- Three-dimensional intact-tissue sequencing of single-cell transcriptional states SCIENCE 2018; 361 (6400): 380-+
N-6-methyladenosine-dependent regulation of messenger RNA stability
2014; 505 (7481): 117-?
N(6)-methyladenosine (m(6)A) is the most prevalent internal (non-cap) modification present in the messenger RNA of all higher eukaryotes. Although essential to cell viability and development, the exact role of m(6)A modification remains to be determined. The recent discovery of two m(6)A demethylases in mammalian cells highlighted the importance of m(6)A in basic biological functions and disease. Here we show that m(6)A is selectively recognized by the human YTH domain family 2 (YTHDF2) 'reader' protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m(6)A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies. The carboxy-terminal domain of YTHDF2 selectively binds to m(6)A-containing mRNA, whereas the amino-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. Our results indicate that the dynamic m(6)A modification is recognized by selectively binding proteins to affect the translation status and lifetime of mRNA.
View details for DOI 10.1038/nature12730
View details for Web of Science ID 000329163300035
View details for PubMedID 24284625
N-6-methyladenosine Modulates Messenger RNA Translation Efficiency
2015; 161 (6): 1388-1399
N(6)-methyladenosine (m(6)A) is the most abundant internal modification in mammalian mRNA. This modification is reversible and non-stoichiometric and adds another layer to the dynamic control of mRNA metabolism. The stability of m(6)A-modified mRNA is regulated by an m(6)A reader protein, human YTHDF2, which recognizes m(6)A and reduces the stability of target transcripts. Looking at additional functional roles for the modification, we find that another m(6)A reader protein, human YTHDF1, actively promotes protein synthesis by interacting with translation machinery. In a unified mechanism of m(6)A-based regulation in the cytoplasm, YTHDF2-mediated degradation controls the lifetime of target transcripts, whereas YTHDF1-mediated translation promotion increases translation efficiency, ensuring effective protein production from dynamic transcripts that are marked by m(6)A. Therefore, the m(6)A modification in mRNA endows gene expression with fast responses and controllable protein production through these mechanisms.
View details for DOI 10.1016/j.cell.2015.05.014
View details for Web of Science ID 000355935000017
View details for PubMedID 26046440
High-Resolution N-6-Methyladenosine (m(6)A) Map Using Photo-Crosslinking-Assisted m(6)A Sequencing
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
2015; 54 (5): 1587-1590
N(6) -methyladenosine (m(6) A) is an abundant internal modification in eukaryotic mRNA and plays regulatory roles in mRNA metabolism. However, methods to precisely locate the m(6) A modification remain limited. We present here a photo-crosslinking-assisted m(6) A sequencing strategy (PA-m(6) A-seq) to more accurately define sites with m(6) A modification. Using this strategy, we obtained a high-resolution map of m(6) A in a human transcriptome. The map resembles the general distribution pattern observed previously, and reveals new m(6) A sites at base resolution. Our results provide insight into the relationship between the methylation regions and the binding sites of RNA-binding proteins.
View details for DOI 10.1002/anie.201410647
View details for Web of Science ID 000348713900034
View details for PubMedID 25491922
- Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine CELL RESEARCH 2014; 24 (12): 1493-1496
Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain
NATURE CHEMICAL BIOLOGY
2014; 10 (11): 927-929
N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA. Our structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m(6)A)C sequences by YTHDC1.
View details for DOI 10.1038/NCHEMBIO.1654
View details for Web of Science ID 000343621500014
View details for PubMedID 25242552
Dynamic RNA Modifications in Posttranscriptional Regulation
2014; 56 (1): 5-12
Cellular RNAs can be chemically modified over a hundred different ways. These modifications were once thought to be static, discrete, and utilized to fine-tune RNA structure and function. However, recent studies have revealed that some modifications, like mRNA methylation, can be reversed, and these reversible modifications may play active roles in regulating diverse biological processes. In this perspective, we summarize examples of dynamic RNA modifications that affect biological functions. We further propose that reversible modifications might occur on tRNA, rRNA, and other noncoding RNAs to regulate gene expression analogous to the reversible mRNA methylation.
View details for DOI 10.1016/j.molcel.2014.09.001
View details for Web of Science ID 000344484400003
View details for PubMedID 25280100
Reading RNA methylation codes through methyl-specific binding proteins
2014; 11 (6): 669-672
N (6)-methyladenosine (m (6)A) is a prevalent modification of eukaryotic mRNAs. It regulates yeast cell fate and is essential to the development and fertility of metazoans. Although its presence in mRNA has been known since the early 1970s, the function of m (6)A remained a mystery until the spate of discoveries in the past three years. Here, we focus on the discovery of m (6)A "readers" (proteins that specifically recognize m (6)A), and their functions in tuning mRNA stability, as well as the broader significance of such m (6)A-dependent regulation of gene expression.
