Explanipedia

Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance Open

Minli Ruan, Sean M. Engels, Sean M. Engels, Xiaoyan Li, Rosella Stower , et al. · 2025

Pseudouridine (Ψ) is an abundant post-transcriptional modification found across all classes of RNA. It has been widely speculated that Ψ inclusion in mRNAs might provide an avenue for cells to control gene expression post-transcriptionally…

Functional Proximity across an mRNA Open

Breanne M. Hatfield, Chase A. Weidmann, Christina A. McCutchin, Patrick S. Irving, Irma M. Nelson , et al. · 2025

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…

SHAPE-based chemical probes for studying preQ1-RNA interactions in living bacteria Open

José A. Reyes Franceschi, Emilio L. Cárdenas, Barbara Klein, Chase A. Weidmann, Amanda L. Garner · 2025

Interrogating RNA-small molecule interactions inside cells is critical for advancing RNA-targeted drug discovery. In particular, chemical probing technologies that both identify small molecule-bound RNAs and define their binding sites in t…

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

Xiaoxiao Hao, Yuechuan Chen, Divya Sahu, Roza Przanowska, Mujawar Aaiyas , et al. · 2025

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…

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

Xiaoxiao Hao, Yuechuan Chen, Divya Sahu, Roza Przanowska, Mujawar Aaiyas , et al. · 2024

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…

Simultaneous mapping of RNA secondary, tertiary, and quaternary structure in living cells by multi-site DMS probing Open

Irfana Saleem, Thomas P. Miller, Lucas Kearns, David Mitchell, Ritwika Bose , et al. · 2024

Identifying tertiary structures and protein binding sites on RNA molecules remains a key challenge in RNA biology. We report a new chemical probing strategy termed multi-site DMS-MaP (msDMS-MaP) that exploits base tautomerization during mu…

Template switching enables chemical probing of native RNA structures Open

Ian Hall, Martin R. O’Steen, Scott E. Gold, Sarah C. Keane, Chase A. Weidmann · 2024

RNAs are often studied in nonnative sequence contexts to facilitate structural studies. However, seemingly innocuous changes to an RNA sequence may perturb the native structure and generate inaccurate or ambiguous structural models. To fac…

The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex Open

Robert P. Connacher, Richard T. Roden, Kai-Lieh Huang, Amanda J Korte, Saathvika Yeruva , et al. · 2024

The essential Drosophila RNA-binding protein Brain Tumor (Brat) represses specific genes to control embryogenesis and differentiation of stem cells. In the brain, Brat functions as a tumor suppressor that diminishes neural stem cell prolif…

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox Open

Chase A. Weidmann, Anthony M. Mustoe, Kevin M. Weeks · 2024

Functional Validation of SAM Riboswitch Element A fromListeria monocytogenes Open

Ian Hall, Kaitlyn Zablock, Raeleen Sobetski, Chase A. Weidmann, Sarah C. Keane · 2024

SreA is one of seven candidate S -adenosyl methionine (SAM) class I riboswitches identified in Listeria monocytogenes , a saprophyte and opportunistic foodborne pathogen. SAM is essential to all domains of life, serving as a ubiquitous met…

Measuring Proximity-Mediated Function of mRNA Regulatory Proteins by Engineered Tethering Open

Breanne M. Hatfield, Chase A. Weidmann, Kevin M. Weeks · 2023

Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis Open

Anthony M. Mustoe, Chase A. Weidmann, Kevin M. Weeks · 2023

RNA molecules convey biological information both in their linear sequence and in their base-paired secondary and tertiary structures. Chemical probing experiments, which involve treating an RNA with a reagent that modifies conformationally…

Structural analysis of MALAT1 long noncoding RNA in cells and in evolution Open

Anaïs Monroy‐Eklund, Colin D. Taylor, Chase A. Weidmann, Christina L. Burch, Alain Laederach · 2023

Although not canonically polyadenylated, the long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is stabilized by a highly conserved 76-nt triple helix structure on its 3′ end. The entire MALAT1 transcript is…

Global 5′-UTR RNA structure regulates translation of a SERPINA1 mRNA Open

Philip J. Grayeski, Chase A. Weidmann, Jayashree Kumar, Lela Lackey, Anthony M. Mustoe , et al. · 2022

SERPINA1 mRNAs encode the protease inhibitor α-1-antitrypsin and are regulated through post-transcriptional mechanisms. α-1-antitrypsin deficiency leads to chronic obstructive pulmonary disease (COPD) and liver cirrhosis, and specific vari…

