Journal of Genetics and Genomics最新文献

Maize (Zea mays), which is a vital source of food, feed, and energy feedstock globally, has significant potential for higher yields. However, environmental stress conditions, including drought and salt stress, severely restrict maize plant growth and development, leading to great yield losses. Leucine-rich repeat receptor-like kinases (LRR-RLKs) function in biotic and abiotic stress responses in the model plant Arabidopsis (Arabidopsis thaliana), but their roles in abiotic stress responses in maize are not entirely understood. In this study, we determine that the LRR-RLK ZmMIK2, a homolog of the Arabidopsis LRR-RK MALE DISCOVERER 1 (MDIS1)- INTERACTING RECEPTOR LIKE KINASE 2 (MIK2), functions in resistance to both drought and salt stress in maize. Zmmik2 plants exhibit enhanced resistance to both stresses, whereas overexpressing ZmMIK2 confers the opposite phenotypes. Furthermore, we identify C2-DOMAIN-CONTAINING PROTEIN 1 (ZmC2DP1), which interacts with the intracellular region of ZmMIK2. Notably, that region of ZmMIK2 mediates the phosphorylation of ZmC2DP1, likely by increasing its stability. Both ZmMIK2 and ZmC2DP1 are mainly expressed in roots. As with ZmMIK2, knockout of ZmC2DP1 enhanced resistance to both drought and salt stress. We conclude that ZmMIK2-ZmC2DP1 act as a negative regulatory module in maize drought- and salt-stress responses.

Hematopoiesis is crucial for organismal health, and Drosophila serves as an effective genetic model due to conserved regulatory mechanisms with vertebrates. In larvae, hematopoiesis primarily occurs in the lymph gland, which contains distinct zones, including the cortical zone, intermediate zone, medullary zone, and posterior signaling center (PSC). Rab1 is vital for membrane trafficking and maintaining the localization of cell adhesion molecules, yet its role in hematopoietic homeostasis is not fully understood. This study investigates the effects of Rab1 dysfunction on β-integrin trafficking within circulating hemocytes and lymph gland cells. Rab1 impairment disrupts the endosomal trafficking of β-integrin, leading to its abnormal localization on cell membranes, which promotes lamellocyte differentiation and altered progenitor dynamics in circulating hemocytes and lymph glands, respectively. We also show that the mislocalization of β-integrin was dependent on the adhesion protein DE-cadherin. The reduction of β-integrin at cell boundaries in PSC cells leads to fewer PSC cells and lamellocyte differentiation. Furthermore, Rab1 regulates the trafficking of β-integrin via the Q-SNARE protein Syntaxin 17 (Syx17). Our findings indicate that Rab1 and Syx17 regulate distinct trafficking pathways for β-integrin in different hematopoietic compartments and maintain hematopoietic homeostasis of Drosophila.

The CRISPR-Cas technology has revolutionized our ability to understand and engineer organisms, evolving from a singular Cas9 model to a diverse CRISPR toolbox. A critical bottleneck in developing new Cas proteins is identifying protospacer adjacent motif (PAM) sequences. Due to the limitations of experimental methods, bioinformatics approaches have become essential. However, existing PAM prediction programs are limited by the small number of spacers in CRISPR-Cas systems, resulting in low accuracy. To address this, we develop PAMPHLET, a novel pipeline that uses homology searches to identify additional spacers, significantly increasing the number of spacers up to 18-fold. PAMPHLET is validated on 20 CRISPR-Cas systems and successfully predicts PAM sequences for 18 protospacers. These predictions are further validated using the DocMF platform, which characterizes protein-DNA recognition patterns via next-generation sequencing. The high consistency between PAMPHLET predictions and DocMF results for novel Cas proteins demonstrates potential of PAMPHLET to enhance PAM sequence prediction accuracy, expedite the discovery process, and accelerate the development of CRISPR tools.

When plants respond to drought stress, dynamic cellular changes occur, accompanied by alterations in gene expression, which often act through trans-regulation. However, the detection of trans-acting genetic variants and networks of genes is challenged by the large number of genes and markers. Using a tensor decomposition method, we identify trans-acting expression quantitative trait loci (trans-eQTLs) linked to gene modules, rather than individual genes, which were associated with maize drought response. Module-to-trait association analysis demonstrates that half of the modules were relevant to drought-related traits. Genome-wide association studies of the expression patterns of each module identify 286 trans-eQTLs linked to drought-responsive modules, the majority of which cannot be detected based on individual gene expression. Notably, the trans-eQTLs located in the regions selected during maize improvement tend towards relatively strong selection. We further prioritize the genes that affected the transcriptional regulation of multiple genes in trans, as exemplified by two transcription factor genes. Our analyses highlight that multidimensional reduction could facilitate the identification of trans-acting variations in gene expression in response to dynamic environments and serve as a promising technique for high-order data processing in future crop breeding.

In the mammalian genome, most CpGs are methylated. However, CpGs within the CpG islands (CGIs) are largely unmethylated, which are important for gene expression regulation. The mechanism underlying the low methylation levels at CGIs remains largely elusive. KDM2 proteins (KDM2A and KDM2B) are H3K36me2 demethylases known to bind specifically at CGIs. Here, we report that depletion of each or both KDM2 proteins, or mutation of all their JmjC domains that harbor the H3K36me2 demethylation activity, leads to an increase in DNA methylation at selective CGIs. The Kdm2a/2b double knockout shows a stronger increase in DNA methylation compared to the single mutant of Kdm2a or Kdm2b, indicating that KDM2A and KDM2B redundantly regulate DNA methylation at CGIs. In addition, the increase of CGI DNA methylation upon mutations of KDM2 proteins is associated with the chromatin environment. Our findings reveal that KDM2A and KDM2B function redundantly in regulating DNA methylation at a subset of CGIs in an H3K36me2 demethylation-dependent manner.

Fungi are a diverse kingdom, characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions. In this review, we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance. We examine key features and the heterogeneity of genomes across different fungal species, including but not limited to their chromosome content, DNA composition, distribution and arrangement of their content across chromosomes, and other major traits. We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions. Fungal genomes exhibit large variation in size, gene content, and structural features such as abundance of transposable elements (TEs), compartmentalization into gene-rich and TE-rich regions, and presence or absence of dispensable chromosomes. Genomic structural variations are equally diverse in fungi, ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds, to targeted deletion of effector encoding genes that may promote virulence. Finally, the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicide. Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.

Programmed silencing of γ-globin genes in adult erythropoiesis is mediated by several chromatin remodeling complexes, which determine the stage-specific genome architecture in this region. Identification of cis- or trans-acting mutations contributing to the diverse extent of Hb F might illustrate the underlying mechanism of γ-β globin switching. Here, we recruit a cohort of 1142 β-thalassemia patients and dissect the natural variants in the whole β-globin gene cluster through a targeted next-generation sequencing panel. A previously unreported SNP rs7948668, predicted to disrupt the binding motif of IKAROS as a key component of chromatin remodeling complexes, is identified to be significantly associated with higher levels of Hb F and age at onset. Gene-editing on this SNP leads to elevation of Hb F in both HUDEP-2 and primary CD34⁺ cells while the extent of elevation is amplified in the context of β-thalassemia mutations, indicating epistasis effects of the SNP in the regulation of Hb F. Finally, we perform ChIP-qPCR and 4C assays to prove that this variant disrupts the binding motif of IKAROS, leading to enhanced competitiveness of HBG promoters to locus control regions. This study highlights the significance of common regulatory SNPs and provides potential targets for treating of β-hemoglobinopathy.