N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas.

N(6)-methyldeoxyadenosine (6mA or m(6)A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here, we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms.

DNA Methylation on N6-Adenine in C. elegans.

In mammalian cells, DNA methylation on the fifth position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC, as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N(6)-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylations of histone H3K4 and adenines and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes.

N6-methyladenine DNA modification in Drosophila.

DNA N(6)-methyladenine (6mA) modification is commonly found in microbial genomes and plays important functions in regulating numerous biological processes in bacteria. However, whether 6mA occurs and what its potential roles are in higher-eukaryote cells remain unknown. Here, we show that 6mA is present in Drosophila genome and that the 6mA modification is dynamic and is regulated by the Drosophila Tet homolog, DNA 6mA demethylase (DMAD), during embryogenesis. Importantly, our biochemical assays demonstrate that DMAD directly catalyzes 6mA demethylation in vitro. Further genetic and sequencing analyses reveal that DMAD is essential for development and that DMAD removes 6mA primarily from transposon regions, which correlates with transposon suppression in Drosophila ovary. Collectively, we uncover a DNA modification in Drosophila and describe a potential role of the DMAD-6mA regulatory axis in controlling development in higher eukaryotes.

N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA.

N6-Methyldeoxyadenosine (6mA) has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA (gDNA). However, the biological functions of 6mA in mammals have yet to be adequately explored, largely due to its low abundance in most mammalian genomes. Here, we report that mammalian mitochondrial DNA (mtDNA) is enriched for 6mA. The level of 6mA in HepG2 mtDNA is at least 1,300-fold higher than that in gDNA under normal growth conditions, corresponding to approximately four 6mA modifications on each mtDNA molecule. METTL4, a putative mammalian methyltransferase, can mediate mtDNA 6mA methylation, which contributes to attenuated mtDNA transcription and a reduced mtDNA copy number. Mechanistically, the presence of 6mA could repress DNA binding and bending by mitochondrial transcription factor (TFAM). Under hypoxia, the 6mA level in mtDNA could be further elevated, suggesting regulatory roles for 6mA in mitochondrial stress response. Our study reveals DNA 6mA as a regulatory mark in mammalian mtDNA.

The m6A reader SlYTH2 negatively regulates tomato fruit aroma by impeding the translation process.

N6-methyladenosine (m6A) is a fundamentally important RNA modification for gene regulation, whose function is achieved through m6A readers. However, whether and how m6A readers play regulatory roles during fruit ripening and quality formation remains unclear. Here, we characterized SlYTH2 as a tomato m6A reader protein and profiled the binding sites of SlYTH2 at the transcriptome-wide level. SlYTH2 undergoes liquid-liquid phase separation and promotes RNA-protein condensate formation. The target mRNAs of SlYTH2, namely m6A-modified SlHPL and SlCCD1B associated with volatile synthesis, are enriched in SlYTH2-induced condensates. Through polysome profiling assays and proteomic analysis, we demonstrate that knockout of SlYTH2 expedites the translation process of SlHPL and SlCCD1B, resulting in augmented production of aroma-associated volatiles. This aroma enrichment significantly increased consumer preferences for CRISPR-edited fruit over wild type. These findings shed light on the underlying mechanisms of m6A in plant RNA metabolism and provided a promising strategy to generate fruits that are more attractive to consumers.

Chemical and Enzyme-Mediated Chemical Reactions for Studying Nucleic Acids and Their Modifications.

Nucleic acids are genetic information-carrying molecules inside cells. Apart from basic nucleotide building blocks, there exist various naturally occurring chemical modifications on nucleobase and ribose moieties, which greatly increase the encoding complexity of nuclei acids, contribute to the alteration of nucleic acid structures, and play versatile regulation roles in gene expression. To study the functions of certain nucleic acids in various biological contexts, robust tools to specifically label and identify these macromolecules and their modifications, and to illuminate their structures are highly necessary. In this review, we summarize recent technique advances of using chemical and enzyme-mediated chemical reactions to study nucleic acids and their modifications and structures. By highlighting the chemical principles of these techniques, we aim to present a perspective on the advancement of the field as well as to offer insights into developing specific chemical reactions and precise enzyme catalysis utilized for nucleic acids and their modifications.

SUMOylation regulates pre-mRNA splicing to overcome DNA damage in fungi.

