Structure-guided discovery of highly efficient cytidine deaminases with sequence-context independence.

The applicability of cytosine base editors is hindered by their dependence on sequence context and by off-target effects. Here, by using AlphaFold2 to predict the three-dimensional structure of 1,483 cytidine deaminases and by experimentally characterizing representative deaminases (selected from each structural cluster after categorizing them via partitional clustering), we report the discovery of a few deaminases with high editing efficiencies, diverse editing windows and increased ratios of on-target to off-target effects. Specifically, several deaminases induced C-to-T conversions with comparable efficiency at AC/TC/CC/GC sites, the deaminases could introduce stop codons in single-copy and multi-copy genes in mammalian cells without double-strand breaks, and some residue conversions at predicted DNA-interacting sites reduced off-target effects. Structure-based generative machine learning could be further leveraged to expand the applicability of base editors in gene therapies.

A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues.

Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55-182 SEs (5-17% in total) and 99-309 BDs (8-16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.

Enhancing Lithium-Storage Performance via Graphdiyne/Graphene Interface by Self-Supporting Framework Synthesized.

The self-supporting graphdiyne/exfoliated graphene (GDY/EG) composites materials were prepared by the solvothermal method and applied as lithium-ion batteries (LIBs). Graphdiyne (GDY) is a new type of carbon allotrope with a natural macroporous structure, but its conductivity is poor. A small amount of highly conductive graphene can improve surface conductivity and facilitate electron transport. The layered GDY/graphene heterogeneous interface can reduce the electron aggregation polarization, enhance the ability to obtain electrons from the electrolyte, and form a more uniform solid-electrolyte interface (SEI) film. The structural performance and electrochemical performance have been systematically studied. The results showed that the GDY/EG composite electrode has a reversible capacity of 1253 mA h g-1 after 600 cycles at a current density of 0.5 A g-1. When the current density is 5 A g-1, the GDY/EG composite electrode can still maintain a reversible capacity of 324 mA h g-1 after 2000 cycles, and the electrode can still maintain a good morphology after recycling. GDY/EG has a high reversible capacity, excellent rate capability, and cycle stability. A small amount of EG and inner foam copper form a double-layer conductivity, which changes the storage method of lithium ions and facilitates the rapid diffusion of lithium ions.

SEIPIN overexpression in the liver may alleviate hepatic steatosis by influencing the intracellular calcium level.

SEIPIN deficiency leads to a severe lipodystrophic phenotype with loss of fat tissue. Interestingly, SEIPIN knockout in non-adipocytes is reported to promote intracellular triacylglycerol (TG) accumulation. However, the underlying mechanisms remain unclear at present. Here, we have shown that SEIPIN knockdown and overexpression exert opposite effects on hepatic lipometabolism. Our experimental data suggest that depletion of SEIPIN induces an increase in intracellular TG via activation of ER stress while its overexpression triggers a decrease in the intracellular TG content via increasing PGC-1α, which drives increased mitochondrial activity. Adeno-associated virus-mediated SEIPIN overexpression alleviated high fat diet-induced hepatosteatosis in mice. The collective results indicate that the effects of SEIPIN on TG and PGC-1α are dependent on calcium concentrations, signifying regulatory activity on hepatic lipometabolism through alterations in the intracellular calcium level, and support the potential utility of modulating intracellular SEIPIN and calcium levels as novel therapeutic strategies for fatty liver.

Fluorinated graphdiyne as a significantly enhanced fluorescence material.

The chemical modification of graphdiyne (GDY) using light elements is a possible route to regulate its unique structure and optoelectronic properties. In this paper it is shown that directly heating a mixture of xenon difluoride and GDY produces partially fluorinated GDY with covalent C-F bonding and localized sp2-carbon hybridization because of the breaking of the acetylenic bond. It is seen that the fluorescence of GDY is significantly enhanced because of the fluorine doping. All the fluorinated GDYs with different doping ratios of fluorine exhibit photoluminescence from bright blue to green when the excitation wavelength varies from 260 nm to 480 nm. In addition, the doped GDY with 15.2% fluorine doping shows a strong photoluminescence and the quantum efficiency is 3.7%. The enhanced fluorescence is considered to be induced by defect states because of the doping of fluorine, suggesting its potential applications in luminescence devices, such as biological sensing and flexible light-emitting diodes.

Top-down strategy synthesis of fluorinated graphdiyne for lithium ion battery.

