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An optimized chemical-genetic method for cell-specific metabolic labeling of RNA

Ubiquitous mammalian enzymes can scavenge uracil analogs, leading to non-specific background in cell-type-specific RNA labeling. This work reveals the enzymes involved and describes the uridine/cytidine kinase 2 and 2′-azidouridine pair as a highly specific and non-toxic alternative.

Sarah Nainar
Bonnie J. Cuthbert
Robert C. Spitale
Research03 Feb 2020
Nature Methods

Volume: 17, P: 311-318
Erratum: Structural imprints in vivo decode RNA regulatory mechanisms

Robert C. Spitale
Ryan A. Flynn
Howard Y. Chang
Amendments and Corrections30 Sept 2015
Nature

Volume: 527, P: 264
Erratum: Light-activated chemical probing of nucleobase solvent accessibility inside cells

Chao Feng
Dalen Chan
Robert C Spitale
Amendments and Corrections14 Feb 2018
Nature Chemical Biology

Volume: 14, P: 325
Reply to: On gene silencing by the X10-23 DNAzyme

Robert C. Spitale
John C. Chaput
Research18 Jul 2022
Nature Chemistry

Volume: 14, P: 859-861
Light-activated chemical probing of nucleobase solvent accessibility inside cells

A method called Light Activated Structural Examination of RNA (LASER) enables monitoring of the solvent accessibility of purine nucleobases and identifies rapid structural changes of cellular RNA–protein interactions and intracellular RNA structures.

Chao Feng
Dalen Chan
Robert C Spitale
Research15 Jan 2018
Nature Chemical Biology

Volume: 14, P: 276-283
Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modification

Nguyen et al. identify TDP-43 and METTL3 as key regulators of disrupted RNA splicing in Huntington’s disease, offering insight into how TDP-43 mislocalization and aberrant m6A RNA modification and localization relate to disease pathogenesis.

Thai B. Nguyen
Ricardo Miramontes
Leslie M. Thompson
ResearchOpen Access06 Jan 2025
Nature Neuroscience

Volume: 28, P: 280-292
Technologies to probe functions and mechanisms of long noncoding RNAs

In this Perspective, Spitale, Chang and Chu discuss recent technological advances that will aid in the functional characterization of long noncoding RNAs, which up to now has posed a substantial challenge.

Ci Chu
Robert C Spitale
Howard Y Chang
Reviews07 Jan 2015
Nature Structural & Molecular Biology

Volume: 22, P: 29-35
RNA SHAPE analysis in living cells

Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) is a proven methodology for in vitro RNA secondary structure analysis. The identification of a new acylating agent permits the use of SHAPE to probe folded RNAs within living cells.

Robert C Spitale
Pete Crisalli
Howard Y Chang
Research25 Nov 2012
Nature Chemical Biology

Volume: 9, P: 18-20
Probing the dynamic RNA structurome and its functions

In this Review, Spitale and Incarnato discuss how the application of sequencing-based RNA structure mapping methods to entire transcriptomes in living cells is providing insight into the RNA structurome, the dynamics of RNA ensembles and how RNA structure regulates cellular processes.

Robert C. Spitale
Danny Incarnato
Reviews08 Nov 2022
Nature Reviews Genetics

Volume: 24, P: 178-196
Imaging of Titan from the Cassini spacecraft

Carolyn C. Porco
Emily Baker
Robert West
Research10 Mar 2005
Nature

Volume: 434, P: 159-168
A biologically stable DNAzyme that efficiently silences gene expression in cells

RNA-cleaving DNA enzymes (DNAzymes) have the potential to function as therapeutic agents by silencing the expression of disease-associated proteins. Xeno-nucleic acids were used to improve the catalytic activity and biological stability of a highly evolved DNAzyme known as 10–23. The enzyme exhibits a robust multiple-turnover activity in cultured mammalian cells.

Yajun Wang
Kim Nguyen
John C. Chaput
Research25 Mar 2021
Nature Chemistry

Volume: 13, P: 319-326
The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery

Here the authors characterize the sequence-specific effect of an anticancer compound on mRNA cleavage, providing insights into the mechanism of mRNA 3′ processing.

Liang Liu
Angela M Yu
Yongsheng Shi
Research12 Dec 2023
Nature Structural & Molecular Biology

Volume: 30, P: 1947-1957
Fear extinction is regulated by the activity of long noncoding RNAs at the synapse

Synaptic activity controls the extinction of conditioned fear. Here the authors discovered a new way that the brain controls memories of fear: a long noncoding RNA called Gas5 that coordinates the activity of RNA granules in the synaptic compartment.

Wei-Siang Liau
Qiongyi Zhao
Timothy W. Bredy
ResearchOpen Access22 Nov 2023
Nature Communications

Volume: 14, P: 1-16
The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction

Li et al. have discovered a necessary role for the DNA modification N6-methyldeoxyadenosine (m6dA) in regulating experience-dependent gene expression and the formation of fear extinction memory. These findings expand the scope of DNA modifications in the adult brain.

Xiang Li
Qiongyi Zhao
Timothy W. Bredy
Research18 Feb 2019
Nature Neuroscience

Volume: 22, P: 534-544
Structural imprints in vivo decode RNA regulatory mechanisms

The single-stranded nature of RNAs synthesized in the cell gives them great scope to form different structures, but current methods to measure RNA structure in vivo are limited; now, a new methodology allows researchers to examine all four nucleotides in mouse embryonic stem cells.

