{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:11:46Z","timestamp":1785413506158,"version":"3.56.0"},"reference-count":53,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Gansu Province Major Science and Technology Projects","award":["25ZDNA004"],"award-info":[{"award-number":["25ZDNA004"]}]},{"name":"Technology Support Project from Department of Agriculture and Rural Affairs of Gansu Province","award":["KJZC-2026-7"],"award-info":[{"award-number":["KJZC-2026-7"]}]},{"name":"China Agriculture Research System","award":["CARS-37"],"award-info":[{"award-number":["CARS-37"]}]},{"award":["CARS-37"],"award-info":[{"award-number":["CARS-37"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The sheep Y chromosome encodes genes essential for testicular development and spermatogenesis, yet their transcriptional dynamics across developmental and pathological states remain largely uncharacterized. Here, we profiled Y-linked gene expression using RNA-seq datasets from Hu sheep testes across postnatal development (0, 3, 6, 12 months) and from divergent testicular (large, normal, small, cryptorchid) and epididymal (large, small) weights. Developmental trajectory analysis of 134 expressed Y-linked genes revealed three distinct patterns: progressive activation from birth to sexual maturity (dominated by multicopy families ZNF280BY, HSFY, PRAMEY, TSPY3), progressive decrease, and stage-specific expression. Differential expression identified 41 Y-linked genes consistently downregulated in small, cryptorchid, and pre-pubertal testes compared with normal or large mature testes. Hierarchical clustering showed that 6-month-old small testes transcriptionally clustered with cryptorchid testes, not with immature or normal testes. In the epididymis, only one Y-linked gene was differentially expressed between large and small groups. Among X\u2013Y gametolog pairs, most showed positive expression correlations in testes, whereas DDX3X\/DDX3Y exhibited a significant negative correlation (\u03c1 = \u22120.450, p = 0.0185); strikingly, this pair reversed to a positive correlation in the epididymis (\u03c1 = 0.607, p = 3.29 \u00d7 10\u22125). In conclusion, Y-linked transcriptional profiles distinguish testicular pathology from normal maturation, and DDX3X\/DDX3Y regulation is strictly tissue-specific.<\/jats:p>","DOI":"10.3390\/ani16132107","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T13:19:31Z","timestamp":1783430371000},"page":"2107","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Y-Linked Expression Signatures Distinguish Dysfunctional Testicular States in Sheep"],"prefix":"10.3390","volume":"16","author":[{"given":"Yangkai","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yali","family":"Song","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jialei","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2155-6863","authenticated-orcid":false,"given":"Wanhong","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangpeng","family":"Yue","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1016\/j.cell.2014.09.052","article-title":"Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes","volume":"159","author":"Soh","year":"2014","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/nrg3366","article-title":"Y-chromosome evolution: Emerging insights into processes of Y-chromosome degeneration","volume":"14","author":"Bachtrog","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e67345","DOI":"10.7554\/eLife.67345","article-title":"Y chromosome functions in mammalian spermatogenesis","volume":"10","author":"Subrini","year":"2021","journal-title":"eLife"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1126\/science.ads6495","article-title":"Systematic identification of Y-chromosome gene functions in mouse spermatogenesis","volume":"387","author":"Subrini","year":"2025","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"8277","DOI":"10.1038\/s41467-024-52384-5","article-title":"Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content","volume":"15","author":"Olagunju","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1146\/annurev-genet-112414-055311","article-title":"The biology and evolution of mammalian Y chromosomes","volume":"49","author":"Hughes","year":"2015","journal-title":"Annu. Rev. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Yang, Y., Chang, T.C., Yasue, H., Bharti, A.K., Retzel, E.F., and Liu, W.S. (2011). ZNF280BY and ZNF280AY: Autosome derived Y-chromosome gene families in Bovidae. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-13"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Wang, Y., Chen, Y., Zhu, Z., Zeng, X., Ha, W., Su, L., Hu, L., Liu, Y., Li, B., and Loor, J. (2026). Divergent amplification of Y-linked dosage-sensitive genes triggers regulatory mismatch underlying cattle\u2013yak male sterility. Biomolecules, 16.","DOI":"10.3390\/biom16030471"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"evad205","DOI":"10.1093\/gbe\/evad205","article-title":"Transcript isoform diversity of ampliconic genes on the Y chromosome of great apes","volume":"15","author":"Tomaszkiewicz","year":"2023","journal-title":"Genome Biol. Evol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"12373","DOI":"10.1073\/pnas.1221104110","article-title":"Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development","volume":"110","author":"Chang","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nature13206","article-title":"Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators","volume":"508","author":"Bellott","year":"2014","journal-title":"Nature"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/s41559-024-02627-x","article-title":"Evolutionary divergence between homologous X\u2013Y chromosome genes shapes sex-biased biology","volume":"9","author":"DeCasien","year":"2025","journal-title":"Nat. Ecol. Evol."