Single-cell and spatial transcriptomic investigation reveals the spatiotemporal specificity of the beta-defensin gene family during mouse sperm maturation.

Low sperm motility is a significant contributor to male infertility. beta-defensins have been implicated in host defence and the acquisition of sperm motility; however, the regulatory mechanisms governing their gene expression patterns and functions remain poorly understood. In this study, we performed single-cell RNA and spatial transcriptome sequencing to investigate the cellular composition of testicular and epididymal tissues and examined their gene expression characteristics. In the epididymis, we found that epididymal epithelial cells display a region specificity of gene expression in different epididymal segments, including the beta-defensin family genes. In particular, Defb15, Defb18, Defb20, Defb25 and Defb48 are specific to the caput; Defb22, Defb23 and Defb26 to the corpus; Defb2 and Defb9 to the cauda of the epididymis. To confirm this, we performed mRNA fluorescence in situ hybridisation (FISH) targeting certain exon region of beta-defensin genes, and found some of their expression matched the sequencing results and displayed a close connection with epididimosome marker gene Cd63. In addition, we paid attention to the Sertoli cells and Leydig cells in the testis, along with fibroblasts and smooth muscle cells in the epididymis, by demonstrating their gene expression profile and spatial information. Our study provides a single-cell and spatial landscape for analysing the gene expression characteristics of testicular and epididymal environments and has important implications for the study of spermatogenesis and sperm maturation.

The landscape of the long non-coding RNAs in developing mouse retinas.

BACKGROUND: The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available. RESULTS: Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways. CONCLUSIONS: In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.

Exploring the Spatiotemporal Evolution and Socioeconomic Determinants of PM2.5 Distribution and Its Hierarchical Management Policies in 366 Chinese Cities.

From 2013 to 2017, progress has been made by implementing the Air Pollution Prevention and Control Action Plan. Under the background of the 3 Year Action Plan to Fight Air Pollution (2018-2020), the pollution status of PM2.5, a typical air pollutant, has been the focus of continuous attention. The spatiotemporal specificity of PM2.5 pollution in the Chinese urban atmospheric environment from 2018 to 2020 can be summarized to help conclude and evaluate the phased results of the battle against air pollution, and further, contemplate the governance measures during the period of the 14th Five-Year Plan (2021-2025). Based on PM2.5 data from 2018 to 2020 and taking 366 cities across China as research objects, this study found that PM2.5 pollution has improved year by year from 2018 to 2020, and that the heavily polluted areas were southwest Xinjiang and North China. The number of cities with a PM2.5 concentration in the range of 25-35 µg/m3 increased from 34 in 2018 to 86 in 2019 and 99 in 2020. Moreover, the spatial variation of the PM2.5 gravity center was not significant. Concretely, PM2.5 pollution in 2018 was more serious in the first and fourth quarters, and the shift of the pollution's gravity center from the first quarter to the fourth quarter was small. Global autocorrelation indicated that the space was positively correlated and had strong spatial aggregation. Local Moran's I and Local Geti's G were applied to identify hotspots with a high degree of aggregation. Integrating national population density, hotspots were classified into four areas: the Beijing-Tianjin-Hebei region, the Fenwei Plain, the Yangtze River Delta, and the surrounding areas were selected as the key hotspots for further geographic weighted regression analysis in 2018. The influence degree of each factor on the average annual PM2.5 concentration declined in the following order: (1) the proportion of secondary industry in the GDP, (2) the ownership of civilian vehicles, (3) the annual grain planting area, (4) the annual average population, (5) the urban construction land area, (6) the green space area, and (7) the per capita GDP. Finally, combined with the spatiotemporal distribution of PM2.5, specific suggestions were provided for the classified key hotspots (Areas A, B, and C), to provide preliminary ideas and countermeasures for PM2.5 control in deep-water areas in the 14th Five-Year Plan.

Near-infrared optogenetic engineering of photothermal nanoCRISPR for programmable genome editing.