Robert C. Spitale
Ryan A. Flynn
Howard Y. Chang
Research18 Mar 2015
Nature

Volume: 519, P: 486-490
Understanding the transcriptome through RNA structure

The ways in which an RNA molecule folds to form structures can be crucial to its function, and so methods for studying RNA structures make an important contribution to understanding transcriptomes. Experimental approaches in this field are being advanced by coupling them to high-throughput sequencing.

Yue Wan
Michael Kertesz
Howard Y. Chang
Reviews18 Aug 2011
Nature Reviews Genetics

Volume: 12, P: 641-655
Progress and challenges for chemical probing of RNA structure inside living cells

Miles Kubota
Catherine Tran
Robert C Spitale
Reviews17 Nov 2015
Nature Chemical Biology

Volume: 11, P: 933-941
Landscape and variation of RNA secondary structure across the human transcriptome

An RNA secondary structure (RSS) map of coding and noncoding RNA from a human family (two parents and their child) is produced; this reveals that approximately 15% of all transcribed single nucleotide variants (SNVs) alter local RNA structure, and these SNVs are depleted in certain locations, suggesting that particular RNA structures are important at those sites.

Yue Wan
Kun Qu
Howard Y. Chang
Research29 Jan 2014
Nature

Volume: 505, P: 706-709
RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

DEAD-box RNA helicase DDX21 is involved in both the transcription and RNA processing of ribosomal genes in human cells, sensing the transcriptional status of both RNA polymerase I and RNA polymerase II and associating with non-coding RNAs involved in ribonucleoprotein formation, possibly allowing for coordinated regulation of protein synthesis.

Eliezer Calo
Ryan A. Flynn
Joanna Wysocka
Research24 Nov 2014
Nature

Volume: 518, P: 249-253
Control of somatic tissue differentiation by the long non-coding RNA TINCR

The human long non-coding RNA TINCR binds to STAU1 and controls epidermal differentiation by stabilizing key differentiation mRNAs, by means of a TINCR-binding motif found enriched in epidermal differentiation genes.

Markus Kretz
Zurab Siprashvili
Paul A. Khavari
Research02 Dec 2012
Nature

Volume: 493, P: 231-235
Clobetasol promotes neuromuscular plasticity in mice after motoneuronal loss via sonic hedgehog signaling, immunomodulation and metabolic rebalancing

Nunzio Vicario
Federica M. Spitale
Rosario Gulino
ResearchOpen Access16 Jun 2021
Cell Death & Disease

Volume: 12, P: 1-13
Evolving insights into RNA modifications and their functional diversity in the brain

The study of the mechanisms controlling RNA metabolism in neurons represents a new frontier in the understanding of gene–environment interactions and how they regulate brain function. In this Perspective, the authors describe the recent surge in newly identified epitranscriptomic processes and highlight their potential importance in coordinating the molecular underpinnings of cognition and memory.

Sarah Nainar
Paul R Marshall
Timothy W Bredy
Reviews27 Sept 2016
Nature Neuroscience

Volume: 19, P: 1292-1298
Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression

Loredana Zocchi
Aditi Mehta
Claudia A. Benavente
ResearchOpen Access18 Feb 2020
Oncogenesis

Volume: 9, P: 1-15
Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

icSHAPE allows transcriptome-wide RNA structure profiling in living cells. It uses a clickable SHAPE reagent to enable biotin-based enrichment of SHAPE-modified RNA, reducing the necessary sequencing depth.

Ryan A Flynn
Qiangfeng Cliff Zhang
Howard Y Chang
Protocols14 Jan 2016
Nature Protocols

Volume: 11, P: 273-290
Dose-escalation trial of budesonide in surfactant for prevention of bronchopulmonary dysplasia in extremely low gestational age high-risk newborns (SASSIE)

Cindy T. McEvoy
Philip L. Ballard
Roberta A. Ballard
Research01 Feb 2020
Pediatric Research

Volume: 88, P: 629-636

Search

An optimized chemical-genetic method for cell-specific metabolic labeling of RNA

Erratum: Structural imprints in vivo decode RNA regulatory mechanisms

Erratum: Light-activated chemical probing of nucleobase solvent accessibility inside cells

Reply to: On gene silencing by the X10-23 DNAzyme

Light-activated chemical probing of nucleobase solvent accessibility inside cells

Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modification

Technologies to probe functions and mechanisms of long noncoding RNAs

RNA SHAPE analysis in living cells

Probing the dynamic RNA structurome and its functions

Imaging of Titan from the Cassini spacecraft

A biologically stable DNAzyme that efficiently silences gene expression in cells

The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery

Fear extinction is regulated by the activity of long noncoding RNAs at the synapse

The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction

Structural imprints in vivo decode RNA regulatory mechanisms

Understanding the transcriptome through RNA structure

Progress and challenges for chemical probing of RNA structure inside living cells

Landscape and variation of RNA secondary structure across the human transcriptome

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Clobetasol promotes neuromuscular plasticity in mice after motoneuronal loss via sonic hedgehog signaling, immunomodulation and metabolic rebalancing

Evolving insights into RNA modifications and their functional diversity in the brain

Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

Dose-escalation trial of budesonide in surfactant for prevention of bronchopulmonary dysplasia in extremely low gestational age high-risk newborns (SASSIE)

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