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Romeo-Cardeillac C, Trovero MF, Radío S, Smircich P, Rodríguez-Casuriaga R, Geisinger A, Sotelo-Silveira J. Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis. BMC Genomics 2024; 25:295. [PMID: 38509455 PMCID: PMC10953240 DOI: 10.1186/s12864-024-10170-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Mammalian testis is a highly complex and heterogeneous tissue. This complexity, which mostly derives from spermatogenic cells, is reflected at the transcriptional level, with the largest number of tissue-specific genes and long noncoding RNAs (lncRNAs) compared to other tissues, and one of the highest rates of alternative splicing. Although it is known that adequate alternative-splicing patterns and stage-specific isoforms are critical for successful spermatogenesis, so far only a very limited number of reports have addressed a detailed study of alternative splicing and isoforms along the different spermatogenic stages. RESULTS In the present work, using highly purified stage-specific testicular cell populations, we detected 33,002 transcripts expressed throughout mouse spermatogenesis not annotated so far. These include both splice variants of already annotated genes, and of hitherto unannotated genes. Using conservative criteria, we uncovered 13,471 spermatogenic lncRNAs, which reflects the still incomplete annotation of lncRNAs. A distinctive feature of lncRNAs was their lower number of splice variants compared to protein-coding ones, adding to the conclusion that lncRNAs are, in general, less complex than mRNAs. Besides, we identified 2,794 unannotated transcripts with high coding potential (including some arising from yet unannotated genes), many of which encode unnoticed putative testis-specific proteins. Some of the most interesting coding splice variants were chosen, and validated through RT-PCR. Remarkably, the largest number of stage-specific unannotated transcripts are expressed during early meiotic prophase stages, whose study has been scarcely addressed in former transcriptomic analyses. CONCLUSIONS We detected a high number of yet unannotated genes and alternatively spliced transcripts along mouse spermatogenesis, hence showing that the transcriptomic diversity of the testis is considerably higher than previously reported. This is especially prominent for specific, underrepresented stages such as those of early meiotic prophase, and its unveiling may constitute a step towards the understanding of their key events.
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Affiliation(s)
- Carlos Romeo-Cardeillac
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - María Fernanda Trovero
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santiago Radío
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
| | - Adriana Geisinger
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay.
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), 11,400, Montevideo, Uruguay.
| | - José Sotelo-Silveira
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay.
- Department of Cell and Molecular Biology, Facultad de Ciencias, UdelaR, 11,400, Montevideo, Uruguay.
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Zhang X, Lin Q, Liao W, Zhang W, Li T, Li J, Zhang Z, Huang X, Zhang H. Identification of New Candidate Genes Related to Semen Traits in Duroc Pigs through Weighted Single-Step GWAS. Animals (Basel) 2023; 13:ani13030365. [PMID: 36766254 PMCID: PMC9913471 DOI: 10.3390/ani13030365] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Semen traits play a key role in the pig industry because boar semen is widely used in purebred and crossbred pigs. The production of high-quality semen is crucial to ensuring a good result in artificial insemination. With the wide application of artificial insemination in the pig industry, more and more attention has been paid to the improvement of semen traits by genetic selection. The purpose of this study was to identify the genetic regions and candidate genes associated with semen traits of Duroc boars. We used weighted single-step GWAS to identify candidate genes associated with sperm motility, sperm progressive motility, sperm abnormality rate and total sperm count in Duroc pigs. In Duroc pigs, the three most important windows for sperm motility-sperm progressive motility, sperm abnormality rate, and total sperm count-explained 12.45%, 9.77%, 15.80%, and 12.15% of the genetic variance, respectively. Some genes that are reported to be associated with spermatogenesis, testicular function and male fertility in mammals have been detected previously. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. We found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm motility and sperm abnormality rate, which confirms the hypothesis of gene pleiotropy. Gene network enrichment analysis showed that STRA8, UBB and CATSPER1 were enriched in the common biological process and participated in male meiosis and spermatogenesis. The SNPs of candidate genes can be given more weight in genome selection to improve the ability of genome prediction. This study provides further insight into the understanding the genetic structure of semen traits in Duroc boars.
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Affiliation(s)
- Xiaoke Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qing Lin
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Weili Liao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wenjing Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Tingting Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiang Huang
- Guangdong Guyue Technology Co., Ltd. Guangzhou 510980, China
- Correspondence: (X.H.); (H.Z.)
| | - Hao Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.H.); (H.Z.)
