverage is needed to obtain unbiased insights about RNA structures and functi...
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Article
Open AccessMagnetic resonance colonography with intestine-absorbable nanoparticle contrast agents in evaluation of colorectal inflammation
To develop a nanoparticle-based MRI protocol based on transrectal administration of intestine-absorbable nanoparticle contrast agents to evaluate ulcerative colitis (UC).
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Article
RNA structure probing uncovers RNA structure-dependent biological functions
RNA molecules fold into complex structures that enable their diverse functions in cells. Recent revolutionary innovations in transcriptome-wide RNA structural probing of living cells have ushered in a new era ...
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Article
Open AccessLong noncoding RNA ILF3-AS1 aggravates papillary thyroid carcinoma progression via regulating the miR-4306/PLAGL2 axis
It have been proven that long non-coding RNAs (lncRNAs) serve as regulators in carcinogenesis. Interleukin enhancer binding factor 3 antisense RNA 1 (ILF3-AS1) has been illuminated as a prognostic factor in so...
