TRNA fragments (tRFs) are small non-coding RNAs generated from cleaved tRNA molecules, playing key roles in gene regulation and cellular processes. Produced by ribonucleases like angiogenin and Dicer, tRFs vary in length and function in gene silencing and stress responses. They interact with Argonaute proteins and affect mRNA levels, and are emerging as potential diagnostic and therapeutic targets for diseases such as cancer and neurodegenerative disorders. Given that the skin is the largest organ in mammals, it serves as an ideal model for studying development and various diseases. Therefore, this study investigates tRF expression in sheep skin tissues to understand their regulatory roles during growth and development. This study analyzed skin tissue from five 1-month-old lambs and five 24-month-old adult Tan sheep using small RNA sequencing and proteomics. Raw sequencing data were filtered and aligned to identify various tsRNAs, while proteomic data were assessed for differential expression. Principal Component Analysis (PCA) revealed distinct separation between juvenile and adult samples based on tsRNA expression patterns, indicating intra-group similarity and inter-group differences. Differentially expressed tsRNAs were identified, with 19 highly expressed tsRNAs at 1 month of age. Proteomic screening identified 932 highly expressed and 835 lowly expressed proteins in the 1-month-old group, with functional enrichment highlighting immunity and inflammation pathways. Predictive analysis of tsRNA target genes intersected with 20 differentially expressed proteins involved in mitochondrial metabolism and stress response. This study reveals that tsRNAs significantly influence developmental and immune processes in sheep, with distinct expression patterns between juveniles and adults. Future research should validate these findings and further elucidate the functional mechanisms of tsRNA regulation.

Background: While the growth-immunity trade-off has been extensively studied in plant biology, its existence, underlying immunometabolic mechanisms, and practical implications in animals remain poorly characterized. Chronic immune activation diverts essential bioenergetic resources away from somatic development, highlighting a critical need for interventions capable of modulating this physiological balance. The potent anti-inflammatory properties of 18β-glycyrrhetinic acid (GA), an active component of licorice, provide a unique opportunity to elucidate this regulatory mechanism. Methods: To elucidate the regulatory logic of this trade-off in ruminants, we integrated large-scale physiological profiling, multi-tissue bulk transcriptomics, single-cell RNA sequencing (scRNA-seq), limited proteolysis-coupled mass spectrometry (LiP-MS), and molecular docking. We evaluated a large lamb cohort (n = 448) to determine the systemic and molecular effects of maternal 18β-glycyrrhetinic acid (GA) supplementation on offspring. Results: Gestational GA administration significantly dampened systemic inflammatory tone and oxidative stress, redirecting metabolic resources to somatic growth. This resulted in marked improvements in offspring birth weight (by 7.09%), weaning weight (by 10.66%), skeletal muscle fiber development, and secondary hair follicle maturation. Inter-tissue communication analysis pinpointed the lymph node as the primary signaling hub for GA-mediated inter-organ regulation. Specifically, scRNA-seq revealed that GA preferentially acts on adaptive T-cell subpopulations within the lymph nodes. Furthermore, LiP-MS and molecular docking identified key NF-κB pathway components—specifically PARP1, DDX1, RIPK1, HSPA1A, FLOT1, FLNA, REL, and TRADD—as direct physical binding targets of GA. By engaging these molecular targets, GA suppresses hyperactivated NF-κB signaling in T cells, reducing pro-inflammatory cytokine production and the bioenergetic costs of immune maintenance. Conclusion: This study establishes the operational animal growth-immunity trade-off paradigm and demonstrates that maternal GA intervention successfully optimizes livestock growth performance and systemic homeostasis through precise immunometabolic regulation.