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Donizetti A, Venditti M, Arcaniolo D, Aliperti V, Carrese AM, De Sio M, Minucci S, Caraglia M, Aniello F. The long non-coding RNA transcript, LOC100130460 (CAND1.11) gene, encodes a novel protein highly expressed in cancer cells and tumor human testis tissues. Cancer Biomark 2023; 38:343-353. [PMID: 37661873 DOI: 10.3233/cbm-230160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
BACKGROUND Testis-specific genes encoding for long non-coding RNA (lncRNA) have been detected in several cancers; many produce proteins with restricted or aberrant expression patterns in normal or cancer tissues. OBJECTIVE To characterize new lncRNA involved in normal and/or pathological differentiation of testicular cells. METHODS Using bioinformatics analysis, we found that lncRNA LOC100130460 (CAND1.11) is expressed in normal and tumor testis; its expression was assessed in several human cell lines by qRT-PCR. CAND1.11 protein, produced by a single nucleotide mutation, was studied by western blot and immunofluorescence analysis on normal, classic seminoma, and Leydig cell tumor testicular tissues. RESULTS CAND1.11 gene is primate-specific; its expression was low in SH-SY5Y cells and increased when differentiated with retinoic acid treatment. CAND1.11 expression in PC3 cells was higher than in PNT2 cells. CAND1.11 protein is present in the human testis and overexpressed in testicular cancer tissues. CONCLUSIONS This report is one of the few providing evidence that a lncRNA produces a protein expressed in normal human tissues and overexpressed in several testicular cancers, suggesting its involvement in regulating cell proliferation and differentiation. Although further studies are needed to validate the results, our data indicate that CAND1.11 could be a potential new prognostic biomarker to use in proliferation and cancer.
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Affiliation(s)
- Aldo Donizetti
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Massimo Venditti
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Davide Arcaniolo
- Dipartimento della Donna, del Bambino e di Chirurgia Generale e Specialistica, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Vincenza Aliperti
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Anna Maria Carrese
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Marco De Sio
- Dipartimento della Donna, del Bambino e di Chirurgia Generale e Specialistica, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Sergio Minucci
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Michele Caraglia
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Francesco Aniello
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
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Otsuka K, Yang H, Matsubara S, Shiraishi A, Kurihara M, Satake H, Kimura AP. Evidence for a functional role of Start, a long noncoding RNA, in mouse spermatocytes. PLoS One 2022; 17:e0273279. [PMID: 36006924 PMCID: PMC9409574 DOI: 10.1371/journal.pone.0273279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
A mouse testis-specific long noncoding RNA (lncRNA), Start, is localized in the cytosol of Leydig cells and in the nucleus of pachytene spermatocytes. We previously showed that Start regulates steroidogenesis through controlling the expression of Star and Hsd3b1 genes in Leydig cells, but its function in germ cells was not known. Here we verified that a spermatocyte-specific protease gene, Prss43/Tessp-3, was downregulated in Start-knockout testes. To investigate the transcriptional regulatory activity of Start in spermatocytes, we first performed a series of reporter gene assays using a thymidine kinase promoter in spermatocyte-derived GC-2spd(ts) cells. A 5.4-kb genome sequence encompassing Start exhibited enhancer activity for this promoter, and the activity was decreased by knockdown of Start. Deletion of the Start promoter and replacement of the Start sequence abolished the enhancer activity and, consistently, the activity was detected in further experiments only when Start was actively transcribed. We then examined whether the Prss43/Tessp-3 gene could be a target of Start. A reporter gene assay demonstrated that the 5.4-kb sequence exhibited enhancer activity for a Prss43/Tessp-3 promoter in GC-2spd(ts) cells and that the activity was significantly decreased by knockdown of Start. These results suggest that Start functions in transcriptional activation of the Prss43/Tessp-3 gene in spermatocytes. Given that Start is presumed to regulate steroidogenic genes at the posttranscriptional level in Leydig cells, the function in spermatocytes is a novel role of Start. These findings provide an insight into multifunctionality of lncRNAs in the testis.
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Affiliation(s)
- Kai Otsuka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Microbiology and Molecular Genetics, University of California, Davis, California United States of America
| | - Hong Yang
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Misuzu Kurihara
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P. Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
- * E-mail:
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