Pathogenic fungi are subject to DNA damage stress derived from host immune responses during infection. Small ubiquitin-like modifier (SUMO) modification and precursor (pre)-mRNA splicing are both involved in DNA damage response (DDR). However, the mechanisms of how SUMOylation and splicing coordinated in DDR remain largely unknown. Combining with biochemical analysis, RNA-Seq method, and biological analysis, we report that SUMO pathway participates in DDR and virulence in Fusarium graminearum, a causal agent of Fusarium head blight of cereal crops world-wide. Interestingly, a key transcription factor FgSR is SUMOylated upon DNA damage stress. SUMOylation regulates FgSR nuclear-cytoplasmic partitioning and its phosphorylation by FgMec1, and promotes its interaction with chromatin remodeling complex SWI/SNF for activating the expression of DDR-related genes. Moreover, the SWI/SNF complex was found to further recruit splicing-related NineTeen Complex, subsequently modulates pre-mRNA splicing during DDR. Our findings reveal a novel function of SUMOylation in DDR by regulating a transcription factor to orchestrate gene expression and pre-mRNA splicing to overcome DNA damage during the infection of F. graminearum, which advances the understanding of the delicate regulation of DDR by SUMOylation in pathogenic fungi, and extends the knowledge of cooperation of SUMOylation and pre-mRNA splicing in DDR in eukaryotes.

RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation.

N(6)-methyladenosine (m(6)A) is the most prevalent and internal modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, although its functional relevance remained a mystery for decades. This modification is installed by the m(6)A methylation "writers" and can be reversed by demethylases that serve as "erasers." In this review, we mainly summarize recent progress in the study of the m(6)A mRNA methylation machineries across eukaryotes and discuss their newly uncovered biological functions. The broad roles of m(6)A in regulating cell fates and embryonic development highlight the existence of another layer of epigenetic regulation at the RNA level, where mRNA is subjected to chemical modifications that affect protein expression.

Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle.

The natural chemical modifications of messenger RNA (mRNA) in living organisms have shown essential roles in both physiology and pathology. The mapping of mRNA modifications is critical for interpreting their biological functions. In another dimension, the synthesized nucleoside analogs can enable chemical labeling of cellular mRNA through a metabolic pathway, which facilitates the study of RNA dynamics in a pulse-chase manner. In this regard, the sequencing tools for mapping both natural modifications and nucleoside tags on mRNA at single base resolution are highly necessary. In this work, we review the progress of chemical sequencing technology for determining both a variety of naturally occurring base modifications mainly on mRNA and a few on transfer RNA and metabolically incorporated artificial base analogs on mRNA, and further discuss the problems and prospects in the field.

N4 -Allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Markers, and In Situ Imaging.

DNA tagging with base analogues has found numerous applications. To precisely record the DNA labelling information, it would be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases following a mild, efficient and bioorthogonal chemical treatment. Here we reported such a DNA tag, N4 -allyldeoxycytidine (a4 dC), for labeling and identifying DNA by in vitro assays. The iodination of a4 dC led to fast and complete formation of 3, N4 -cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4 dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic marker N4 -methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4 dC. Our study sheds light on the design of next generation DNA tags with chemical sequencing power.

Resonant energy transfer between rare earth atomic layers in nanolaminate films.

Förster resonant energy transfer between atoms separated at a distance of a few nanometers has strong relevance to different properties of matter. In this work, the resonant energy transfer rate is derived from the electric potential in a system with one dipole interacting with a separated 2D plane of dipoles. It shows an R-2 (R: distance between dipole and 2D plane of dipoles) dependency on the distance of dipole layers, which is different from previous theoretical evaluations with an R-4 dependency. The electroluminescence (EL) properties are studied in different rare earth (Re: Tm, Tb, Ho, Yb, Er) distributed single atomic layer doped Al2O3 nanolaminates prepared by atomic layer deposition, in which the distance between single atomic layers of Re3+ is modulated at the atomic scale. Our theoretical results are consistent with the changes of EL intensity and decay time with the distance between the single atomic rare earth doping layers. This result is crucial for increasing the accuracy in biosensing and design of photonic materials.

A metabolic labeling method detects m6A transcriptome-wide at single base resolution.

