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.

-acetyltransferase NAT10 controls cell fates via connecting mRNA cytidine acetylation to chromatin signaling.

Cell fate transition involves dynamic changes of gene regulatory network and chromatin landscape, requiring multiple levels of regulation, yet the cross-talk between epitranscriptomic modification and chromatin signaling remains largely unknown. Here, we uncover that suppression of -acetyltransferase 10 (NAT10), the writer for mRNA -acetylcytidine (acC) modification, can notably affect human embryonic stem cell (hESC) lineage differentiation and pluripotent reprogramming. With integrative analysis, we identify that NAT10-mediated acC modification regulates the protein levels of a subset of its targets, which are strongly enriched for fate-instructive chromatin regulators, and among them, histone chaperone ANP32B is experimentally verified and functionally relevant.

An RNA Methylation-Sensitive AIEgen-Aptamer Reporting System for Quantitatively Evaluating mA Methylase and Demethylase Activities.

-Methyladenosine (mA) chemical modification determines the fate of the mammalian cellular mRNA to modulate crucial physiological and pathological processes. Dysregulations of mA methylase and demethylase have been linked to cancer diseases. Therefore, evaluations of enzyme mutants' activities and related inhibitors for discovery of targeted therapeutic strategies are very necessary.

Construction and application of a new watermelon germplasm with the phenotype of dwarf and branchless.

Watermelon (Citrullus lanatus) is a widely cultivated cucurbitaceae crop appreciated by consumers worldwide. However, the long vine and abundant lateral branches of currently cultivated watermelon varieties hinder light simplification and mechanized cultivation, affecting plant spacing and row spacing requirements. To address this, the development of watermelon with dwarf and branchless traits has become a crucial direction for the industry.

aA-seq: -allyladenosine-based cellular messenger RNA metabolic labelling and sequencing.

The integration of RNA metabolic labelling by nucleoside analogues with high-throughput RNA sequencing has been harnessed to study RNA dynamics. The immunoprecipitation purification or chemical pulldown technique is generally required to enrich the analogue-labelled RNAs. Here we developed an aA-seq method, which takes advantage of allyladenosine (aA) metabolic labelling on cellular mRNAs and profiles them in an immunoprecipitation-free and mutation-based manner.

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.

N -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, N -allyldeoxycytidine (a dC), for labeling and identifying DNA by in vitro assays.

New Chromatin Run-On Reaction Enables Global Mapping of Active RNA Polymerase Locations in an Enrichment-free Manner.

The development of a simple and cost-effective method to map the distribution of RNA polymerase II (RNPII) genome-wide at a high resolution is highly beneficial to study cellular transcriptional activity. Here we report a mutation-based and enrichment-free global chromatin run-on sequencing (mGRO-seq) technique to locate active RNPII sites genome-wide at near-base resolution. An adenosine triphosphate (ATP) analog named -allyladenosine triphosphate (aATP) was designed and could be incorporated into nascent RNAs at RNPII-located positions during a chromatin run-on reaction.