1
|
Yu M, Zhang S, Ma Z, Qiang J, Wei J, Sun L, Kocher TD, Wang D, Tao W. Disruption of Zar1 leads to arrested oogenesis by regulating polyadenylation via Cpeb1 in tilapia (Oreochromis niloticus). Int J Biol Macromol 2024; 260:129632. [PMID: 38253139 DOI: 10.1016/j.ijbiomac.2024.129632] [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] [Received: 07/11/2023] [Revised: 11/21/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
Oogenesis is a complex process regulated by precise coordination of multiple factors, including maternal genes. Zygote arrest 1 (zar1) has been identified as an ovary-specific maternal gene that is vital for oocyte-to-embryo transition and oogenesis in mouse and zebrafish. However, its function in other species remains to be elucidated. In the present study, zar1 was identified with conserved C-terminal zinc finger domains in Nile tilapia. zar1 was highly expressed in the ovary and specifically expressed in phase I and II oocytes. Disruption of zar1 led to the failed transition from oogonia to phase I oocytes, with somatic cell apoptosis. Down-regulation and failed polyadenylation of figla, gdf9, bmp15 and wee2 mRNAs were observed in the ovaries of zar1-/- fish. Cpeb1, a gene essential for polyadenylation that interacts with Zar1, was down-regulated in zar1-/- fish. Moreover, decreased levels of serum estrogen and increased levels of androgen were observed in zar1-/- fish. Taken together, zar1 seems to be essential for tilapia oogenesis by regulating polyadenylation and estrogen synthesis. Our study shows that Zar1 has different molecular functions during gonadal development by the similar signaling pathway in different species.
Collapse
Affiliation(s)
- Miao Yu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shiyi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhisheng Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jing Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lina Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, United States of America
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| |
Collapse
|
2
|
Cui H, Zhu H, Ban W, Li Y, Chen R, Li L, Zhang X, Chen K, Xu H. Characterization of Two Gonadal Genes, zar1 and wt1b, in Hermaphroditic Fish Asian Seabass ( Lates calcarifer). Animals (Basel) 2024; 14:508. [PMID: 38338151 PMCID: PMC10854929 DOI: 10.3390/ani14030508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Zygote arrest-1 (Zar1) and Wilms' tumor 1 (Wt1) play an important role in oogenesis, with the latter also involved in testicular development and gender differentiation. Here, Lczar1 and Lcwt1b were identified in Asian seabass (Lates calcarifer), a hermaphrodite fish, as the valuable model for studying sex differentiation. The cloned cDNA fragments of Lczar1 were 1192 bp, encoding 336 amino acids, and contained a zinc-binding domain, while those of Lcwt1b cDNA were 1521 bp, encoding a peptide of 423 amino acids with a Zn finger domain belonging to Wt1b family. RT-qPCR analysis showed that Lczar1 mRNA was exclusively expressed in the ovary, while Lcwt1b mRNA was majorly expressed in the gonads in a higher amount in the testis than in the ovary. In situ hybridization results showed that Lczar1 mRNA was mainly concentrated in oogonia and oocytes at early stages in the ovary, but were undetectable in the testis. Lcwt1b mRNA was localized not only in gonadal somatic cells (the testis and ovary), but also in female and male germ cells in the early developmental stages, such as those of previtellogenic oocytes, spermatogonia, spermatocytes and spermatids. These results indicated that Lczar1 and Lcwt1b possibly play roles in gonadal development. Therefore, the findings of this study will provide a basis for clarifying the mechanism of Lczar1 and Lcwt1b in regulating germ cell development and the sex reversal of Asian seabass and even other hermaphroditic species.
