Journal of Genetics and Genomics最新文献

Stable transgene expression in the mammary gland is crucial for recombinant protein production in livestock, yet it is frequently hampered by transgene silencing and random integration. To address this, we profile chromatin accessibility in goat mammary epithelial cells (GMECs) using ATAC-seq and identify 15 highly accessible genomic regions. Three of these regions are confirmed to support stable transgene expression. Notably, we identify a goat-derived ubiquitous chromatin opening element (UCOE) in the SF3B1-COQ10B intergenic region, with a high GC content (65%) and CpG island enrichment. This UCOE improves hfCas12Max-mediated integration of large DNA fragments and maintains high-level expression of human lactoferrin (hLTF) in GMECs. Subsequently, we precisely integrate the UCOE-hLTF cassette into the highly accessible loci and generate a transgenic goat via somatic cell nuclear transfer, without detectable off-target effects. Our pipeline, which integrates chromatin accessibility profiling, UCOE discovery, and precision editing, demonstrates the role of CpG island-containing UCOEs in preventing transgene silencing. The study provides valuable tools for enhancing recombinant protein production and supports the breeding of dairy goats for milk with high lactoferrin content, while advancing the understanding of the interactions between chromatin, regulatory elements, and transgenes in molecular breeding.

Although chimeric antigen receptor (CAR) T-cell therapy has markedly improved outcomes for many patients with B-cell malignancies, a subset experiences limited benefit due to primary or secondary resistance. Building on CRISPR/Cas9 genome-wide screening in malignant B-cells, we identify NPRL2 and NPRL3 as key regulators of tumor sensitivity to CAR-T cytotoxicity. This study aims to investigate the impact and mechanisms of tumor-intrinsic NPRL2 and NPRL3 on the efficacy of CAR-T cell therapy. In a tandem CD19/20 CAR-T clinical trial for relapsed/refractory (R/R) B-cell lymphoma (NCT03097770), high tumor NPRL2 or NPRL3 expression correlates with therapeutic resistance in patients. Consistently, in vitro experiments confirm that tumor cells overexpressing NPRL2/NPRL3 exhibit resistance to CAR-T-mediated cytolysis. Mechanistically, NPRL2/NPRL3 suppresses mTORC1 activity within tumor cells, negatively regulating the conjugation between tumor cells and CAR-T cells, consequently impairing CAR-T cell activation and cytotoxic function, ultimately facilitating immune escape. As therapeutic strategies, either genetic ablation of tumor-intrinsic NPRL2/NPRL3 or pharmacological activation of mTORC1 enhances CAR-T cell activation, cytotoxic degranulation, and tumor clearance both in vitro and in vivo. In conclusion, targeting tumor NPRL2/NPRL3 or directly activating mTOR represents a promising combinational strategy to potentiate CAR-T efficacy and overcome resistance in clinical practice.

Chloroplast translation systems have evolved specialized regulatory mechanisms distinct from those of their prokaryotic ancestors. However, critical gaps persist in understanding how these systems coordinate translation efficiency with photosynthetic apparatus assembly-a process central to plant development. Here, we identify Arabidopsis BACTERIAL LARGE RIBOSOMAL SUBUNIT PROTEIN 31 (bL31c) as a critical chloroplast ribosomal protein that interacts with the translation elongation factor RAB GTPASE HOMOLOG 8D (RAB8D) to ensure translation elongation efficiency. Knocking down bL31c disrupts chloroplast translation, causing preferential depletion of photosystem I (PSI) subunits, a functional imbalance between PSI and PSII, and paradoxical accumulation of the PSI-LHCI-LHCII supercomplex. Comparative analysis reveals evolutionary conservation of the bL31c-EF-Tu functional module in Cyanobacteria but not in E. coli, demonstrating lineage-specific adaptation of translation surveillance mechanisms. Crucially, pharmacological inhibition of translation elongation in wild-type plants phenocopies the photosystem stoichiometry defects observed in bl31c mutants, establishing defective ribosome processivity as the primary driver of photosystem imbalance. Our findings uncover a plant-specific ribosomal checkpoint mechanism that dynamically coordinates protein synthesis with photosynthetic complex assembly, providing important insights into the evolutionary rewiring of organellar gene expression systems in eukaryotes.

