As researchers open up to the reality of RNA modification, an expanded epitranscriptomics toolbox takes shape.
A role for DNA modification in gene regulation is well established, but much less is known about how RNA modification affects RNA fate and influences the way genes are expressed. This web collection features articles from various Nature journals that highlight this exciting new research area of ‘epitranscriptomics’.
We hope you will enjoy the read!
Illustration by Viktor Koen based on concepts developed for Gidi Rechavi’s group, Sheba Medical Center, Tel Aviv University.
Reviews, News and Comment
Although it has been known for decades that RNA is subjected to numerous covalent modifications, there has been a recent surge in interest driven by sequencing-based transcriptome-wide detection methods and the realization that RNA modifications have important roles in diverse biological processes. This Review describes the range of detection strategies for RNA modifications, their particular strengths and limitations, and how responsible and complementary application of these techniques will be required to ensure the quality and interpretability of the rapidly accumulating data sets.
The chemical modifications and structural features of mRNAs are highly dynamic. Together, they regulate the composition and function of the transcriptome by shaping RNA–protein interactions at different stages of the gene expression process.
This Review describes the latest methods for profiling common epitranscriptomic marks, their scale, resolution and ability to quantify. It also discusses remaining challenges.
Reversible mRNA methylation is an emerging mode of eukaryotic post-transcriptional gene regulation. N6-methyladenosine (m6A) affects mRNA processing, translation and decay during cell differentiation, embryonic development and stress responses. Other mRNA modifications — N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine — together with m6A code a new layer of information that controls protein synthesis.
Five experts discuss topical aspects of RNA modifications, highlighting where the research field stands, recommendations for best practices and visions for the future of epitranscriptomics studies.
This Perspective highlights recent progress on the location, functions and mechanisms of N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNA. In particular, the authors discuss how m6A modification affects the mammalian RNA life cycle at multiple stages.
Pseudouridine is the most abundant internal post-transcriptional modification of spliceosomal small nuclear RNAs and ribosomal RNAs. Transcriptome-wide maps of RNA pseudouridylation have recently established that pseudouridines are also found in mRNAs, potentially representing a new mechanism of proteomic diversification.
Diverse types of RNA in various species are modified by methylation to form N6-methyladenosine (m6A). This Review describes how progress in the characterization of m6A distributions and of proteins that 'write', 'erase' and 'read' this mark is revealing roles for reversible m6A methylation in dynamic gene expression control.
The results of transcriptome-wide N6-methyladenosine (m6A) mapping techniques have resolved many of the long-standing concerns regarding the physiological relevance of m6A, which suggests that this modification regulates mRNA fate and function. The identification of adenosine methylases and demethylases provides insights into the cellular pathways that involve m6A and indicates a role of m6A in physiological processes.
Post-transcriptional RNA modifications can be dynamic and might have functions beyond fine-tuning the structure and function of RNA. Understanding these RNA modification pathways and their functions may allow researchers to identify new layers of gene regulation at the RNA level.
Methylation at the 6 position of adenosine (m6A) in RNA is rapidly and transiently induced at DNA damage sites in response to ultraviolet irradiation.
The N 6-methyladenosine (m6A) modification facilitates maternally driven clearance of zebrafish maternal mRNAs through the m6A-binding protein Ythdf2, ensuring proper and timely embryonic development.
Fat mass and obesity-associated protein (FTO) preferentially demethylates m6Am, a modified adenosine that, when present at the 5′ end of certain mRNAs, positively influences mRNA stability by preventing DCP2-mediated decapping.
The methylation of adenosine residues on the long non-coding RNA XIST is essential for X-chromosome transcriptional repression during female mammalian development.
The structure of the METTL3–METTL14 complex, which mediates N6-adenosine methylation of RNA, suggests that the METTL3 subunit is the catalytic core while METTL14 serves to bind RNA.
Infection with HIV-1 triggers an increase in N6-methyladenosine (m6A) modification of both viral and host mRNAs, which impacts viral replication and nuclear export of viral RNA.
Here the m1A modification is discovered in messenger RNA and mapped at the transcriptome-wide level; the modification is conserved, dynamic, accumulates in structured regions around translation initiation sites upstream of the first splice site, and correlates with higher protein expression.
