Functional & Integrative Genomics最新文献

Epigenome editing has become a leading-edge technology of programmable, heritable and reversible control of gene expression in plants without changing the DNA sequence. CRISPR/dCas9 systems along with transcription activator-like effectors (TALEs) and zinc finger systems have made it possible to manipulate DNA methylation, histone modifications, and RNA epigenetic marks in a precise and locus-specific fashion. These tools have been used on major regulatory genes of flowering time, stress adjustment, and yield maximization in model and crop plants. This review synthesizes the current status of plant epigenome editing advances and highlights mechanistic innovations including SunTag, CRISPRoff/on and RNA m6A editing. It also emphasizes new paradigm shifts in chromatin reprogramming, including transcription-resistive chromatin states, locus-specific H3K27me3 demethylation, and nanobody-mediated chromatin targeting. Furthermore, it considers the consequences of these shifts in the context of trait stability and epigenetic inheritance. Moreover, the relative evaluation of dCas9-, TALE-, and ZFP-based platforms indicated that there are still enduring problems in the performance of delivery, off-target effects, and transgenerational stability. The review concludes with a conceptual framework connecting epigenome editing to climate-smart crop improvement and outlines future research priorities focused on combinatorial multi-omics integration and the development of environmentally responsive editing platforms.

Starch is the main storage carbohydrate in barley, and disrupting starch biosynthesis can alter the type of storage carbohydrate accumulated. Here, the starch synthase gene, SSIIa, which is associated with amylopectin biosynthesis, was knocked out in waxy (GBSSI-knockout) barley through genome editing to generate a double mutant (gbssI ssIIa) of both SSIIa and GBSSI genes. Wild-type Golden Promise (GP), gbssI ssIIa, and waxy plants exhibited similar phenotypes in terms of plant height, tiller number, spike length, and grains per spike. The starch content in gbssI ssIIa grains was only 3.87%, significantly less than in waxy (33.13%) and GP (62.83%). Consequently, the soluble sugar content of gbssI ssIIa was increased to 23.03%, reaching the level typically classified as super sweet. The fructan content in gbssI ssIIa was 5.09%, significantly higher than in waxy (0.95%) and GP (0.47%). The elevated expression of 6-FFT may partially explain the increased fructan content. β-glucan levels were only marginally affected, showing comparable content in gbssI ssIIa and waxy. Additionally, monosaccharide and oligosaccharide levels were increased, as revealed by GC-MS analysis. This study provides a new strategy for generating sweet cereal crops with higher soluble sugar, β-glucan, and fructan content by simultaneously knocking out GBSSI and SSIIa genes.

Hyperpigmentation of the visceral peritoneum (HVP) is a sex-biased phenotype that reduces carcass value in yellow-feathered broilers. While GWAS studies have identified candidate loci, the cellular origin and molecular mechanisms driving HVP remain unknown. This study employed single-cell RNA sequencing to profile black, faded, and normal peritoneal tissues from bearded chickens at 40 and 120 d of age, functionally validating findings with fibroblast lines and primary melanocytes. We identified nine cell types, with melanocytes significantly elevated in HVP tissue. UMAP visualization shows nearly overlapping melanocyte and Schwann-cell clusters, suggesting that HVP melanocytes may share a common origin with Schwann cells along the ventromedial migratory pathway of neural-crest cells (NCCs). Aberrant melanocyte aggregation and migration drive HVP pathogenesis. CellChat analysis demonstrated pivotal roles for the SEMA3C-PLXND1 axis, which directs NCCs migration, and the TNC-SDC1 axis, which enhances melanocytes adhesion, in fibroblasts-melanocytes crosstalk. Transcription factor analysis highlighted HOX family regulation of NCCs to melanocytes differentiation. Experimentally, Downregulation of SDC1 reduced melanin synthesis but significantly enhanced the migratory capacity of melanocytes, while estradiol promoted melanogenesis and modulated extracellular matrix. HVP development involves four interconnected mechanisms: RA-HOX-mediated aberrant NCCs differentiation, SEMA3C-PLXND1-driven melanocyte barrier breaching, TNC-SDC1-mediated peritoneal colonization, and estrogen-coordinated melanin deposition. These findings provide a theoretical framework for breeding against HVP in broilers.

Cadmium (Cd) contamination in agricultural soils poses a significant threat to the safety of pepper (Capsicum annuum L.) products. The development of low-Cd-accumulating pepper varieties is a promising strategy to ensure food safety. To identify potential genetic targets involved in regulating Cd accumulation in pepper fruits, we conducted a genome-wide selective sweep analysis in high- and low-Cd-accumulating pepper materials. By integrating genome-wide selective sweep analysis with gene expression profiling, we identified CaDTX12 (Capana11g002353), a gene encoding a detoxification efflux carrier (DTX). Heterologous expression of CaDTX12 significantly enhanced Cd accumulation in both yeast and Arabidopsis. Silencing of CaDTX12 via VIGS resulted in a 27.8% reduction in Cd content in pepper fruits. Two genotypic variants of CaDTX12 were identified (X15-CaDTX12 and X55-CaDTX12). Among these, X15-CaDTX12 represents the functional allele, exhibiting significantly higher Cd accumulation capacity compared with X55-CaDTX12. The CaDTX12 protein is localized to the tonoplast membrane. Furthermore, CaDTX12 exhibited a consistent expression pattern with that of CaDTX1, CaHMA1, CaHMA3, CaNRAMP3, CaZIP11, and CaSOD-Fe, and the silencing of CaDTX12 led to the downregulation of these associated genes. In conclusion, our findings suggest that CaDTX12 functions in Cd transport on the vacuolar membrane, and together with proteins including CaDTX1, CaHMA1, CaHMA3, CaNRAMP3, CaZIP11, and CaSOD-Fe, it collectively promotes Cd accumulation in pepper fruits and enhances Cd tolerance. These findings provide novel insights into the molecular mechanisms underlying Cd accumulation in pepper fruits and offer potential genetic targets for developing low-Cd-accumulating pepper varieties through breeding programs.

