37 Result(s)
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Qiangfeng Cliff Zhang
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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
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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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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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
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
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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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
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 AccessRNA structure probing reveals the structural basis of Dicer binding and cleavage
It is known that an RNA’s structure determines its biological function, yet current RNA structure probing methods only capture partial structure information. The ability to measure intact (i.e., full length) R...
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Open AccessPredicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures
Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation, and dynamically reflect specific cellular conditions. However, presently available tools for predicting RBP–R...
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Article
IRIS: A method for predicting in vivo RNA secondary structures using PARIS data
RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs, yet in vivo RNA secondary structures remain enigmatic. PARIS (Psoralen Analysis of RNA Interact...
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Article
Identification of mecciRNAs and their roles in the mitochondrial entry of proteins
Mammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitoc...
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Article
Prediction and differential analysis of RNA secondary structure
RNA structure is the crucial basis for RNA function in various cellular processes. Over the last decade, high throughput structure profiling (SP) experiments have brought enormous insight into RNA secondary st...
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Article
Open AccessRNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structu...
