Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

  title={Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq},
  author={Dan Dominissini and Sharon Moshitch-Moshkovitz and Schraga Schwartz and Mali Salmon-Divon and Lior Ungar and Sivan Osenberg and Karen Cesarkas and Jasmine Jacob-Hirsch and Ninette Amariglio and Martin Kupiec and Rotem Sorek and Gideon Rechavi},
An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. [] Key Result We identify over 12,000 m6A sites characterized by a typical consensus in the transcripts of more than 7,000 human genes. Sites preferentially appear in two distinct landmarks—around stop codons and within long internal exons—and are highly conserved between human and mouse.

Novel RNA regulatory mechanisms revealed in the epitranscriptome

It is reported that recent work has shown RNA modifications like m6A, collectively called the “epitranscriptome,” are a pervasive feature of mammalian cells and likely play a role in development and disease.

Mapping and significance of the mRNA methylome

The advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics are summarized.

Dynamic landscape and evolution of m6A methylation in human

A resource of human m6A profile is provided for future studies of m 6A functions, and a role ofm6A modification in human evolutionary adaptation and disease susceptibility is suggested.

Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation

It is revealed that m7G is enriched at the 5′UTR region and AG-rich contexts, a feature that is well-conserved across different human/mouse cell lines and mouse tissues, and highlighted as a novel epitranscriptomic marker with regulatory roles in translation.

Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome

m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) is developed and used to demonstrate that antibodies to m6A can induce specific mutational signatures at m 6A residues after ultraviolet light–induced antibody-RNA cross- linking and reverse transcription.

m6A: A novel hallmark of translation

The elucidation of the mechanism underlying stress-induced 5’UTR methylation was discovered and several surprising features of the mA "reader" YTHDF2 were discovered, including the fact that mA resembles mG, and it was speculated that the stress- induced 5‘UTRmethylation permits the translation machinery to identify stressinduced messages from preexisting mRNAs, thereby achieving selective translation.

Genome-wide identification of mRNA 5-methylcytosine in mammals

A quantitative atlas of RNA m5C sites in human and mouse tissues based on a new discovery pipeline allows the identification of sequence motifs and structural features associated with the modification and provides a resource for future studies.

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome.

m6A-SAC-seq is a quantitative method to dissect the dynamics and functional roles of m6A sites in diverse biological processes using limited input RNA.

Most m6A RNA Modifications in Protein‐Coding Regions Are Evolutionarily Unconserved and Likely Nonfunctional

It is suggested that most m6A modifications in protein‐coding regions are nonfunctional and nonadaptive, probably resulting from off‐target activities of m6a methyltransferases.



Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing.

A method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus, and observing a high frequency of methylation at PuGm6ACU sequences is described.

Systematic identification of abundant A-to-I editing sites in the human transcriptome

A computational search for ADAR editing sites in the human transcriptome is described, using millions of available expressed sequences and indicates the role of editing in controlling dsRNA stability.

Sequence specificity of the human mRNA N6-adenosine methylase in vitro.

The results demonstrate that the N6-adenosine methylase has a strict sequence specificity, and that there is no requirement for extended sequences or secondary structures for methylation.

Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine

The principles of molecular recognition and nucleic acid chemistry are exploited to establish the experimental parameters for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine, two abundant modifications in eukaryotic rRNA/tRNA and mRNA, respectively.

Mapping of N6-methyladenosine residues in bovine prolactin mRNA.

Using a combination of in vitro RNA labeling and antibody selection, this technique was able to detect m6A in purified stable mRNAs that cannot be readily labeled in cells with greater sensitivity than was possible by previous techniques.

N6-methyladenosine residues in an intron-specific region of prolactin pre-mRNA

The results indicate the final intron-specific sequence (intron D) of a prolactin RNA molecule does indeed possess m6A residues, and when mapped to specific T1 oligonucleotides, the predominant site of methylation was found to be within the consensus sequence AGm6ACU.

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor[W][OA]

The results reported here provide direct evidence for an essential function for N6-methyladenosine in a multicellular eukaryote, and the interaction with At FIP37 suggests possible RNA processing events that might be regulated or altered by this base modification.

Deciphering the splicing code

The assembly of a ‘splicing code’ is described, which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons and facilitates the discovery and detailed characterization of regulatedAlternative splicing events on a genome-wide scale.

A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

A highly precise mass spectrometric method is developed to quantify tRNA modifications in Saccharomyces cerevisiae and reveals several novel biosynthetic pathways for RNA modifications and led to the discovery of signature changes in the spectrum of t RNA modifications in the damage response to mechanistically different toxicants.