We herein report an optogenetically activatable CRISPR-Cas9 nanosystem for programmable genome editing in the second near-infrared (NIR-II) optical window. The nanosystem, termed nanoCRISPR, is composed of a cationic polymer-coated Au nanorod (APC) and Cas9 plasmid driven by a heat-inducible promoter. The APC not only serves as a carrier for intracellular plasmid delivery but also can harvest external NIR-II photonic energy and convert it into local heat to induce the gene expression of the Cas9 endonuclease. Due to high transfection activity, the APC shows strong ability to induce a significant level of disruption in different genomic loci upon optogenetic activation. Moreover, the precise control of genome-editing activity can be simply programmed by finely tuning exposure time and irradiation time in vitro and in vivo and also enables editing at multiple time points, thus proving the sensitivity and inducibility of such an editing modality. The NIR-II optical feature of nanoCRISPR enables therapeutic genome editing at deep tissue, by which treatment of deep tumor and rescue of fulminant hepatic failure are demonstrated as proof-of-concept therapeutic examples. Importantly, this modality of optogenetic genome editing can significantly minimize the off-target effect of CRISPR-Cas9 in most potential off-target sites. The optogenetically activatable CRISPR-Cas9 nanosystem we have developed offers a useful tool to expand the current applications of CRISPR-Cas9, and also defines a programmable genome-editing strategy toward high precision and spatial specificity.

Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes.

BACKGROUND: Chinese cordyceps, also known as Chinese caterpillar fungus (Ophiocordyceps sinensis, syn. Cordyceps sinensis), is of particular interest for its cryptic life cycle and economic and ecological importance. The large-scale artificial cultivation was succeeded recently after several decades of efforts and attempts. However, the induction of primordium, sexual development of O. sinensis and the molecular basis of its lifestyle still remain cryptic. RESULTS: The developmental transcriptomes were analyzed for six stages covering the whole developmental process, including hyphae (HY), sclerotium (ST), primordium (PR), young fruiting body (YF), developed fruiting body (DF) and mature fruiting body (MF), with a focus on the expression of sexual development-related genes. Principal component analysis revealed that the gene expression profiles at the stages of primordium formation and fruiting body development are more similar than those of the undifferentiated HY stage. The PR and MF stages grouped together, suggesting that primordium differentiation and sexual maturation have similar expression patterns. Many more DEGs were identified between the ST and HY stages, covering 47.5% of the O. sinensis genome, followed by the comparisons between the ST and PR stages. Using pairwise comparisons and weighted gene coexpression network analysis, modules of coexpressed genes and candidate hub genes for each developmental stage were identified. The four mating type loci genes expressed during primordium differentiation and sexual maturation; however, spatiotemporal specificity of gene expression indicated that they also expressed during the anamorphic HY stage. The four mating type genes were not coordinately expressed, suggesting they may have divergent roles. The expression of the four mating type genes was highest in the fertile part and lowest in the sclerotium of the MF stage, indicating that there is tissue specificity. Half of genes related to mating signaling showed as the highest expression in the ST stage, indicating fruiting was initiated in the ST stage. CONCLUSIONS: These results provide a new perspective to understanding of the key pathways and hub genes, and sexual development-related gene profile in the development of Chinese cordyceps. It will be helpful for underlying sexual reproduction, and add new information to existing models of fruiting body development in edible fungi.

Spatiotemporal aspect of cytokinin-auxin interaction in hormonal regulation of the root meristem.

Hormonal regulation of root development is a long known phenomenon. In the past decades, the molecular mechanisms of individual hormonal pathways and their impact on root development have been studied. Recent genetic and molecular studies suggest importance of interactions of the individual hormonal pathways and their components. In our paper we show impact of endogenous cytokinin on the root architecture and its interaction with auxin in Arabidopsis thaliana. In this addendum we discuss our results in the light of significant recent papers that deal with cytokinin-auxin interactions and we point out spatiotemporal specificity of these interactions in the root development.