},{"key":"ref_13","unstructured":"Hamilton, C.K., Verduzco-Gomez, A.R., Favetta, L.A., Blondin, P., and King, W.A. (2013). Holstein bull fertility linked to more copies of a testis-specific protein in the genome. Proceedings of the 2013 Annual Meeting, University of Guelph."},{"key":"ref_14","first-page":"6","article-title":"Detection of single nucleotide polymorphism of holandric genes and association with sperm nuclear maturity in bovines","volume":"67","author":"Kaur","year":"2014","journal-title":"Indian J. Dairy Sci."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Fu, X., Yang, Y., Yan, Z., Liu, M., and Wang, X. (2022). Transcriptomic study of spermatogenesis in the testis of Hu sheep and Tibetan sheep. Genes, 13.","DOI":"10.3390\/genes13122212"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Xi, B., Zhao, S., Zhang, R., Lu, Z., Li, J., An, X., and Yue, Y. (2024). Transcriptomic study of different stages of development in the testis of sheep. Animals, 14.","DOI":"10.3390\/ani14192767"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Xu, H., Sun, W., Pei, S., Li, W., Li, F., and Yue, X. (2022). Identification of key genes related to postnatal testicular development based on transcriptomic data of testis in Hu sheep. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.773695"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"110949","DOI":"10.1016\/j.ygeno.2024.110949","article-title":"Integration analysis of transcriptome and metabolome revealed the potential mechanism of spermatogenesis in Tibetan sheep (Ovis aries) at extreme high altitude","volume":"116","author":"Zhang","year":"2024","journal-title":"Genomics"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Su, J., Zhang, Y., Su, H., Wang, C., Wang, D., Yang, Y., Li, X., Qi, W., Li, H., and Li, X. (2022). Dosage compensation of the X chromosome during sheep testis development revealed by single-cell RNA sequencing. Animals, 12.","DOI":"10.3390\/ani12172169"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"107306","DOI":"10.1016\/j.anireprosci.2023.107306","article-title":"Study on the changes of LHR, FSHR and AR with the development of testis cells in Hu sheep","volume":"256","author":"Su","year":"2023","journal-title":"Anim. Reprod. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/s42003-026-09729-1","article-title":"Single-nucleus RNA sequencing provides insights into the genetic mechanisms underlying reproductive adaptability in Tibetan sheep (Ovis aries)","volume":"9","author":"Wang","year":"2026","journal-title":"Commun. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Atawalna, J., Essel, D.C.J., Nettey, N., and Amponsah, P.M. (2022). Correlation between testicular morphometric parameters and sperm reserves in Ghanaian West African Dwarf rams. Vet. Med. Int., 8421334.","DOI":"10.1155\/2022\/8421334"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Abba, Y., and Igbokwe, I.O. (2015). Testicular and related size evaluations in Nigerian Sahel goats with optimal cauda epididymal sperm reserve. Vet. Med. Int., 357519.","DOI":"10.1155\/2015\/357519"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"233","DOI":"10.4314\/sajas.v37i4.4100","article-title":"Relationship of testicular development with age, body weight, semen characteristics and testosterone in Kivircik ram lambs","volume":"37","author":"Elmaz","year":"2007","journal-title":"S. Afr. J. Anim. Sci."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Wang, X., Deng, F., Chen, Y., Liu, X., Li, D., Tang, X., Lai, H., Li, Q., Fu, W., and Liu, G. (2025). Developmental phase-specific molecular signatures and signaling pathways in cryptorchidism-induced testicular damage. Biomolecules, 15.","DOI":"10.3390\/biom15111584"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Nassif, C., Mara, L., Chessa, F., Cossu, I., Gallus, M., Melis, F., Cannas, A., and Dattena, M. (2026). Cryptorchidism in Sarda sheep: Incidence, morphology, ultrasonography and behavioral insights. Animals, 16.","DOI":"10.3390\/ani16081253"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Pei, S.W., Liu, Y.K., Wang, Z.Y., Yuan, Z.H., Li, W.H., Li, F.D., and Yue, X.P. (2025). Identification of key genes related to unilateral cryptorchidism in sheep by comprehensive transcriptomics and proteomics analyses. BMC Genom., 26.","DOI":"10.1186\/s12864-024-11166-5"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.theriogenology.2020.10.014","article-title":"Effect of feeding linseed diet on testis development, antioxidant capacity, and epididymal cauda sperm concentration in Chinese Hu lamb","volume":"159","author":"Li","year":"2021","journal-title":"Theriogenology"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.12688\/f1000research.21142.2","article-title":"Falco: High-speed FastQC emulation for quality control of sequencing data","volume":"8","author":"Smith","year":"2021","journal-title":"F1000Research"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: An efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"5","DOI":"10.6026\/97320630002005","article-title":"Mfuzz: A software package for soft clustering of microarray data","volume":"2","author":"Kumar","year":"2007","journal-title":"Bioinformation"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1146\/annurev-animal-020518-115332","article-title":"Mammalian sex chromosome structure, gene content, and function in male fertility","volume":"7","author":"Liu","year":"2019","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"61","DOI":"10.4314\/sajas.v32i2.3748","article-title":"Genetic parameters of testicular measurements in Merino rams and the influence of scrotal circumference on total flock fertility","volume":"32","author":"Duguma","year":"2002","journal-title":"S. Afr. J. Anim. