Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle.

Body weight is a polygenic trait with intricate inheritance patterns. Functional genomics enriched with multi-layer annotations offers essential resources for exploring the genetic architecture of complex traits. In this study, we undertook an extensive characterization of regulatory variants for body weight related traits in cattle using a multi-omics approach.

PABPC1 SUMOylation enhances cell survival by promoting mitophagy through stabilizing U-rich mRNAs within stress granules.

Stress granules (SGs) are cytoplasmic, membraneless organelles that modulate mRNA metabolism and cellular adaptation under stress, yet the mechanisms by which they regulate cancer cell survival remain unclear. Here, we identify Poly(A)-Binding Protein Cytoplasmic 1 (PABPC1), a core SG component, as stress-inducible SUMOylation target. Upon various stress conditions, SUMOylated PABPC1 promotes SG assembly and enhances cancer cell survival.

Multi-omics integration analysis reveals the regulatory impact of CNVs for slaughter traits in cattle.

Copy number variations (CNVs) represent a crucial class of genomic variations that modulate gene expression and contribute to phenotypic diversity. In this study, we systematically identified 124,790 CNVs across genome using Bovine HD SNP array. A CNV-based genome-wide association study (GWAS) identified 17 and 3 significant CNV segments associated with lean meat percentage (LMP) and dressing percentage (DP), respectively.

Mitigating Cell Cycle Effects in Multi-Omics Data: Solutions and Analytical Frameworks.

Cell cycle structures vary significantly across cell types, which exhibit distinct phase compositions. Asynchronous DNA replication and dynamic cellular characteristics during the cell cycle result in considerable heterogeneity in DNA dosage, chromatin accessibility, methylation, and expression. Nonetheless, the consequences of cell cycle disruption in the interpretation of multi-omics data remain unclear.

Comprehensive Characterization of Organic Chemicals Associated with Urban Particulate Matter in China.

Atmospheric particulate matter (PM) is considered a health hazard; however, the inadequate identification of the components of PM limits our understanding of its specific toxic pollutants. Herein, by combining three extraction solvents with different polarities (dichloromethane, hexane, and acetonitrile) and three ionization modes (electron ionization and the positive and negative modes of electrospray ionization), we comprehensively analyzed the organic chemicals in the PM and PM samples collected during summer and winter in Beijing. Suspect screening was facilitated by comparison with the mzCloud and the National Institute of Standards and Technology databases for tentatively characterizing chemical identities.

Integrating genomics and transcriptomics reveals candidate genes affecting loin muscle area in Huaxi cattle.

Loin muscle area (LMA) is an indicator of carcass composition and is related to weight gain, animal musculature and meat quality traits. Therefore, integrating multi-omics data to reveal candidate genes affecting LMA has attracted extensive attention. We used the combined analysis method of GWAS and RNA-seq to find the candidate genes that affect the size of LMA.

Mammary gland multi-omics data reveals new genetic insights into milk production traits in dairy cattle.

Although many sequence variants have been discovered in cattle, deciphering the relationship between genome and phenome remains a significant challenge. In this study, we identified functional classes, including mammary-specific genes, lactation-associated genes, novel long non-coding RNAs, miRNAs, RNA editing sites, DNA methylation, histone modifications, and expression quantitative trait loci. We estimated their contributions to genetic variance for milk production traits using 3 million variants in 23,566 Holstein bulls.

Trafficking of the telomerase RNA using a novel genetic approach.

Telomeres are specialized nucleoprotein structures situated at eukaryotic chromosome ends, vital for preserving genetic information during cell replication. Telomerase, a holoenzyme composed of telomerase reverse transcriptase and an RNA template component, is responsible for elongating telomeric DNA. The intracellular trafficking of the telomerase RNA (TER) varies, either staying in the nucleus or exiting to the cytoplasm, depending on the organism.

The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-rich lncRNAs.

Polycomb repressive complex 2 (PRC2) is responsible for depositing H3K27me3 and plays essential roles in gene silencing during development and cancer. Meanwhile, the nuclear exosome targeting (NEXT) complex facilitates the degradation of numerous noncoding RNAs in the nucleoplasm. Here we find that the functional deficiency of the NEXT complex leads to an overall decrease in H3K27me3 levels.

Deciphering the Population Characteristics of Leiqiong Cattle Using Whole-Genome Sequencing Data.

Long-term geographic isolation and breeding programs both influence population characteristics. Leiqiong cattle, a native breed from the southernmost region of China, are renowned for disease and heat resistance, with two subgroups on Hainan Island and the Leizhou Peninsula. However, the genomic differences between them remain unexplored.

Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle.

Fatty acid composition (FA) is an important indicator of meat quality in beef cattle. We investigated potential functional candidate genes for FA in beef cattle by integrating genomic and transcriptomic dataset through multiple strategies. In this study, we observed 65 SNPs overlapping with five candidate genes (CCDC57, FASN, HDAC11, ALG14, and ZMAT4) using two steps association based on the imputed sequencing variants.