Embryonic pattern formation and cell specification require precise cell division and cell cycle regulation. Splicing factors and the splicing of precursor mRNA (pre-mRNA) play significant roles in embryo development. However, how splicing factors control embryonic patterning via RNA splicing remains unclear. Here, we show that the mutation of SUPPRESSORS OF MEC-8 AND UNC-52 1 (SMU1), a conserved subunit of the spliceosomal B complex, causes compromised cell fate of the hypophysis and quiescent center (QC), failed embryonic root apical meristem (RAM) formation, as evidenced by altered WUSCHEL-RELATED HOMEOBOX 5 (WOX5) expression and perturbed auxin signaling. This results in smu1 embryo lethality. The splicing efficiency of three out of four CYCLIN-DEPENDENT KINASE ACTIVATOR (CAK) genes is decreased, leading to reduced protein levels in smu1 embryos. These CAK genes are required for hypophysis specification and embryonic RAM formation. SMU1 binds CAK transcripts in vitro and in vivo. Restoring the expression of either CAK gene partially rescues the defects in smu1 embryos, leading to the formation of QC-like cells, continued embryo development, and even the production of viable seeds. Our data suggest that SMU1 binds to CAK transcripts and promotes their splicing, enabling cell cycle progression to promote embryonic RAM formation.

Liver cancer ranks sixth in cancer incidence and third in cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) is the primary histological subtype, and hepatitis B virus (HBV) carriers have a higher risk of HCC. Although several susceptibility loci for HCC have been identified in East Asian populations through genome-wide association studies (GWAS), the underlying biological mechanisms of this malignancy remain incompletely understood. Here, we conduct a two-stage GWAS including 2413 cases and 2794 HBV-positive controls from a high-incidence region in Southern China. The function of the susceptibility locus is investigated by bioinformatic and experimental approaches, supported by a xenograft model. We identify a 4p14 locus significantly associated with the risk of HCC (rs55718051, OR [95% CI] = 0.73 [0.67-0.80], P_meta = 9.14 × 10^-11), and 18q23 locus with borderline significance (rs12964643: OR [95% CI] = 0.75 [0.67-0.83], P_meta = 1.11 × 10^-7). Functional experiments indicate the role of rs55718051 in FAM114A1 expression regulation, possibly through interaction of FOXA1. Knockdown of FAM114A1 significantly enhances the oncogenic phenotypes in liver cancer cells, suggesting its potential tumor suppressor role. Our findings expand the understanding of HCC susceptibility and suggest FAM114A1 as a potential suppressor in HBV-related HCC carcinogenesis.

Cilia are vital subcellular organelles whose assembly is regulated by master transcription factors, such as Foxj1 and Rfx. However, the mechanisms of epigenetic regulation over cilia stability remain largely unclear. Here, we investigate the epigenetic control by manipulating chromatin remodeling genes in zebrafish. We demonstrate that the depletion of multiple components of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex induces ciliopathy-like phenotypes in zebrafish embryos. Specifically, the loss of Actl6a, an essential component of the SWI/SNF complex, leads to cilia disassembly and cystic kidney defects, without affecting cilia motility. Our multi-omics analyses (RNA-seq, ATAC-seq, and FitCUT&RUN) consistently reveal that in Actl6a-depleted pronephros or embryos, a critical set of cilia genes, including the master regulators foxj1a and rfx2, exhibit concordant downregulation across the transcriptional level, chromatin accessibility, and SWI/SNF binding. Consistently, the depletion of foxj1a or rfx2 causes cilia assembly defects and cystic kidney formation in zebrafish. Furthermore, overexpression of either foxj1a or rfx2 mRNA substantially rescues the cystic kidney and cilia disassembly defects observed in actl6a^-/- mutant embryos. Collectively, these findings reveal that the SWI/SNF complex maintains cilia stability and kidney homeostasis by directly modulating the expression of the key ciliogenesis transcription factors foxj1a and rfx2.