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.theriogenology.2022.12.010","article-title":"Identification of Y-SNPs within ovine MSY region and their association with testicular size","volume":"197","author":"Pei","year":"2023","journal-title":"Theriogenology"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/age.13166","article-title":"A mutation modulating DDX3Y gene expression cosegregates with the major Y-chromosomal haplogroups and with testis size in Hu sheep","volume":"53","author":"Zhang","year":"2022","journal-title":"Anim. Genet."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1016\/j.fertnstert.2025.03.024","article-title":"Genetic and genomic insights into male reproductive tract development","volume":"123","author":"Held","year":"2025","journal-title":"Fertil. Steril."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1016\/S0031-3955(16)37015-8","article-title":"Primary and secondary testicular insufficiency","volume":"37","author":"Lee","year":"1990","journal-title":"Pediatr. Clin. N. Am."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Su, J., Yang, Y., Wang, D., Su, H., Zhao, F., Zhang, C., Zhang, M., Li, X., He, T., and Li, X. (2025). A dynamic transcriptional cell atlas of testes development after birth in Hu sheep. BMC Biol., 23.","DOI":"10.1186\/s12915-025-02186-y"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"117946","DOI":"10.1016\/j.theriogenology.2026.117946","article-title":"Molecular mechanism of testicular oxidative stress-induced ferroptosis in Leydig cells caused by cryptorchidism in yak","volume":"261","author":"Zeng","year":"2026","journal-title":"Theriogenology"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1530\/rep.0.1250769","article-title":"Proliferation and functional maturation of Sertoli cells, and their relevance to disorders of testis function in adulthood","volume":"125","author":"Sharpe","year":"2003","journal-title":"Reproduction"},{"key":"ref_44","unstructured":"Maxie, M.G. (2016). Male genital system. Jubb, Kennedy & Palmer\u2019s Pathology of Domestic Animals, W.B. Saunders. [6th ed.]."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1177\/0300985820906891","article-title":"Severe degenerative changes in cryptorchid testes in Japanese Black cattle","volume":"57","author":"Fuke","year":"2020","journal-title":"Vet. Pathol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/7771","article-title":"Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome","volume":"21","author":"Lahn","year":"1999","journal-title":"Nat. Genet."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1093\/gbe\/evaa088","article-title":"Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels","volume":"12","author":"Vegesna","year":"2020","journal-title":"Genome Biol. Evol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1093\/humrep\/deaf041","article-title":"Clinical presentation of congenital hypogonadotropic hypogonadism in males with delayed puberty according to genetic etiology: A systematic review and meta-analysis after reclassification of gene variants","volume":"40","author":"Castro","year":"2025","journal-title":"Hum. Reprod."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1038\/s41598-025-33814-w","article-title":"Quantitative dissection of sexual dimorphism in mice through Y-linked gene knockouts and multivariate phenotyping","volume":"16","author":"Tanaka","year":"2026","journal-title":"Sci. Rep."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1101\/gr.261248.120","article-title":"Quantitative analysis of Y-chromosome gene expression across 36 human tissues","volume":"30","author":"Godfrey","year":"2020","journal-title":"Genome Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/s42003-023-04714-4","article-title":"DDX3Y is likely the key spermatogenic factor in the AZFa region that contributes to human non-obstructive azoospermia","volume":"6","author":"Dicke","year":"2023","journal-title":"Commun. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1261\/rna.078926.121","article-title":"DDX3X and DDX3Y are redundant in protein synthesis","volume":"27","author":"Venkataramanan","year":"2021","journal-title":"RNA"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2588","DOI":"10.1016\/j.molcel.2022.04.022","article-title":"Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation","volume":"82","author":"Shen","year":"2022","journal-title":"Mol. Cell"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/13\/2107\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T12:14:23Z","timestamp":1783512863000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/13\/2107"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,7]]},"references-count":53,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["ani16132107"],"URL":"https:\/\/doi.org\/10.3390\/ani16132107","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,7]]}}}