Hepatocellular carcinoma (HCC) progression is driven by cancer stem cells (CSCs) with self-renewal and immune evasion capacities. Here, we identify a novel HIF-1α/YTHDF2/PFKL axis that orchestrates metabolic reprogramming in myeloid-derived suppressor cells (MDSCs) to sustain CSC malignancy. Bioinformatics and TCGA analyses revealed HIF-1α and YTHDF2 overexpression correlated with poor HCC prognosis. Mechanistically, HIF-1α binds the YTHDF2 promoter under hypoxia, activating its transcription (validated by ChIP and luciferase assays). YTHDF2, an m6A “reader,” stabilizes PFKL mRNA—a glycolytic rate-limiting enzyme—by recognizing m6A sites (predicted by SRAMP, confirmed via MeRIP/RIP). Functional assays demonstrated that YTHDF2 knockdown reduced PFKL expression, suppressed MDSC glycolysis (decreased ECAR, lactate/ATP production), and attenuated CD8⁺T cell inhibition. Conversely, YTHDF2 overexpression amplified these effects. In vitro, HIF-1α-silenced MDSCs impaired CSC spherogenesis and PD-L1 expression, rescued by PFKL overexpression. In vivo, HIF-1α knockdown inhibited tumor growth and CD8⁺T cell infiltration, while PFKL restoration reversed these phenotypes. Our study unveils HIF-1α-driven m6A modification as a critical link between MDSC metabolism and CSC immune evasion, proposing the HIF-1α/YTHDF2/PFKL axis as a therapeutic target for HCC.

Graphical Abstract

Schematic illustration of the molecular mechanism by which HIF-1α activation of YTHDF2 transcription mediates m6A modification, stabilizing PFKL mRNA and ultimately promoting glycolysis in MDSCs, thereby enhancing CSC self-renewal and immune evasion in liver cancer.

Wheat (Triticum aestivum L.) is widely grown and consumed cereal crop around the world, but most wheat-producing regions suffer from rust diseases, especially stripe and leaf rust, which has caused a devastating global pandemic and severely reduced grain yields. The most effective way to control rust problem in wheat is to sow and breed durable, rust resistant wheat varieties. Conventional breeding for disease-resistant crops primarily relies on resistance (R) genes; however, the effectiveness of R gene-mediated resistance is often compromised by mutations in the pathogen. In this study, we employed CRISPR-Cas9-based genome editing as an advanced breeding tool to enhance rust resistance in the bread wheat cultivar Galaxy-13 by knocking out the homologs of the susceptibility allele TaLr34, specifically targeting the conserved regions within exon 11. Out of 21 transformed plants, five carried successful editing and exhibited resistance to moderate resistance against leaf rust. The TaLr34 mutants were evaluated for leaf rust resistance under both glasshouse and field conditions over three consecutive growing seasons at multiple geographical locations. Our results demonstrate that CRISPR-Cas9-mediated knockout of TaLr34 provides a robust strategy for achieving durable leaf rust resistance in the high-yielding elite wheat cultivar Galaxy-13 without compromising grain yield and agronomic performance.

The TCP (Teosinte branched1/Cincinnata/Proliferating Cell Factor) gene family encodes plant-specific transcription factors that are essential for regulating various aspects of growth, development, and environmental stress responses. To elucidate the roles of TCP genes in regulating the development of mustard (Brassica juncea), this study conducted a genome-wide identification and comprehensive analysis of TCP family members. A total of 72 TCP genes were identified in the genome of leaf mustard, distributed unevenly across 17 chromosomes. Based on conserved domain characteristics, the BjTCPs were classified into two subfamilies. Cis-acting element analysis of the promoter regions revealed numerous elements associated with hormonal responses, light signaling, stress tolerance, and development. Expression pattern analysis demonstrated that BjTCP genes exhibit different expression profiles. Functional validation through CRISPR/Cas9-mediated gene editing and transformation experiments indicated that BjTCP18 acts as a negative regulator in the branching development of mustard. This study provides a theoretical foundation and candidate gene resources for further elucidation of the influence of the TCP gene family on regulatory processes and the role of the BjTCP18 gene in regulating branching development in mustard.

Di (2-ethylhexyl) phthalate (DEHP) is extremely application in industrial production. DEHP and its metabolites can induce epigenetic changes, such as selective gene expression regulation and post-transcriptional gene regulation, leading to adverse outcome pathways in living organisms. Our findings, bioinformatics tools, and miRNA-mRNA prediction suggested that corticotropin-releasing hormone (CRH) could be miR-101a’s target gene. Although the regulatory relationship between miR-101a and CRH has not been experimentally established, the present study aimed to investigate this interaction in zebrafish embryos exposed to low concentrations of DEHP. Both DLR™ and DFP™ reporter assays confirmed the biological association between miR-101a and CRH mRNA. Validation experiments revealed that overexpression or knockdown of miR-101a in ZF4 cells resulted in changes in CRH mRNA expression. These findings represent that miR-101a adversely impacts CRH at the levels of mRNA.This study improves the discovery of the molecular toxicology of DEHP exposure, and miR-101a is predicted to be a novel toxicological biomarker for chemical hazards.