Collapse
Affiliation(s)
- Han Cui
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Haoyu Zhu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Wenzhuo Ban
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Yulin Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Ruyi Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Lingli Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Xiaoling Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Kaili Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Hongyan Xu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| |
Collapse
|
3
|
Shi R, Li X, Cheng P, Yang Q, Chen Z, Chen S, Wang N. Characterization of growth differentiation factor 9 and bone morphogenetic factor 15 in Chinese tongue sole (Cynoglossus semilaevis): Sex-biased expression pattern and promoter regulation. Theriogenology 2022; 182:119-128. [DOI: 10.1016/j.theriogenology.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
|
4
|
Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
Collapse
Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
| |
Collapse
|
5
|
Deutschmeyer VE, Richter AM. The ZAR1 protein in cancer; from epigenetic silencing to functional characterisation and epigenetic therapy of tumour suppressors. Biochim Biophys Acta Rev Cancer 2020; 1874:188417. [PMID: 32828887 DOI: 10.1016/j.bbcan.2020.188417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
ZAR1, zygote arrest 1, is a zinc finger protein (C-terminus), which was initially identified in mouse oocytes. Later it was found that its expression is present in various human tissues e.g. lung and kidney. Interestingly, it was observed that in various tumour types the ZAR1 transcript is missing due to hypermethylation of its CpG island promoter, but not ZAR2. Since methylation of the ZAR1 promoter is described as a frequent event in tumourigenesis, ZAR1 could serve as a useful diagnostic marker in cancer screens. ZAR1 was described as a useful prognostic/diagnostic cancer marker for lung cancer, kidney cancer, melanoma and possibly liver carcinoma. Furthermore, ZAR1 was reactivated as a tumour suppressor by epigenetic therapy using CRISPR-dCas9 method. This method holds the potential to precisely target not only ZAR1 and reactivate tumour suppressors in a tailored cancer therapy. ZAR1 is highly conserved amongst vertebrates, especially its zinc finger, which is the relevant domain for its protein and RNA binding ability. ZAR1 is implicated in various cellular mechanisms including regulation of oocyte/embryo development, cell cycle control and mRNA binding, though little was known about the underlying mechanisms. ZAR1 was reported to regulate and activate translation through the binding to TCS translation control sequences in the 3'UTRs of its target mRNA the kinase WEE1. ZAR1 has a tumour suppressing function by inhibiting cell cycle progression. Here we review the current literature on ZAR1 focusing on structural, functional and epigenetic aspects. Characterising the cellular mechanisms that regulate the signalling pathways ZAR1 is involved in, could lead to a deeper understanding of tumour development and, furthermore, to new strategies in cancer treatment.
Collapse
Affiliation(s)
| | - Antje M Richter
- Institute for Genetics, University of Giessen, 35392 Giessen, Germany; Max-Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.
| |
Collapse
|
6
|
Kottmann JS, Jørgensen MGP, Bertolini F, Loh A, Tomkiewicz J. Differential impacts of carp and salmon pituitary extracts on induced oogenesis, egg quality, molecular ontogeny and embryonic developmental competence in European eel. PLoS One 2020; 15:e0235617. [PMID: 32634160 PMCID: PMC7340298 DOI: 10.1371/journal.pone.0235617] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
Low egg quality and embryonic survival are critical challenges in aquaculture, where assisted reproduction procedures and other factors may impact egg quality. This includes European eel (Anguilla anguilla), where pituitary extract from carp (CPE) or salmon (SPE) is applied to override a dopaminergic inhibition of the neuroendocrine system, preventing gonadotropin secretion and gonadal development. The present study used either CPE or SPE to induce vitellogenesis in female European eel and compared impacts on egg quality and offspring developmental competence with emphasis on the maternal-to-zygotic transition (MZT). Females treated with SPE produced significantly higher proportions of floating eggs with fewer cleavage abnormalities and higher embryonic survival. These findings related successful embryogenesis to higher abundance of mRNA transcripts of genes involved in cell adhesion, activation of MZT, and immune response (dcbld1, epcam, oct4, igm) throughout embryonic development. The abundance of mRNA transcripts of cldnd, foxr1, cea, ccna1, ccnb1, ccnb2, zar1, oct4, and npm2 was relatively stable during the first eight hours, followed by a drop during MZT and low levels thereafter, indicating transfer and subsequent clearance of maternal mRNA. mRNA abundance of zar1, epcam, and dicer1 was associated with cleavage abnormalities, while mRNA abundance of zar1, sox2, foxr1, cldnd, phb2, neurod4, and neurog1 (before MZT) was associated with subsequent embryonic survival. In a second pattern, low initial mRNA abundance with an increase during MZT and higher levels persisting thereafter indicating the activation of zygotic transcription. mRNA abundance of ccna1, npm2, oct4, neurod4, and neurog1 during later embryonic development was associated with hatch success. A deviating pattern was observed for dcbld1, which mRNA levels followed the maternal-effect gene pattern but only for embryos from SPE treated females. Together, the differences in offspring production and performance reported in this study show that PE composition impacts egg quality and embryogenesis and in particular, the transition from initial maternal transcripts to zygotic transcription.
