Kevin M. Weeks
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View article: A small cationic probe for accurate, punctate discovery of RNA tertiary structure
A small cationic probe for accurate, punctate discovery of RNA tertiary structure Open
RNA molecules fold into intricate three-dimensional tertiary structures that are central to their biological functions. Yet reliably discovering new motifs that form true tertiary interactions remains a major challenge. Here we show that R…
View article: Functional Proximity across an mRNA
Functional Proximity across an mRNA Open
Extensive RNA-protein interactions occur throughout the lifecycle of an mRNA that up- and down-regulate mRNA translation and degradation. Modulating interactions between regulatory proteins and mRNAs can have large effects on gene expressi…
View article: Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP
Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP Open
Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, these sites must be in proximity. Inverted repeat …
View article: A 36-base hairpin within lncRNA DRAIC, which is modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes
A 36-base hairpin within lncRNA DRAIC, which is modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes Open
A tumor-suppressive long-noncoding RNA (lncRNA) DRAIC (downregulated RNAin cancers) inhibits NF-κB activity and physically interacts with IKKα, a kinase component of the IKK complex, in several cancer types. Here we explore the precise mol…
View article: Ligand-binding pockets in RNA and where to find them
Ligand-binding pockets in RNA and where to find them Open
RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules—via well-defined ligand-binding p…
View article: <i>fpocketR</i> : A platform for identification and analysis of ligand-binding pockets in RNA
<i>fpocketR</i> : A platform for identification and analysis of ligand-binding pockets in RNA Open
Small molecules that bind specific sites in RNAs hold promise for altering RNA function, manipulating gene expression, and expanding the scope of druggable targets beyond proteins. Identifying binding sites in RNA that can engage ligands w…
View article: Ligand-binding pockets in RNA, and where to find them
Ligand-binding pockets in RNA, and where to find them Open
RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules – via well-defined ligand binding…
View article: Scaffold-enabled high-resolution cryo-EM structure determination of RNA
Scaffold-enabled high-resolution cryo-EM structure determination of RNA Open
Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are compounded for small RNAs as cryo-EM is inherent…
View article: A 36-base hairpin within lncRNA <i>DRAIC</i> , which is modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes
A 36-base hairpin within lncRNA <i>DRAIC</i> , which is modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes Open
A tumor-suppressive long noncoding RNA (lncRNA) DRAIC ( d own-regulated RN A in c ancers) inhibits NF-κB activity and physically interacts with IKKα, a kinase component of the IKK complex, in several cancer types. Here we explore the preci…
View article: Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP
Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP Open
Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these sites must be in pro…
View article: Protein binding in an mRNA 5′-UTR sterically hinders translation
Protein binding in an mRNA 5′-UTR sterically hinders translation Open
Structures in the 5′ untranslated regions (UTRs) of mRNAs can physically modulate translation efficiency by impeding the scanning ribosome or by sequestering the translational start site. We assessed the impact of stable protein binding in…
View article: Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing
Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing Open
Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, information about base pairing, conformational en…
View article: RNAvigate: efficient exploration of RNA chemical probing datasets
RNAvigate: efficient exploration of RNA chemical probing datasets Open
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and mu…
View article: Scaffold-enabled high-resolution cryo-EM structure determination of RNA
Scaffold-enabled high-resolution cryo-EM structure determination of RNA Open
Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are compounded for small RNAs as cryo-EM is inherent…
View article: RNAvigate: efficient exploration of RNA chemical probing datasets
RNAvigate: efficient exploration of RNA chemical probing datasets Open
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and mu…
View article: Immune-induced remodelling of mRNA structurome regulates uORF-mediated translation
Immune-induced remodelling of mRNA structurome regulates uORF-mediated translation Open
To survive stress, eukaryotes selectively translate stress-related transcripts while inhibiting growth-associated protein production. How this translational reprogramming occurs under biotic stress has not been systematically studied. To i…
View article: RNAvigate: Efficient exploration of RNA chemical probing datasets
RNAvigate: Efficient exploration of RNA chemical probing datasets Open
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA including local nucleotide flexibility, RNA secondary structure, protein- and ligand-binding, through-space interaction networks, and mu…
View article: Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication
Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication Open
The genomes of RNA viruses encode the information required for replication in host cells both in their linear sequence and in complex higher-order structures. A subset of these RNA genome structures show clear sequence conservation, and ha…