The “nine-curve” crimped wool is a key economic trait of Tan sheep, which peaks at 35 days of age and disappears in adulthood. However, the regulatory mechanisms underlying this age-dependent trait remain unclear. This study aimed to decipher these mechanisms by analyzing the skin of Tan sheep across critical developmental stages. We integrated small RNA sequencing, mRNA sequencing, and proteomics, combined with phenotypic observation and histological analysis, to examine the skin tissues of Tan sheep at three critical developmental stages (embryonic day 120, trait initiation stage; 35 days of age, trait peak stage; 24 months of age, trait disappearance stage). Phenotypic and histological results confirmed that this crimped trait depends on medullated fibers derived from primary follicles; with individual aging, the ratio of secondary to primary follicles increases, and primary follicles degenerate in adulthood, ultimately leading to the loss of the crimped trait. Transcriptomic analysis showed that the PD-1/PD-L1 immune checkpoint pathway is the core hub mediating “immune-follicle” crosstalk. Proteomic results revealed a “transcriptional reserve-translational delay” characteristic in keratin genes such as KRT5 and KRT71, confirming that the phenotype at 35 days of age is a continuation of the developmental program initiated at embryonic day 120. Small RNA analysis revealed a "miRNA storm" that peaks at embryonic day 120 (41 miRNAs in total, 40 of which are derived from the MEG3 (GTL2)-miRNA cluster on chromosome 18), and the expression level of this storm gradually decreases with age. Multi-omics integration analysis found that these MEG3-miRNAs can target six key genes (HOXC6, RILPL2, RAB10, ARL1, MX1, and ST7) and are significantly enriched in immune-inflammatory related pathways, suggesting that they may participate in the development and remodeling of wool follicles by regulating immune-inflammatory responses, thereby affecting the formation of the crimped trait. This study identifies MEG3-miRNAs as key epigenetic regulators of wool crimping and highlights the role of the immune microenvironment in follicle remodeling. We propose that these MEG3-miRNAs likely inhibit immune activation at embryonic day 120 to support primary follicle development, whereas postnatal reduction of these miRNAs relieves immune suppression, triggering overactivation and primary follicle degeneration. This study provides guidance for Tan sheep breeding, reveals conserved epigenetic‒immune synergy in mammalian skin appendages, and offers a model for studying human age-related hair disorders and cross-species age-dependent traits. The online version contains supplementary material available at 10.1186/s12864-026-12688-w.

The molecular architecture of the growth-regulating hypothalamus-pituitary-muscle (H-P-M) axis is poorly understood. We performed integrative transcriptomic analysis of the hypothalamus, pituitary, and longissimus dorsi muscle from Liangshan black sheep with superior growth performance to dissect this regulatory network. Analysis of 3,422 differentially expressed genes (DEGs) identified across pairwise tissue comparisons revealed a three-tiered regulatory architecture: (1) tissue-specific interfaces defining spatial hierarchy, (2) relay modules for temporal dynamics, and (3) shared core hubs (131 genes) establishing neuro-endocrine-muscle integration. This study provides a multi-level regulatory map of the H-P-M axis, identifying key pathways such as pituitary calcium signaling and hub genes (e.g., NPY), with 12 of 14 candidate genes validated by quantitative PCR. These findings deepen the understanding of neuroendocrine control over skeletal muscle growth and offer novel molecular targets for genetic improvement in livestock.

Heme oxygenase-1 (HO-1), encoded by HMOX1, catalyzes the rate-limiting step of heme degradation and generates biliverdin, carbon monoxide, and ferrous iron, thereby linking heme turnover with redox regulation and stress-associated signaling. In birds, biliverdin is retained as a major heme-derived product, but the cellular consequences of HMOX1 perturbation remain insufficiently defined. Here, CRISPR/Cas9-mediated editing was used to generate a heterogeneous HMOX1-edited population in Chicken hepatocellular carcinoma-derived cells. The selected sgRNA reduced HO-1 protein abundance by approximately 47%, and no detectable cleavage was observed at the seven predicted high-risk off-target loci examined. Compared with vector-control cells, HMOX1-edited cells exhibited intracellular heme accumulation, reduced biliverdin levels, increased oxidation-sensitive fluorescence, and reduced CCK-8 absorbance values, indicating disruption of heme–biliverdin metabolic and redox homeostasis. RNA sequencing identified 2650 differentially expressed genes, including 951 upregulated and 1699 downregulated genes. Downregulated genes were mainly enriched in immune, cytokine, MAPK/stress, and extracellular signaling-associated pathways, whereas DNA replication and cell-cycle-related genes were increased. Enrichment-term association and STRING functional-association analyses further identified a coordinated module involving IL1B, JUN, NFKBIA, IRF1, TGFB1, IL10, CCL5, and PTGS2. Independent RT-qPCR analysis confirmed selected expression trends. These findings show that heterogeneous HMOX1 editing and reduced HO-1 abundance are associated with disruption of the avian heme–biliverdin metabolic axis and coordinated remodeling of basal immune, stress, extracellular signaling, and cell-cycle-associated transcriptional programs in Chicken hepatocellular carcinoma-derived cells.