RNA Methylation
Methods and Protocols
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Article
Time-resolved single-cell RNA-seq using metabolic RNA labelling
Single-cell RNA genomics technologies are revolutionizing biomedical science by profiling single cells with unprecedented resolution, providing fundamental insights into the role of different cellular states a...
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Article
Open AccessSpt6 is a maintenance factor for centromeric CENP-A
Replication and transcription of genomic DNA requires partial disassembly of nucleosomes to allow progression of polymerases. This presents both an opportunity to remodel the underlying chromatin and a danger ...
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Protocol
Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates
The study of RNA dynamics, specifically RNA transcription and decay rates, has gained increasing attention in recent years because various mechanisms have been discovered that affect mRNA half-life, thereby ul...
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Publisher Correction: RNA modification: Getting a hold on cytosine methylation in mRNA
In the version of this article initially published, the author order (Liu, J., Huang, T., Chen, W., Gu, N. & Zhang, R.) for the linked Resource (ref. 7) was incorrect, and all named citations of that reference...
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Article
Getting a hold on cytosine methylation in mRNA
Cytosine methylation (m5C) is one of the more disputed base modifications of the epitranscriptome, mostly because current methods for detection are prone to artifacts. A new approach to increase detection accurac...
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Protocol
Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine
A powerful method to determine the methylation status of specific cytosine residues within RNA is bisulfite sequencing. In combination with high-throughput sequencing methods cytosine methylation can be determ...
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Open AccessRNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity
Chemical modifications of RNA have been attracting increasing interest because of their impact on RNA fate and function. Therefore, the characterization of enzymes catalyzing such modifications is of great imp...
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Open AccessDistinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosi...
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Protocol
Detection of 5-Methylcytosine in Specific Poly(A) RNAs by Bisulfite Sequencing
RNA bisulfite sequencing (RNA-BS-seq) represents a method for the detection of methylated cytosines in RNA. Developed originally for the analysis of DNA methylation, a modified version of this method can be us...
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Protocol
Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite Sequencing
While low-throughput RNA bisulfite sequencing is the method of choice to assess the methylation status of specific cytosines in candidate RNAs, the combination of bisulfite treatment of RNA with today’s high-t...
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Article
Open AccessRecent insights from in vitro single-molecule studies into nucleosome structure and dynamics
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a shor...
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Article
Open AccessEmbryonic stem cell differentiation requires full length Chd1
The modulation of chromatin dynamics by ATP-dependent chromatin remodeling factors has been recognized as an important mechanism to regulate the balancing of self-renewal and pluripotency in embryonic stem cel...
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Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly
CHD1 is a chromodomain-containing protein in the SNF2-like family of ATPases. Here we show that CHD1 exists predominantly as a monomer and functions as an ATP-utilizing chromatin assembly factor. This reaction...
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Strategies for the reconstitution of chromatin
In eukaryotes, chromatin is the natural form of DNA in the nucleus. For hundreds of millions of years, DNA-binding factors have evolved with chromatin. It is therefore more desirable to study the molecular mec...
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Article
A maize histone deacetylase and retinoblastoma-related protein physically interact and cooperate in repressing gene transcription
In mammalian cells the product of the human retinoblastoma tumour suppressor gene (pRb) can recruit Rpd3-like histone deacetylases to repress transcription. In this study, we investigated whether this mechanis...
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Article
Comparative analysis of HD2 type histone deacetylases in higher plants
Zea mays (L.) histone deacetylase HD2 was identified as a new type of histone deacetylase (HDAC) unrelated to the well-known Rpd3p and Hda1p families but with sequence homology to peptidyl-proly...