Collapse
Affiliation(s)
- Johanna S. Kottmann
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Adrian Loh
- School of Science, University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Jonna Tomkiewicz
- National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
7
|
Peng L, Fu W, Wu X, He S, Zhao H, Liu J, Liu W, Xiao Y. Bisexual Fertile Triploid Zebrafish (Danio rerio): a Rare Case. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:443-455. [PMID: 32307628 DOI: 10.1007/s10126-020-09964-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
Previous studies have suggested that artificially induced triploid zebrafish are exclusively male-biased. Owing to greatly inhibited gonadal development for the artificially induced triploid fish, they are regarded to be sterile in general. In this article, partially fertile bisexual triploid zebrafish are produced by suppressing extrusion of the second polar body by heat shock. Histological observation confirms that the early gonadal development of these triploid zebrafish is normal. Backcrossing and self-crossing are used to demonstrate that both the female and male triploid zebrafish have partial reproductive ability. Their dynamic of chromosomes during meiosis is revealed from the chromosome preparations of gonads. Examination of the expressed gonadal development-related genes shows some molecular evidence of the normal gonadal development in the triploid zebrafish. Clearly, these fertile bisexual triploid zebrafish can provide a unique system to study sex determination, as well as aneuploidy associated human diseases such as infertility and pregnancy loss.
Collapse
Affiliation(s)
- Liangyue Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xianlong Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Sheng He
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Han Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jinhui Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Wenbin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
- School of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
| |
Collapse
|
8
|
Abstract
Growth differentiation factor 9 (GDF9) has been shown to be involved in regulating follicular development and reproduction in many mammalian species. However, related information about the effect of the GDF9 gene on reproductive traits of New Zealand white rabbits was rarely reported. In this study, rabbits were distributed into two groups (poor and prolific offspring productions) and cloning and quantitative real-time PCR (qPCR) were employed to characterize the rabbit GDF9 gene. By cloning, 2515-bp genomic DNA and 1359-bp cDNA sequences were obtained. Comparing the two cDNA sequences, three potential mutation sites (C.539C>T,C.562G>C and C.718C>G) in exon 2 of the GDF9 gene were found, and the corresponding amino acids changed (P.183T>M, P.188E>Q and P.240L>V). The qPCR results revealed that GDF9 was not tissue-specific, but rather expressed in all collected tissues. The expression level of the GDF9 gene was highest in the ovary, and was significantly increased (P< 0.05) compared with the other tissues. The liver had the second highest expression, and the heart and spleen had the least expression in New Zealand white rabbits. In the prolific group, the expression quantity of the GDF9 gene significantly increased (P < 0.05) in the heart, spleen, ovary, liver and uterus (P < 0.01) than the other groups. The amino acid sequence identities of human, sheep, goat, mouse, cattle, pig, cat, donkey, Nancy Ma's night monkey and olive baboon were 72, 68, 69, 66, 69, 71, 67, 73, 75 and 73%, respectively. Bioinformatics analysis was executed, and a random coil was determined to be the primary secondary structure.
Collapse
|
9
|
Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes). Sci Rep 2017; 7:40241. [PMID: 28071684 PMCID: PMC5223123 DOI: 10.1038/srep40241] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/05/2016] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary. Of the miRNAs exhibiting the highest overabundance in the ovary, 20 were selected for further analysis. Using a combination of QPCR and in silico analyses, we identified 8 novel miRNAs that are predominantly expressed in the ovary, including 2 miRNAs (miR-4785 and miR-6352) that exhibit strict ovarian expression. Of these 8 miRNAs, 7 were previously uncharacterized in fish. The strict ovarian expression of miR-4785 and miR-6352 suggests an important role in oogenesis and/or early development, possibly involving a maternal effect. Together, these results indicate that, similar to protein-coding genes, a significant number of ovarian-predominant miRNA genes are found in fish.