As a novel carbon allotrope, graphdiyne exhibits excellent electrochemical properties such as high specific capacities, outstanding rate performances, and long cycle lives. These properties are attributed to its sp- and sp2-hybridized bonding and a natural large pore structure. Doping with light elements is a facile way to improve the electrochemical performance of graphdiyne. Herein, we report the preparation of fluorine-doped graphdiyne by exposure to XeF2 under a mild temperature. Compared to pristine graphdiyne, the capacities are doubled. We obtained reversible capacities of fluorinated graphdiyne up to 1080 mA h g-1 after 600 cycles at a current density of 500 mA g-1. At a higher current density of 1000 mA g-1, it still retained a high specific capacity of 693 mA h g-1 after 1000 cycles. Using in situ quantitative nanomechanical probe atomic force microscopy, we further analyzed the surface morphologies and elastic modulus to understand the mechanism of the electrochemical improvement. The fluorinated graphdiyne elastic modulus is doubled in contrast to pristine graphdiyne. The performance improvements are attributed to the improvement in conductivity and enhancement of the mechanical properties.

FTO reduces mitochondria and promotes hepatic fat accumulation through RNA demethylation.

Fat mass and obesity-associated protein (FTO) is a RNA demethylase, whether FTO regulates fat metabolism through its demethylation is unclear. The results of this study confirmed that N6-methyladenosine (m6 A) is associated with fat accumulation both in vivo and in vitro. The data showed that FTO down-regulated m6 A levels, decreased mitochondrial content, and increased triglyceride (TG) deposition. However, an FTO (R316A) mutant lacking demethylation activity could not regulate mitochondria and TG content, indicating that FTO affects mitochondrial content and fat metabolism by modulating m6 A levels in hepatocytes. In addition, the regulatory roles of cycloleucine (methylation inhibitor) and betaine (methyl donor) could regulate m6 A levels and fat deposition. This work clarified that the demethylation function of FTO plays an essential role in the fat metabolism of hepatocytes and links the epigenetic modification of RNA with fat deposition, thereby providing a new target (m6 A) for regulation of hepatic fat metabolism.

Cidec differentially regulates lipid deposition and secretion through two tissue-specific isoforms.

Lipid metabolism has important roles in animal growth, development, and reproduction. As a regulator of lipid metabolism, CIDEc promotes unilocular development of lipid droplets and stimulates intracellular lipid deposition, and has two isoforms, CIDEc-l and CIDEc-s. CIDEc-l has ten more N-terminal amino acids than CIDEc-s. However, the functions of two isoforms are largely unknown. In this study, the expression profiles of two isoforms in Bama pigs differed, with cidec-l dominant in the liver and small intestine, and cidec-s dominant in muscle and adipose tissue. Fasting and consuming a high-fat diet resulted in changes in the expression of the two isoforms that were closely related to changes in blood and muscle triglyceride (TG) concentrations. Comparison of gene expression and TG concentration suggested that CIDEc-l accelerated lipid secretion and that CIDEc-s promoted lipid deposition, implying that the two isoforms had different functions. Study In vitro confirmed that CIDEc-s stimulated lipid deposition in C2C12 muscle cells and CIDEc-l promoted lipid secretion in HepG2 liver cells. The results showed that two tissue-specific CIDEc isoforms had different roles in lipid deposition and secretion. They may be potential targets for regulation of fat content.

Transcriptomic analysis of Bama pig's liver in various nutritional states reveals a metabolic difference of fatty acids.

Both fasting and treatment with a high-fat diet (HFD) can dramatically change fat metabolism in the liver and, thus, are commonly used methods to investigate hepatic fat metabolism and related diseases. Here, the gene expression profiles of pig liver under both conditions were investigated and changes in hepatic triacylglycerol (TG) levels under different diet conditions were determined. In this study, both fasting and HFD conditions significantly increased hepatic TG levels and serum levels of cholesterol, TG, high-density lipoprotein, low-density lipoprotein, and apolipoprotein B. Transcriptome sequencing analysis identified 580 differentially expressed genes (DEGs) between the fasting group and the control group (F/C group) and 613 between the HFD group and the control group (H/C group). Kyoto Encyclopedia of Genes and Genomes enrichment analysis found that the DEGs of the F/C group were mainly enriched in the synthesis pathways of fatty acids (FAs) with less than 16 carbons, while the DEGs of the H/C group were mainly enriched in the synthesis pathways of FAs with more than 16 carbons. In order to verify whether changes in the expression levels of the DEGs caused changes in FA metabolism, the composition and saturation of the FAs in liver TG were analyzed, which showed that under fasting conditions, the contents of monounsaturated and polyunsaturated FAs had increased, while the proportion of saturated FAs had decreased. However, the content of polyunsaturated FAs decreased, while the contents of monounsaturated and saturated FAs increased under HFD conditions. These results will help clarify the differences in FA metabolism in the liver under different nutritional states and indicate that the proportion of unsaturated FAs had increased in hepatic fat under fasting conditions.