View details for DOI 10.4161/rna.28829
View details for Web of Science ID 000341971700005
View details for PubMedID 24823649
A METTL3-METTL14 complex mediates mammalian nuclear RNA N-6-adenosine methylation
NATURE CHEMICAL BIOLOGY
2014; 10 (2): 93-95
N(6)-methyladenosine (m(6)A) is the most prevalent and reversible internal modification in mammalian messenger and noncoding RNAs. We report here that human methyltransferase-like 14 (METTL14) catalyzes m(6)A RNA methylation. Together with METTL3, the only previously known m(6)A methyltransferase, these two proteins form a stable heterodimer core complex of METTL3-METTL14 that functions in cellular m(6)A deposition on mammalian nuclear RNAs. WTAP, a mammalian splicing factor, can interact with this complex and affect this methylation.
View details for DOI 10.1038/NGHEMB10.1482
View details for Web of Science ID 000330751600005
View details for PubMedID 24316715
FTO-mediated formation of N-6-hydroxymethyladenosine and N-6-formyladenosine in mammalian RNA
N(6)-methyladenosine is a prevalent internal modification in messenger RNA and non-coding RNA affecting various cellular pathways. Here we report the discovery of two additional modifications, N(6)-hydroxymethyladenosine (hm(6)A) and N(6)-formyladenosine (f(6)A), in mammalian messenger RNA. We show that Fe(II)- and α-ketoglutarate-dependent fat mass and obesity-associated (FTO) protein oxidize N(6)-methyladenosine to generate N(6)-hydroxymethyladenosine as an intermediate modification, and N(6)-formyladenosine as a further oxidized product. N(6)-hydroxymethyladenosine and N(6)-formyladenosine have half-life times of ~3 h in aqueous solution under physiological relevant conditions, and are present in isolated messenger RNA from human cells as well as mouse tissues. These previously unknown modifications derived from the prevalent N(6)-methyladenosine in messenger RNA, formed through oxidative RNA demethylation, may dynamically modulate RNA-protein interactions to affect gene expression regulation.
View details for DOI 10.1038/ncomms2822
View details for Web of Science ID 000318872100155
View details for PubMedID 23653210
Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing
5-methylcytosine is an epigenetic mark that affects a broad range of biological functions in mammals. The chemically inert methyl group prevents direct labelling for subsequent affinity purification and detection. Therefore, most current approaches for the analysis of 5-methylcytosine still have limitations of being either density-biased, lacking in robustness and consistency, or incapable of analysing 5-methylcytosine specifically. Here we present an approach, TAmC-Seq, which selectively tags 5-methylcytosine with an azide functionality that can be further labelled with a biotin for affinity purification, detection and genome-wide mapping. Using this covalent labelling approach, we demonstrate high sensitivity and specificity for known methylated loci, as well as increased CpG dinucleotide coverage at lower sequencing depth as compared with antibody-based enrichment, providing an improved efficiency in the 5-methylcytosine enrichment and genome-wide profiling.
View details for DOI 10.1038/ncomms2527
View details for Web of Science ID 000316616400087
View details for PubMedID 23443545
Blockade of miR-150 Maturation by MLL-Fusion/MYC/LIN-28 Is Required for MLL-Associated Leukemia
2012; 22 (4): 524-535
Expression of microRNAs (miRNAs) is under stringent regulation at both transcriptional and posttranscriptional levels. Disturbance at either level could cause dysregulation of miRNAs. Here, we show that MLL fusion proteins negatively regulate production of miR-150, an miRNA widely repressed in acute leukemia, by blocking miR-150 precursors from being processed to mature miRNAs through MYC/LIN28 functional axis. Forced expression of miR-150 dramatically inhibited leukemic cell growth and delayed MLL-fusion-mediated leukemogenesis, likely through targeting FLT3 and MYB and thereby interfering with the HOXA9/MEIS1/FLT3/MYB signaling network, which in turn caused downregulation of MYC/LIN28. Collectively, we revealed a MLL-fusion/MYC/LIN28⊣miR-150⊣FLT3/MYB/HOXA9/MEIS1 signaling circuit underlying the pathogenesis of leukemia, where miR-150 functions as a pivotal gatekeeper and its repression is required for leukemogenesis.
View details for DOI 10.1016/j.ccr.2012.08.028
View details for Web of Science ID 000310113900012
View details for PubMedID 23079661
Surface Modification of Self-Assembled One-Dimensional Organic Structures: White-Light Emission and Beyond
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2010; 132 (45): 15872-15874
Surface modification is an important method to functionalize micro-/nanostructures, but substrates are mainly confined to robust inorganic compounds. We develop here a facile method to modify the surface of a fragile organic 1D microstructure. The bulk molecules and surface modifier were designed with orthogonal solubility to protect the molecular crystals from destruction under the reaction conditions. As a proof of concept, white-light-emitting 1D microstructures were obtained by grafting red chromophores onto the surface of self-assembled blue-emissive microwires via a heterophase S(N)2 reaction. Spatial distribution of the two species is visualized by fluorescent lifetime mapping, which reveals a core-shell structure. The ability to postfunctionalize organic 1D structures enables many applications, where the surface property plays key roles, such as an organic P-N junction and a biosensor.
View details for DOI 10.1021/ja106354m
View details for Web of Science ID 000284202200013
View details for PubMedID 20973475
- Structural-Property Relationship in Pyrazino[2,3-g]quinoxaline Derivatives: Morphology, Photophysical, and Waveguide Properties CHEMISTRY OF MATERIALS 2010; 22 (12): 3735-3745