Collapse
|
10
|
Geffroy B, Guilbaud F, Amilhat E, Beaulaton L, Vignon M, Huchet E, Rives J, Bobe J, Fostier A, Guiguen Y, Bardonnet A. Sexually dimorphic gene expressions in eels: useful markers for early sex assessment in a conservation context. Sci Rep 2016; 6:34041. [PMID: 27658729 PMCID: PMC5034313 DOI: 10.1038/srep34041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022] Open
Abstract
Environmental sex determination (ESD) has been detected in a range of vertebrate reptile and fish species. Eels are characterized by an ESD that occurs relatively late, since sex cannot be histologically determined before individuals reach 28 cm. Because several eel species are at risk of extinction, assessing sex at the earliest stage is a crucial management issue. Based on preliminary results of RNA sequencing, we targeted genes susceptible to be differentially expressed between ovaries and testis at different stages of development. Using qPCR, we detected testis-specific expressions of dmrt1, amh, gsdf and pre-miR202 and ovary-specific expressions were obtained for zar1, zp3 and foxn5. We showed that gene expressions in the gonad of intersexual eels were quite similar to those of males, supporting the idea that intersexual eels represent a transitional stage towards testicular differentiation. To assess whether these genes would be effective early molecular markers, we sampled juvenile eels in two locations with highly skewed sex ratios. The combined expression of six of these genes allowed the discrimination of groups according to their potential future sex and thus this appears to be a useful tool to estimate sex ratios of undifferentiated juvenile eels.
Collapse
Affiliation(s)
- Benjamin Geffroy
- INRA, UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, 35000 Rennes, France
- INRA, UMR 1224 Ecobiop, Aquapôle, Pôle Gest’Aqua, Quartier Ibarron, 64310, Saint Pée sur Nivelle, France
- UPPA, UMR 1224 Ecobiop, UFR des Sciences de la Côte Basque, allée du parc Montaury, 64600, Anglet, France
| | - Florian Guilbaud
- INRA, UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, 35000 Rennes, France
| | - Elsa Amilhat
- UMR 5110 CNRS - UPVD (CEFREM), Université de Perpignan, Bâtiment R, 58 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Laurent Beaulaton
- Onema, pôle Gest’Aqua, 65 rue de Saint Brieuc, 35042 Rennes Cedex, France
- INRA, 1224 (U3E), Pôle Gest’Aqua, 65 rue de Saint Brieuc, 35042 Rennes Cedex, France
| | - Matthias Vignon
- INRA, UMR 1224 Ecobiop, Aquapôle, Pôle Gest’Aqua, Quartier Ibarron, 64310, Saint Pée sur Nivelle, France
- UPPA, UMR 1224 Ecobiop, UFR des Sciences de la Côte Basque, allée du parc Montaury, 64600, Anglet, France
| | - Emmanuel Huchet
- INRA, UMR 1224 Ecobiop, Aquapôle, Pôle Gest’Aqua, Quartier Ibarron, 64310, Saint Pée sur Nivelle, France
- UPPA, UMR 1224 Ecobiop, UFR des Sciences de la Côte Basque, allée du parc Montaury, 64600, Anglet, France
| | - Jacques Rives
- INRA, UMR 1224 Ecobiop, Aquapôle, Pôle Gest’Aqua, Quartier Ibarron, 64310, Saint Pée sur Nivelle, France
- UPPA, UMR 1224 Ecobiop, UFR des Sciences de la Côte Basque, allée du parc Montaury, 64600, Anglet, France
| | - Julien Bobe
- INRA, UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, 35000 Rennes, France
| | - Alexis Fostier
- INRA, UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, 35000 Rennes, France
| | - Yann Guiguen
- INRA, UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, 35000 Rennes, France
| | - Agnès Bardonnet
- INRA, UMR 1224 Ecobiop, Aquapôle, Pôle Gest’Aqua, Quartier Ibarron, 64310, Saint Pée sur Nivelle, France
- UPPA, UMR 1224 Ecobiop, UFR des Sciences de la Côte Basque, allée du parc Montaury, 64600, Anglet, France
| |
Collapse
|
11
|
Desvignes T, Nguyen T, Chesnel F, Bouleau A, Fauvel C, Bobe J. X-Linked Retinitis Pigmentosa 2 Is a Novel Maternal-Effect Gene Required for Left-Right Asymmetry in Zebrafish. Biol Reprod 2015; 93:42. [PMID: 26134862 DOI: 10.1095/biolreprod.115.130575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/10/2015] [Indexed: 01/05/2023] Open
Abstract
Retinitis pigmentosa 2 (RP2) gene is responsible for up to 20% of X-linked retinitis pigmentosa, a severe heterogeneous genetic disorder resulting in progressive retinal degeneration in humans. In vertebrates, several bodies of evidence have clearly established the role of Rp2 protein in cilia genesis and/or function. Unexpectedly, some observations in zebrafish have suggested the oocyte-predominant expression of the rp2 gene, a typical feature of maternal-effect genes. In the present study, we investigate the maternal inheritance of rp2 gene products in zebrafish eggs in order to address whether rp2 could be a novel maternal-effect gene required for normal development. Although both rp2 mRNA and corresponding protein are expressed during oogenesis, rp2 mRNA is maternally inherited, in contrast to Rp2 protein. A knockdown of the protein transcribed from both rp2 maternal and zygotic mRNA results in delayed epiboly and severe developmental defects, including eye malformations, that were not observed when only the protein from zygotic origin was knocked down. Moreover, the knockdown of maternal and zygotic Rp2 revealed a high incidence of left-right asymmetry establishment defects compared to only zygotic knockdown. Here we show that rp2 is a novel maternal-effect gene exclusively expressed in oocytes within the zebrafish ovary and demonstrate that maternal rp2 mRNA is essential for successful embryonic development and thus contributes to egg developmental competence. Our observations also reveal that Rp2 protein translated from maternal mRNA is important to allow normal heart loop formation, thus providing evidence of a direct maternal contribution to left-right asymmetry establishment.