Stalk lodging is a major problem in maize production, usually causing significant yield losses due to weak stalk strength. Understanding the genetic basis of stalk strength is crucial for improving maize lodging resistance. In this study, we identify 31 quantitative trait loci (QTLs) related to maize stalk strength and clone ZmPRX38 (encoding peroxidase 38) responsible for a hotspot QTL region of stalk strength. ZmPRX38 is highly expressed in maize stalk during vegetative growth stage, and its protein is localized in the cell membrane, cytoplasm and apoplast. Knockout of ZmPRX38 decreases stalk strength and yield in maize, while overexpressing ZmPRX38 increases stalk strength and yield. ZmPRX38 in phenylpropanoid pathway is involved in the biosynthesis of guaiacyl lignin, p-hydroxy-phenyl lignin, and syringyl lignin. Additionally, we identify a favorable haplotype of ZmPRX38, which enhances stalk strength, containing 3 loci distributed in the 5' untranslated region (UTR), exon 1, and 3'UTR of ZmPRX38, respectively. Although 91.46% of maize natural lines contain this favorable haplotype, most of the Huang-gai (HG) lines, a backbone maize germplasm, contain the unfavorable haplotypes. Therefore, targeted improvement of ZmPRX38 by editing unfavorable haplotypes may be an effective strategy for increasing maize stalk strength, thereby improving maize lodging resistance and yield.

CRISPR-based nucleic acid detection technologies have revolutionized infectious disease detection and environmental monitoring by leveraging RNA-DNA complementarity to enable rapid, precise, and cost-effective detection of targets. However, achieving multitarget detection in one tube still presents challenges that necessitate further research. Here, we develop a nucleic acid detection module based on the CRISPR-Cas12i system. Importantly, we find that Cas12i and AapCas12b exhibit opposite trans-cleavage preferences for asymmetrically phosphorothioate-modified single-strand DNA probes, enabling the development of an effective dual-target nucleic acid detection platform by combining these two Cas12 nucleases in one tube. Moreover, this dual-target detection platform exhibits high specificity and sensitivity in genotyping the nucleic acid targets of human papillomavirus (HPV) 16 and HPV18, as well as Influenza A virus (FluA) and Respiratory syncytial virus. Notably, combined with loop-mediated isothermal amplification, this platform achieves high detection rates for clinical samples (18/18 FluA and 18/18 GAPDH internal reference detection rate). Taken together, these results can broaden the application of CRISPR-based Cas12 proteins for multi-target nucleic acid detection in one tube.

Soybean (Glycine max) is a vital foundation of global food security, providing a primary source of high-quality protein and oil for human consumption and animal feed. The rising global population has significantly increased the demand for soybeans, emphasizing the urgency of developing high-yield, stress-tolerant, and nutritionally superior cultivars. The extensive collection of soybean germplasm resources-including wild relatives, landraces, and cultivars-represents a valuable reservoir of genetic diversity critical for breeding advancements. Recent breakthroughs in genomic technologies, particularly high-throughput sequencing and multi-omics approaches, have revolutionized the identification of key genes associated with essential agronomic traits within these resources. These innovations enable precise and strategic utilization of genetic diversity, empowering breeders to integrate traits that improve yield potential, resilience to biotic and abiotic stresses, and nutritional quality. This review highlights the critical role of genetic resources and omics-driven innovations in soybean breeding. It also offers insights into strategies for accelerating the development of elite soybean cultivars to meet the growing demands of global soybean production.