Transcriptome-wide mapping of N6-methyladenosine (m6A) at base resolution remains an issue, impeding our understanding of m6A roles at the nucleotide level. Here, we report a metabolic labeling method to detect mRNA m6A transcriptome-wide at base resolution, called 'm6A-label-seq'. Human and mouse cells could be fed with a methionine analog, Se-allyl-L-selenohomocysteine, which substitutes the methyl group on the enzyme cofactor SAM with the allyl. Cellular RNAs could therefore be metabolically modified with N6-allyladenosine (a6A) at supposed m6A-generating adenosine sites. We pinpointed the mRNA a6A locations based on iodination-induced misincorporation at the opposite site in complementary DNA during reverse transcription. We identified a few thousand mRNA m6A sites in human HeLa, HEK293T and mouse H2.35 cells, carried out a parallel comparison of m6A-label-seq with available m6A sequencing methods, and validated selected sites by an orthogonal method. This method offers advantages in detecting clustered m6A sites and holds promise to locate nuclear nascent RNA m6A modifications.

A Mutation-Based Method for Pinpointing a DNA N6 -Methyladenine Methyltransferase Modification Site at Single Base Resolution.

DNA N6 -methyladenine (6mA) has recently received notable attention due to an increased finding of its functional roles in higher eukaryotes. Here we report an enzyme-assisted chemical labeling method to pinpoint the DNA 6mA methyltransferase (MTase) substrate modification site at single base resolution. A designed allyl-substituted MTase cofactor was applied in the catalytic transfer reaction, and the allyl group was installed to the N6 -position of adenine within a specific DNA sequence to form N6 -allyladenine (6aA). The iodination of 6aA allyl group induced the formation of 1, N6 -cyclized adenine which caused mutations during DNA replication by a polymerase. Thus the modification site could be precisely detected by a mutation signal. We synthesized 6aA deoxynucleoside and deoxynucleotide model compounds and a 6aA-containing DNA probe, and screened nine DNA polymerases to define an optimal system capable of detecting the substrate modification site of a DNA 6mA MTase at single-base resolution.

Electroluminescent Y3Al5O12 nanofilms fabricated by atomic layer deposition on silicon: using Yb as the luminescent dopant and crystallization impetus.

Silicon-based Yb-doped Y3Al5O12 garnet nanofilms are fabricated by atomic layer deposition, which are polycrystalline after annealing at 1150 °C. The sub-nanometer compositional regulation and the Yb2O3 cladding layers, which also work as the luminescent dopants, are critical for the crystallization. Characteristic Yb3+ luminescence at 1030 nm and 970 nm is identified under electrical injection, exhibiting the external quantum efficiency of 0.65% and the fluorescence lifetime of 80-200 µs. The doped Yb3+ are impact-excited by hot electrons stemming from Fowler-Nordheim tunneling mechanism within the Y3Al5O12 matrix, with the excitation cross section of 0.7×10-15 to 6.4×10-15 cm2. This work certifies the manipulation of multi-oxide nanofilms with designed composition and crystallinity, revealing the possibility of developing Si-based optoelectronic devices from crystalline garnet films.

Specific Targeting, Imaging, and Ablation of Tumor-Associated Macrophages by Theranostic Mannose-AIEgen Conjugates.

Tumor-associated macrophages (TAMs) that exist in tumor microenvironment promote tumor progression and have been suggested as a promising therapeutic target for cancer therapy in preclinical studies. Development of theranostic systems capable of specific targeting, imaging, and ablation of TAMs will offer clinical benefits. Here we constructed a theranostic probe, namely, TPE-Man, by attaching mannose moieties to a red-emissive and AIE (aggregation-induced emission)-active photosensitizer. TPE-Man can specifically recognize a mannose receptor that is overexpressed on TAMs by the sugar-receptor interaction and enables fluorescent visualization of the mannose-receptor-positive TAMs in high contrast. The histologic study of mouse tumor sections further verifies TPE-Man's excellent targeting specificity being comparable with the commercial mannose-receptor antibody. TAMs can be effectively eradicated upon exposure to white light irradiation via a photodynamic therapy effect. To our knowledge, this is the first small molecular theranostic probe for TAMs that revealed combined advantages of low cost, high targeting specificity, fluorescent light-up imaging, and efficient photodynamic ablation.

Electrostatic Self-Assembly Enabling Integrated Bulk and Interfacial Sodium Storage in 3D Titania-Graphene Hybrid.