Genome-Wide Scans for Selection Signatures in Ningxia Angus Cattle Reveal Genetic Variants Associated with Economic and Adaptive Traits.

The genetic improvement of beef cattle breeds is crucial for the advancement of the beef cattle industry. Whole-genome resequencing technology has been widely applied in genetic breeding as well as research on selection signatures in beef cattle. In this study, 20× whole-genome resequencing was performed on 282 Angus cattle from the Ningxia region, and a high-quality dataset encompassing extensive genomic variations across the entire genome was constructed.

Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle.

Background: Integrating multi-layered information can enhance the accuracy of genomic prediction for complex traits. However, the improvement and application of effective strategies for genomic prediction (GP) using multi-omics data remains challenging.

Methods: We generated 11 feature sets for sequencing variants from genomics, transcriptomics, metabolomics, and epigenetics data in beef cattle, then we assessed the contribution of functional variants using genomic restricted maximum likelihood (GREML).

Loss of Fbxo45 in AT2 cells leads to insufficient histone supply and initiates lung adenocarcinoma.

Dysregulation of histone supply is implicated in various cancers, including lung adenocarcinoma (LUAD), although the underlying mechanisms remain poorly understood. Here, we demonstrate that knockout of Fbxo45 in mouse alveolar epithelial type 2 (AT2) cells leads to spontaneous LUAD. Our findings reveal that FBXO45 is a novel cell-cycle-regulated protein that is degraded upon phosphorylation by CDK1 during the S/G2 phase.

Accuracy of Genomic Predictions Cross Populations with Different Linkage Disequilibrium Patterns.

Background/objectives: There is a considerable global population of beef cattle, with numerous small-scale groups. Establishing separate reference groups for each breed in breeding practices is challenging, severely limiting the genome selection (GS) application. Combining data from multiple populations becomes particularly attractive and practical for small-scale populations, offering increased reference population size, operational ease, and data sharing.

Evaluation of genomic mating approach based on genetic algorithms for long-term selection in Huaxi cattle.

Background: Genomic mating (GM) can effectively control the growth rate of inbreeding in population and achieve long-term sustainable genetic progress. However, the design of GM method and assessment of its effects during long-term selection have not been fully explored in beef cattle breeding.

Results: In this study, we constructed a simulated population based on the real genotypes of Huaxi cattle, where five generations of simulated breeding were carried out using the genomic optimal contribution selection (GOCS), genetic algorithms strategy and three traditional mating strategies.

A novel regulatory axis of MSI2-AGO2/miR-30a-3p-CGRRF1 drives cancer chemoresistance by upregulating the KRAS/ERK pathway.

The KRAS/ERK pathway is crucial in cancer progression and chemotherapy resistance, yet its upstream regulatory mechanism remains elusive. We identified MSI2 as a new promoter of chemotherapy resistance in cancers. MSI2 directly binds to a specific class of mature miRNAs by recognizing the 'UAG' motif and interacts with the essential effector AGO2, highlighting MSI2 as a novel regulatory factor within the miRNA pathway.

Genome-Wide Gene-Environment Interaction Analysis Identifies Novel Candidate Variants for Growth Traits in Beef Cattle.

Complex traits are widely considered to be the result of a compound regulation of genes, environmental factors, and genotype-by-environment interaction (G × E). The inclusion of G × E in genome-wide association analyses is essential to understand animal environmental adaptations and improve the efficiency of breeding decisions. Here, we systematically investigated the G × E of growth traits (including weaning weight, yearling weight, 18-month body weight, and 24-month body weight) with environmental factors (farm and temperature) using genome-wide genotype-by-environment interaction association studies (GWEIS) with a dataset of 1350 cattle.

Determining toxicity of europium oxide nanoparticles in immune cell components and hematopoiesis in dominant organs in mice: Role of lysosomal fluid interaction.

Extensive application of rare earth element oxide nanoparticles (REE NPs) has raised a concern over the possible toxic health effects after human exposure. Once entering the body, REE NPs are primarily processed by phagocytes in particular macrophages and undergo biotic phosphate complexation in lysosomal compartment. Such biotransformation affects the target organs and in vivo fate of REE NPs after escaping the lysosomes.

Transcriptome Analysis of Compensatory Growth and Meat Quality Alteration after Varied Restricted Feeding Conditions in Beef Cattle.

Compensatory growth (CG) is a physiological response that accelerates growth following a period of nutrient limitation, with the potential to improve growth efficiency and meat quality in cattle. However, the underlying molecular mechanisms remain poorly understood. In this study, 60 Huaxi cattle were divided into one ad libitum feeding (ALF) group and two restricted feeding groups (75% restricted, RF75; 50% restricted, RF50) undergoing a short-term restriction period followed by evaluation of CG.

Genome-Wide Association Analysis Identifies the Gene Affecting Coat Color and Birth Weight in Simmental × Holstein.

Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (, , , , , , , , and ), and these were in , , , , and on BTA5.