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The human AlkB family proteins, such as FTO and ALKBH5, are known to mediate RNA m6A demethylation. However, although ALKBH7 localizes in mitochondria and affects metabolism, the detailed biological function and mechanism have remained unknown for years. We developed Demethylation-Assisted Multiple Methylation sequencing (DAMM-seq) to simultaneously detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) methylations in both steady-state RNA and nascent RNA, and discovered that human ALKBH7 demethylates m22G and m1A within mt-Ile and mt-Leu1 pre-tRNA regions, respectively, in mitochondrial polycistronic RNA. DAMM-seq quantitatively and sensitively monitors the methylation stoichiometry change at pre-tRNA junctions within nascent mt-RNA, revealing the target region where ALKBH7 regulates RNA processing and local structural switch of polycistronic mt-RNAs. A new RNA demethylase in human cells was characterized through the base-resolution quantification of multiple RNA methylations in nascent mt-RNA, resolving the long-standing question about the functional substrate of ALKBH7.

Subgraph representation learning based on Graph Neural Network (GNN) has exhibited broad applications in scientific advancements, such as predictions of molecular structure-property relationships and collective cellular function. In particular, graph augmentation techniques have shown promising results in improving graph-based and node-based classification tasks. Still, they have rarely been explored in the existing GNN-based subgraph representation learning studies. In this study, we develop a novel multi-view augmentation mechanism to improve subgraph representation learning models and thus the accuracy of downstream prediction tasks. Our augmentation technique creates multiple variants of subgraphs and embeds these variants into the original graph to achieve highly improved training efficiency, scalability, and accuracy. Benchmark experiments on several real-world biological and physiological datasets demonstrate the superiority of our proposed multi-view augmentation techniques in subgraph representation learning.

Methods for the precise detection and quantifica-tion of RNA modifications are critical to uncover functional roles of diverse RNA modifications. The internal m7G modification in mammalian cytoplasmic tRNAs is known to affect tRNA function and impact embryonic stem cell self-renewal, tumorigenesis, cancer progression, and other cellular processes. Here, we introduce m7G-quant-seq, a quantitative method that accurately detects internal m7G sites in human cytoplasmic tRNAs at single-base resolution. The efficient chemical reduction and mild depurination can almost completely convert internal m7G sites into RNA abasic sites (AP sites). We demonstrate that RNA abasic sites induce a mixed variation pattern during reverse transcription, including G -> A or C or T mutations as well as deletions. We calculated the total variation ratio to quantify the m7G modification fraction at each methylated site. The calibration curves of all relevant motif contexts allow us to more quantitatively determine the m7G methylation level. We detected internal m7G sites in 22 human cytoplasmic tRNAs from HeLa and HEK293T cells and successfully estimated the corresponding m7G methylation stoichiometry. m7G-quant-seq could be applied to monitor the tRNA m7G methylation level change in diverse biological processes.

pi-Extended helicenes constitute an important class of polycyclic aromatic hydrocarbons with intrinsic chirality. Herein, we report the syntheses of pi-extended [7]helicene 4 and pi-extended [9]helicene 6 through regioselective cyclodehydrogenation in high yields, where a prefusion strategy plays a key role in preventing undesirable aryl rearrangements. The unique helical structures are unambiguously confirmed by X-ray crystal structure analysis. Compared to the parent pristine [7]helicene and [9]helicene, these novel pi-extended helicenes display significantly improved photophysical properties, with a quantum yield of 0.41 for 6. After optical resolution by chiral high-performance liquid chromatography, the chiroptical properties of enantiomers 4-P/M and 6-P/M are investigated, revealing that the small variation in helical length from [7] to [9] can cause an approximately 10-fold increase in the dissymmetry factors. The circularly polarized luminescence brightness of 6 reaches 12.6 M-1 cm(-1) as one of the highest among carbohelicenes.

pi-Extended helicenes constitute an important class of polycyclic aromatic hydrocarbons with intrinsic chirality. Herein, we report the syntheses of pi-extended [7]helicene 4 and pi-extended [9]helicene 6 through regioselective cyclodehydrogenation in high yields, where a prefusion strategy plays a key role in preventing undesirable aryl rearrangements. The unique helical structures are unambiguously confirmed by X-ray crystal structure analysis. Compared to the parent pristine [7]helicene and [9]helicene, these novel pi-extended helicenes display significantly improved photophysical properties, with a quantum yield of 0.41 for 6. After optical resolution by chiral high-performance liquid chromatography, the chiroptical properties of enantiomers 4-P/M and 6-P/M are investigated, revealing that the small variation in helical length from [7] to [9] can cause an approximately 10-fold increase in the dissymmetry factors. The circularly polarized luminescence brightness of 6 reaches 12.6 M-1 cm(-1) as one of the highest among carbohelicenes.

Negatively curved nanographene (NG) 4, having two heptagons and a [5]helicene, was unexpectedly obtained by aryl rearrangement and stepwise cyclodehydrogenations. X-ray crystallography confirmed the saddle-shaped structures of intermediate 3 and NG 4. The favorability of rearrangement over helicene formation following radical cation or arenium cation mechanisms is supported by theoretical calculations. NG 4 demonstrates a reversible mechanochromic color change and solid-state emission, presumably benefiting from its loose crystal packing. After resolution by chiral high-perfomance liquid chromatography, the circular dichroism spectra of enantiomers 4-(P) and 4-(M) were measured and showed moderate Cotton effects at 350 nm (vertical bar Delta epsilon vertical bar = 148 M-1 cm(-1)).

Negatively curved nanographene (NG) 4, having two heptagons and a [5]helicene, was unexpectedly obtained by aryl rearrangement and stepwise cyclodehydrogenations. X-ray crystallography confirmed the saddle-shaped structures of intermediate 3 and NG 4. The favorability of rearrangement over helicene formation following radical cation or arenium cation mechanisms is supported by theoretical calculations. NG 4 demonstrates a reversible mechanochromic color change and solid-state emission, presumably benefiting from its loose crystal packing. After resolution by chiral high-perfomance liquid chromatography, the circular dichroism spectra of enantiomers 4-(P) and 4-(M) were measured and showed moderate Cotton effects at 350 nm (vertical bar Delta epsilon vertical bar = 148 M-1 cm(-1)).