A method called m1A-ID-seq, which involves antibody enrichment and reverse transcriptase–based sequencing of N1-methyladenosine (m1A) RNA modifications, reveals that m1A is a reversible mRNA modification that is abundant in the 5′ UTRs of human genes.
Methylation of adenosine within mRNA coding regions delays tRNA accommodation during translation and thus changes translation dynamics, which might influence protein folding.
Under stress, such as heat shock, the N6-methyladenosine (m6A) modification is shown to accumulate primarily in the 5′ untranslated region of induced mRNAs owing to the translocation of an m6A interacting protein, YTHDF2, into the nucleus, resulting in increased cap-independent translation of these mRNAs, indicating one possible mechanism by which stress-responsive genes can be preferentially expressed.
Unique mutational signatures induced by cross-linking of m6A-specific antibodies to RNA identify m6A and m6Am residues at single-nucleotide resolution, transcriptome-wide.
The addition of the N6-methyladenosine (m6A) mark to primary microRNAs by METTL3 in mammalian cells is found to promote the recognition of these microRNA precursors by DGCR8, a component of the microprocessor complex.
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.
The binding motifs for many RNA-binding proteins are normally buried within structured regions; now, the N6-methyladenosine modification is shown to act as a switch to remodel these regions, expose the motif, and thereby facilitate binding of RNA-binding proteins.
Pseudouridine (ψ) is a C-linked uracil modification originally discovered in tRNA. MS analysis and CeU-Seq, a method that permits chemical tagging, pulldown and sequencing of ψ residues, reveal that these modifications are more abundant in the mammalian transcriptome than previously thought.
N6-methyladenosine (m6A) is an abundant eukaryotic RNA modification that regulates mRNA stability. Biochemical analysis and crystallographic visualization of m6A-YTHDC1 interactions establish this YTH family member as an m6A reader and explain its RNA consensus sequence selectivity.
N6-methyladenosine (m6A) is an abundant internal modification of messenger RNA (mRNA) that has been reported recently in thousands of mammalian mRNAs and long non-coding RNAs (lncRNAs). Zhao and colleagues identify two methyltransferases responsible for this modification in mammalian cells, and demonstrate that they are required for embryonic stem cell self-renewal maintenance through an effect of the modification on the degradation of developmental regulator transcripts.
Modification of mRNA with N 6-methyladenosine (m6A) is proposed to regulate transcript stability. Here, Jia et al. uncover plant-specific features in the m6A methylome of Arabidopsis, such as methylation enrichment around the start codon, and suggest a positive role in gene expression.
The modification of uridine to pseudouridine is widespread in transfer and ribosomal RNAs but not observed so far in a coding RNA; here a new technique is used to detect this modification on a genome-wide scale, leading to the identification of pseudouridylation in messenger RNAs as well as almost 100 new sites in non-coding RNAs.
Certain adenosine residues within mammalian RNAs undergo reversible N6 methylation. Two methyltransferase enzymes, METTL3 and METTL14, as well as the splicing factor WTAP are identified as core components of the multiprotein complex that deposits RNA N6-methyladenosine (m6A) in nuclear RNAs.
The mRNAs of higher eukaryotes are extensively modified internally with N6-methyladenosine, but the specific functional role of this modification has been unclear; here this modification on mRNA is shown to be recognized by several proteins, the modification and its recognition serve to regulate the RNA’s lifetime.
Internal modifications in mRNA and non-coding RNA are necessary for modulating various intracellular signalling pathways. In this study, the authors report novel modifications resulting from oxidative RNA demethylation, which regulate RNA–protein interactions affecting gene expression.
N6-methyladenosine (m6A) is the most prevalent internal modification in messenger RNA; here the human and mouse m6A modification landscape is presented in a transcriptome-wide manner, providing insights into this epigenetic modification.
N6-Methyladenosine is an abundant nucleoside in cellular mRNA that undergoes demethylation under physiological conditions by fat mass and obesity-associated protein (FTO). This new pathway suggests that RNA modifications can be reversible and potentially have an impact on RNA metabolism.