Room-temperature sodium-ion batteries have attracted increased attention for energy storage due to the natural abundance of sodium. However, it remains a huge challenge to develop versatile electrode materials with favorable properties, which requires smart structure design and good mechanistic understanding. Herein, we reported a general and scalable approach to synthesize three-dimensional (3D) titania-graphene hybrid via electrostatic-interaction-induced self-assembly. Synchrotron X-ray probe, transmission electron microscopy, and computational modeling revealed that the strong interaction between titania and graphene through comparably strong van der Waals forces not only facilitates bulk Na+ intercalation but also enhances the interfacial sodium storage. As a result, the titania-graphene hybrid exhibits exceptional long-term cycle stability up to 5000 cycles, and ultrahigh rate capability up to 20 C for sodium storage. Furthermore, density function theory calculation indicated that the interfacial Li+, K+, Mg2+, and Al3+ storage can be enhanced as well. The proposed general strategy opens up new avenues to create versatile materials for advanced battery systems.

N6-Allyladenosine: A New Small Molecule for RNA Labeling Identified by Mutation Assay.

RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N6-allyladenosine (a6A) as a new small molecule for RNA labeling through both metabolic and enzyme-assisted manners. a6A behaves like A and can be metabolically incorporated into newly synthesized RNAs inside mammalian cells. We also show that human RNA N6-methyladenosine (m6A) methyltransferases METTL3/METTL14 can work with a synthetic cofactor, namely allyl-SAM (S-adenosyl methionine with methyl replaced by allyl) in order to site-specifically install an allyl group to the N6-position of A within specific sequence to generate a6A-labeled RNAs. The iodination of N6-allyl group of a6A under mild buffer conditions spontaneously induces the formation of N1,N6-cyclized adenosine and creates mutations at its opposite site during complementary DNA synthesis of reverse transcription. The existing m6A in RNA is inert to methyltransferase-assisted allyl labeling, which offers a chance to differentiate m6A from A at individual RNA sites. Our work demonstrates a new method for RNA labeling, which could find applications in developing sequencing methods for nascent RNAs and RNA modifications.

A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation.

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.

An Efficient, Regioselective Pathway to Cationic and Zwitterionic N-Heterocyclic Cellulose Ionomers.

Cationic derivatives of cellulose and other polysaccharides are attractive targets for biomedical applications due to their propensity for electrostatically binding with anionic biomolecules, such as nucleic acids and certain proteins. To date, however, relatively few practical synthetic methods have been described for their preparation. Herein, we report a useful and efficient strategy for cationic cellulose ester salt preparation by the reaction of 6-bromo-6-deoxycellulose acetate with pyridine or 1-methylimidazole. Dimethyl sulfoxide solvent favored this displacement reaction to produce cationic cellulose acetate derivatives, resulting in high degrees of substitution (DS) exclusively at the C-6 position. These cationic cellulose derivatives bearing substantial, permanent positive charge exhibit surprising thermal stability, dissolve readily in water, and bind strongly with a hydrophilic and anionic surface, supporting their potential for a variety of applications such as permeation enhancement, mucoadhesion, and gene or drug delivery. Expanding upon this chemistry, we reacted a 6-imidazolyl-6-deoxycellulose derivative with 1,3-propane sultone to demonstrate the potential for further elaboration to regioselectively substituted zwitterionic cellulose derivatives.

Polyphenylsilole multilayers--an insight from X-ray electron spectroscopy and density functional theory.

We present a combined investigation by means of X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy of condensed multilayers of two polyphenylsiloles, namely hexaphenylsilole (HPS) and tetraphenylsilole (TPS). Both compounds exhibit very similar spectroscopic signatures, whose interpretation is aided by density functional theory (DFT) calculations. High-resolution XPS spectra of the Si 2p and C 1s core levels of these multilayers indicate a positively charged silicon ion flanked by two negatively charged adjacent carbon atoms in the silole core of both molecules. This result is corroborated quantitatively by DFT calculations on isolated HPS (TPS) molecules, which show a natural bond orbital partial charge of +1.67 e (+1.58 e) on the silicon and -0.34 e (-0.58 e) on the two neighbouring carbon atoms in the silole ring. These charges are conserved in direct contact with a Cu(111) substrate for films of submonolayer coverage, as evidenced by the Si 2p XPS data. The C K-edge NEXAFS spectra of HPS and TPS multilayers exhibit distinct and differing features. Their main characteristics reappear in the simulated spectra and are assigned to the different inequivalent carbon species in the molecule. The angle-dependent measurements hardly reveal any dichroism, i.e., the molecular π-systems are not uniformly oriented parallel or perpendicular with respect to the surface. Changes in the growth conditions of TPS, i.e., a reduction of the substrate temperature from 240 K to 80 K during deposition, lead to a broadening of both XPS and NEXAFS signatures, as well as an upward shift of the Si 2p and C 1s binding energies, indicative of a less ordered growth mode at low temperature.