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Article
Open AccessFear extinction is regulated by the activity of long noncoding RNAs at the synapse
Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synap...
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Article
Probing the dynamic RNA structurome and its functions
RNA is a key regulator of almost every cellular process, and the structures adopted by RNA molecules are thought to be central to their functions. The recent fast-paced evolution of high-throughput sequencing-...
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Article
Open AccessmRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons
N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in metazoans and is particularly abundant in the central nervous system. The extent to which m6A is dynamically regulated and whether m6A....
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Article
Reply to: On gene silencing by the X10-23 DNAzyme
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Article
Open AccessPlaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer’s disease
Disease-associated microglia (DAMs), that surround beta-amyloid plaques, represent a transcriptionally-distinct microglial profile in Alzheimer’s disease (AD). Activation of DAMs is dependent on triggering rec...
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Article
A biologically stable DNAzyme that efficiently silences gene expression in cells
Efforts to use RNA-cleaving DNA enzymes (DNAzymes) as gene-silencing agents in therapeutic applications have stalled due to their low efficacy in clinical trials. Here we report a xeno-nucleic-acid-modified ve...
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Article
An optimized chemical-genetic method for cell-specific metabolic labeling of RNA
Tissues and organs are composed of diverse cell types, which poses a major challenge for cell-type-specific profiling of gene expression. Current metabolic labeling methods rely on exogenous pyrimidine analogs...
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Article
Open AccessChromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression
Retinoblastoma is an aggressive childhood cancer of the develo** retina that initiates by biallelic RB1 gene inactivation. Tumor progression in retinoblastoma is driven by epigenetics, as retinoblastoma genomes...
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Article
The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction
DNA modification is known to regulate experience-dependent gene expression. However, beyond cytosine methylation and its oxidated derivatives, very little is known about the functional importance of chemical m...
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Article
Erratum: Light-activated chemical probing of nucleobase solvent accessibility inside cells
Nat. Chem. Biol.; doi:10.1038/nchembio.2548; published online 15 January 2018; corrected online 22 January 2018 In the version of this article initially published online, the submission date was incorrectly st...
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Article
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 inter...
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Protocol
Assaying RNA Structure Inside Living Cells with SHAPE
RNA molecules have emerged as key players in nearly every facet of gene regulation. Such functions are governed by RNA’s unique ability to fold into intricate secondary and tertiary structures. In order to und...
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Article
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 ...
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Article
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.
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Article
Progress and challenges for chemical probing of RNA structure inside living cells
Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell...
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Article
Erratum: Structural imprints in vivo decode RNA regulatory mechanisms
Nature 519, 486–490 (2015); doi: 10.1038/nature14263 In Fig. 2a of this Letter, an error in the placement of the labels on the pie chart was introduced during the production process. The correct numbers were r...
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Article
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 rese...
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Article
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 ass...
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Article
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.
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Article
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...