Structural conservation of MALAT1 long non-coding RNA in cells and in evolution Open

Anaïs Monroy‐Eklund, Colin D. Taylor, Chase A. Weidmann, Christina L. Burch, Alain Laederach · 2022

Although not canonically polyadenylated, the long non-coding RNA MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is stabilized by a highly conserved 159 nucleotide triple helix structure on its 3’ end. The entire MALAT1 tra…

Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP Open

Samuel W. Olson, Anne‐Marie W. Turner, J. Winston Arney, Irfana Saleem, Chase A. Weidmann , et al. · 2022

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors Open

Roza Przanowska, Chase A. Weidmann, Shekhar Saha, Magdalena A. Cichewicz, Kate Jensen , et al. · 2022

Large-scale allosteric switch in the 7SK RNA regulates transcription in response to growth and stress Open

Samuel W. Olson, Anne‐Marie W. Turner, J. Winston Arney, Irfana Saleem, Chase A. Weidmann , et al. · 2021

Summary 7SK is a highly conserved non-coding RNA that regulates eukaryotic transcription by sequestering positive transcription elongation factor b (P-TEFb). 7SK regulatory function likely entails changes in RNA structure, but characterizi…

Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors Open

Roza Przanowska, Chase A. Weidmann, Shekhar Saha, Magdalena A. Cichewicz, Kate Jensen , et al. · 2021

Summary Many lncRNAs have been discovered using transcriptomic data, however, it is broadly unclear what fraction of lncRNAs are functional and what structural properties affect their phenotype. MUNC lncRNA, also known as DRR eRNA, stimula…

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid Open

Christiane Iserman, Christine Roden, Mark A. Boerneke, Rachel Sealfon, Grace A. McLaughlin , et al. · 2020

Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA Open

Chase A. Weidmann, Anthony M. Mustoe, Parth B. Jariwala, J. Mauro Calabrese, Kevin M. Weeks · 2020

Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins Open

René M. Arvola, Chase A. Weidmann, Traci M. Tanaka Hall, Aaron C. Goldstrohm · 2020

Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as th…

RNP-MaP: In-cell analysis of protein interaction networks defines functional hubs in RNA Open

Chase A. Weidmann, Anthony M. Mustoe, Parth B. Jariwala, J. Mauro Calabrese, Kevin M. Weeks · 2020

RNAs interact with networks of proteins to form complexes (RNPs) that govern many biological processes, but these networks are currently impossible to examine in a comprehensive way. We developed a live-cell chemical probing strategy for m…

Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor Open

Karyn Schmidt, Chase A. Weidmann, Thomas A. Hilimire, Elaine Yee, Breanne M. Hatfield , et al. · 2020

SHAPE Probing Reveals Human rRNAs Are Largely Unfolded in Solution Open

Catherine A. Giannetti, Steven Busan, Chase A. Weidmann, Kevin M. Weeks · 2019

Chemical probing experiments, coupled with empirically determined free energy change relationships, can enable accurate modeling of the secondary structures of diverse and complex RNAs. A current frontier lies in modeling large and structu…

Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies Open

Steven Busan, Chase A. Weidmann, Arnab Sengupta, Kevin M. Weeks · 2019

Chemical probing is an important tool for characterizing the complex folded structures of RNA molecules, many of which play key cellular roles. Electrophilic SHAPE reagents create adducts at the 2'-hydroxyl position on the RNA backbone of …

mRNA structure determines specificity of a polyQ-driven phase separation Open

Erin M. Langdon, Yupeng Qiu, Amirhossein Ghanbari Niaki, Grace A. McLaughlin, Chase A. Weidmann , et al. · 2018

RNA and membraneless organelles Membraneless compartments can form in cells through liquidliquid phase separation (see the Perspective by Polymenidou). But what prevents these cellular condensates from randomly fusing together? Using the R…

mRNA structure determines specificity of a polyQ-driven phase separation Open

Erin M. Langdon, Yupeng Qiu, Amirhossein Ghanbari Niaki, Grace A. McLaughlin, Chase A. Weidmann , et al. · 2017

RNA promotes liquid-liquid phase separation (LLPS) to build membrane-less compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here we report that secondary stru…

Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins Open

René M. Arvola, Chase A. Weidmann, Traci M. Tanaka Hall, Aaron C. Goldstrohm · 2017

Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as th…

Combinatorial Control of Messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins Open

René M. Arvola, Chase A. Weidmann, Traci M. Tanaka Hall, Aaron C. Goldstrohm · 2017

Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as th…

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