Collapse
Affiliation(s)
- Thomas Desvignes
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas Les Flots, France
| | - Thaovi Nguyen
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France
| | | | - Aurélien Bouleau
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas Les Flots, France
| | | | - Julien Bobe
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France
| |
Collapse
|
12
|
Robertson LS, McCormick SD. Transcriptional profiling of the parr-smolt transformation in Atlantic salmon. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:351-60. [PMID: 22951584 DOI: 10.1016/j.cbd.2012.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 07/31/2012] [Accepted: 07/31/2012] [Indexed: 01/03/2023]
Abstract
The parr-smolt transformation in Atlantic salmon (Salmo salar) is a complex developmental process that culminates in the ability to migrate to and live in seawater. We used GRASP 16K cDNA microarrays to identify genes that are differentially expressed in the liver, gill, hypothalamus, pituitary, and olfactory rosettes of smolts compared to parr. Smolts had higher levels of gill Na(+)/K(+)-ATPase activity, plasma cortisol and plasma thyroid hormones relative to parr. Across all five tissues, stringent microarray analyses identified 48 features that were differentially expressed in smolts compared to parr. Using a less stringent method we found 477 features that were differentially expressed at least 1.2-fold in smolts, including 172 features in the gill. Smolts had higher mRNA levels of genes involved in transcription, protein biosynthesis and folding, electron transport, oxygen transport, and sensory perception and lower mRNA levels for genes involved in proteolysis. Quantitative RT-PCR was used to confirm differential expression in select genes identified by microarray analyses and to quantify expression of other genes known to be involved in smolting. This study expands our understanding of the molecular processes that underlie smolting in Atlantic salmon and identifies genes for further investigation.
Collapse
|
13
|
Monget P, Bobe J, Gougeon A, Fabre S, Monniaux D, Dalbies-Tran R. The ovarian reserve in mammals: a functional and evolutionary perspective. Mol Cell Endocrinol 2012; 356:2-12. [PMID: 21840373 DOI: 10.1016/j.mce.2011.07.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/25/2011] [Accepted: 07/27/2011] [Indexed: 01/15/2023]
Abstract
The constitution and the control of the ovarian reserve is of importance in mammals and women. In particular, the number of primordial follicles at puberty is positively correlated with the number of growing follicles and their response to gonadotropin treatments. The size of this ovarian reserve depends on genes involved in germ cell proliferation and differentiation, sexual differentiation, meiosis, germ cell degeneration, formation of primordial follicles, and on a potential mechanism of self-renewal of germ stem cells. In this review, we present the state of the art of the knowledge of genes and factors involved in all these processes. We first focus on the almost 70 genes identified mainly by mouse invalidation models, then we discuss the most plausible hypothesis concerning the possibility of the existence of germ cell self-renewal by neo-oogenesis in animal species and human, with a special interest for the role of corresponding genes in evolutionary distinct model species. All of the genes pointed out here are candidates susceptible to explain fertility defects such as the premature ovarian failure in human.
Collapse
Affiliation(s)
- Philippe Monget
- INRA, UMR85, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France.
| | | | | | | | | | | |
Collapse
|
14
|
Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach. Gene 2012; 500:32-9. [PMID: 22465513 DOI: 10.1016/j.gene.2012.03.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 03/09/2012] [Accepted: 03/12/2012] [Indexed: 11/23/2022]
Abstract
Rainbow trout, Oncorhynchus mykiss, is an important aquaculture species worldwide and, in addition to being of commercial interest, it is also a research model organism of considerable scientific importance. Because of the lack of a whole genome sequence in that species, transcriptomic analyses of this species have often been hindered. Using next-generation sequencing (NGS) technologies, we sought to fill these informational gaps. Here, using Roche 454-Titanium technology, we provide new tissue-specific cDNA repertoires from several rainbow trout tissues. Non-normalized cDNA libraries were constructed from testis, ovary, brain and gill rainbow trout tissue samples, and these different libraries were sequenced in 10 separate half-runs of 454-Titanium. Overall, we produced a total of 3million quality sequences with an average size of 328bp, representing more than 1Gb of expressed sequence information. These sequences have been combined with all publicly available rainbow trout sequences, resulting in a total of 242,187 clusters of putative transcript groups and 22,373 singletons. To identify the predominantly expressed genes in different tissues of interest, we developed a Digital Differential Display (DDD) approach. This approach allowed us to characterize the genes that are predominantly expressed within each tissue of interest. Of these genes, some were already known to be tissue-specific, thereby validating our approach. Many others, however, were novel candidates, demonstrating the usefulness of our strategy and of such tissue-specific resources. This new sequence information, acquired using NGS 454-Titanium technology, deeply enriched our current knowledge of the expressed genes in rainbow trout through the identification of an increased number of tissue-specific sequences. This identification allowed a precise cDNA tissue repertoire to be characterized in several important rainbow trout tissues. The rainbow trout contig browser can be accessed at the following publicly available web site (http://www.sigenae.org/).
Collapse
|
15
|
An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Res Notes 2012; 5:111. [PMID: 22353237 PMCID: PMC3305648 DOI: 10.1186/1756-0500-5-111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 02/21/2012] [Indexed: 12/30/2022] Open
Abstract
Background The striped bass and its relatives (genus Morone) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome. Results Sequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: SRX007394). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display in silico comparisons to zebrafish (Danio rerio) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs. Conclusions This first large reference sequence database available for the ecologically and economically important temperate basses (genus Morone) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).
Collapse
|
16
|
García-López Á, Sánchez-Amaya MI, Halm S, Astola A, Prat F. Bone morphogenetic protein 15 and growth differentiation factor 9 expression in the ovary of European sea bass (Dicentrarchus labrax): cellular localization, developmental profiles, and response to unilateral ovariectomy. Gen Comp Endocrinol 2011; 174:326-34. [PMID: 21978589 DOI: 10.1016/j.ygcen.2011.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 09/22/2011] [Accepted: 09/22/2011] [Indexed: 11/29/2022]
Abstract
Vertebrate oocytes actively contribute to follicle development by secreting a variety of growth factors, among which bone morphogenetic protein 15 (BMP15/Bmp15) and growth differentiation factor 9 (GDF9/Gdf9) have been paid particular attention. In the present study, we describe the cellular localization, the developmental profiles, and the response to unilateral ovariectomy (a procedure implying the surgical removal of one of the ovaries) of protein and mRNA steady-state levels of Bmp15 and Gdf9 in the ovary of European sea bass, an important fish species for marine aquaculture industry. In situ hybridization and immunohistochemistry demonstrated that the oocyte is the main production site of Bmp15 and Gdf9 in European sea bass ovary. During oocyte development, Bmp15 protein expression started to be detected only from the lipid vesicle stage onwards but not in primary pre-vitellogenic (i.e. perinucleolar) oocytes as the bmp15 mRNA already did. Gdf9 protein and gdf9 mRNA expression were both detected in primary perinucleolar oocytes and followed similar decreasing patterns thereafter. Unilateral ovariectomy induced a full compensatory growth of the remaining ovary in the 2-month period following surgery (Á. García-López, M.I. Sánchez-Amaya, C.R. Tyler, F. Prat 2011). The compensatory growth elicited different changes in the expression levels of mRNA and protein of both factors, although the involvement of Bmp15 and Gdf9 in the regulatory network orchestrating such process remains unclear at present. Altogether, our results establish a solid base for further studies focused on elucidating the specific functions of Bmp15 and Gdf9 during primary and secondary oocyte growth in European sea bass.
Collapse
Affiliation(s)
- Ángel García-López
- Departamento de Biología Marina y Acuicultura, Instituto de Ciencias Marinas de Andalucía (CSIC), Avda. República Saharaui 2, E-11510 Puerto Real, Cádiz, Spain.
| | | | | | | | | |
Collapse
|
17
|
Liu Z, Chen A, Yang Z, Wei H, Leng X. Molecular characterization of growth differentiation factor 9 and its spatio-temporal expression pattern in gibel carp (Carassius auratus gibelio). Mol Biol Rep 2011; 39:3863-70. [PMID: 21779806 DOI: 10.1007/s11033-011-1165-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 06/30/2011] [Indexed: 11/29/2022]
Abstract
Growth differentiation factor 9 (GDF9) is a member of the transforming growth factor β (TGF-β) superfamily with a key role in regulating follicle development. In this study, the GDF9 full-length genomic DNA and cDNA were isolated and characterized from the gibel carp ovary using rapid-amplification of cDNA ends (RACE) and LD-PCR. The full-length genomic DNA and cDNA sequences of GDF9 are 3979 and 2044 bp which code 428 amino acid residues with a specific RKKR protease cleavage site of TGF-β superfamily. Sequence analysis showed that gibel carp was similar to zebrafish and other fish species. Spatio-temporal expression analysis using real-time quantitative PCR revealed that GDF9 mRNA was largely expressed in ovary and testis. GDF9 is mainly present at stage I follicles indicating its important role in early follicles development. The same result was obtained in immunohistochemistry localization of GDF9 protein. Within the follicle, the follicle layer cells were barely expressed whereas GDF9 mRNA was mostly expressed in the oocytes. Supplemented with human chorionic gonadotropin (hCG) in isolated follicles, the expression of GDF9 mRNA was increased firstly and then decreased. The results of this study indicated that GDF9 gene played a role in fish during development of follicles, especially in the early stage follicles.
Collapse
Affiliation(s)
- Zhiwei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University, Huchenghuan Road 999, Lingang New District, Shanghai, 201306, People's Republic of China
| | | | | | | | | |
Collapse
|
18
|
Herbert JMJ, Buffa FM, Vorschmitt H, Egginton S, Bicknell R. A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp. BMC Genomics 2009; 10:490. [PMID: 19852815 PMCID: PMC2771047 DOI: 10.1186/1471-2164-10-490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 10/23/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Physiological processes occur in many species for which there is yet no sequenced genome and for which we would like to identify the genetic basis. For example, some species increase their vascular network to minimise the effects of reduced oxygen diffusion and increased blood viscosity associated with low temperatures. Since many angiogenic and endothelial genes have been discovered in man, functional homolog relationships between carp, zebrafish and human were used to predict the genetic basis of cold-induced angiogenesis in Cyprinus Carpio (carp). In this work, carp sequences were collected and built into contigs. Human-carp functional homolog relationships were derived via zebrafish using a new Conditional Stepped Reciprocal Best Hit (CSRBH) protocol. Data sources including publications, Gene Ontology and cDNA libraries were then used to predict the identity of known or potential angiogenic genes. Finally, re-analyses of cold carp microarray data identified carp genes up-regulated in response to low temperatures in heart and muscle. RESULTS The CSRBH approach outperformed all other methods and attained 8,726 carp to human functional homolog relationships for 16,650 contiguous sequences. This represented 3,762 non-redundant genes and 908 of them were predicted to have a role in angiogenesis. The total number of up-regulated differentially expressed genes was 698 and 171 of them were putatively angiogenic. Of these, 5 genes representing the functional homologs NCL, RHOA, MMP9, GRN and MAPK1 are angiogenesis-related genes expressed in response to low temperature. CONCLUSION We show that CSRBH functional homologs relationships and re-analyses of gene expression data can be combined in a non-model species to predict genes of biological interest before a genome sequence is fully available. Programs to run these analyses locally are available from http://www.cbrg.ox.ac.uk/~jherbert/.
Collapse
Affiliation(s)
- John M J Herbert
- Cancer Research UK Angiogenesis Group, Institute for Biomedical Research, Schools of Immunity and Infection and Cancer studies, College of Medicine and Dentistry, University of Birmingham, Birmingham, B15 2TT, UK.
| | | | | | | | | |
Collapse
|