1
|
Wang P, Liu Z, Zhang X, Huo H, Wang L, Dai H, Yang F, Zhao G, Huo J. Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function. Genomics 2024; 116:110819. [PMID: 38432498 DOI: 10.1016/j.ygeno.2024.110819] [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: 11/02/2023] [Revised: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds. Furthermore, we found 1622 co-differentially expressed genes (co-DEGs), 122 co-differentially expressed lncRNAs (co-DELs), 39 co-differentially expressed miRNAs (co-DEMs) in BMI vs introduced commercial breeds (DU and LW). Functional analysis revealed that these co-DEGs and co-DELs/co-DEMs target genes were enriched in male sexual function pathways, including MAPK, AMPK, TGF-β/Smad, Hippo, NF-kappa B, and PI3K/Akt signaling pathways. Additionally, we established 10,536 lncRNA-mRNA, 11,248 miRNA-mRNA pairs, and 62 ceRNA (lncRNA-miRNA-mRNA) networks. The ssc-miR-1343 had the most interactive factors in the ceRNA network, including 20 mRNAs and 3 lncRNAs, consisting of 56 ceRNA pairs. These factors played extremely important roles in the regulation of testis function as key nodes in the interactive regulatory network. Our results provide insight into the functional roles of lncRNAs and miRNAs in porcine testis and offer a valuable resource for understanding the differences between Chinese indigenous and introduced Western pigs.
Collapse
Affiliation(s)
- Pei Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhipeng Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xia Zhang
- College of Life Science, Lyuliang University, Lvliang 033001, China
| | - Hailong Huo
- Yunnan Open University, Kunming 650500, China
| | - Lina Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hongmei Dai
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Fuhua Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
| |
Collapse
|
2
|
Semik-Gurgul E, Gurgul A, Szmatoła T. Transcriptome and methylome sequencing reveals altered long non-coding RNA genes expression and their aberrant DNA methylation in equine sarcoids. Funct Integr Genomics 2023; 23:268. [PMID: 37552338 PMCID: PMC10409845 DOI: 10.1007/s10142-023-01200-2] [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: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Recent publications confirmed that long non-coding RNAs (lncRNAs) perform an essential function in gene-specific transcription regulation. Nevertheless, despite its important role, lncRNA has not yet been described in equine sarcoids, the skin neoplasia of horses. Therefore, the aim of this study is to deepen the knowledge about lncRNA expression in the pathogenesis of equine sarcoids and provide new insight into the regulatory function of lncRNA in the bovine papillomavirus-dependent neoplasia of horse dermal tissues. RNA sequencing (RNA-seq) data from 12 equine sarcoid samples and the corresponding controls were reanalyzed in this study. A total of 3396 differentially expressed (DE) lncRNAs and 128 DElncRNA-DE genes (DEGs) pairs were identified. Differentially expressed lncRNAs predicted target genes were enriched in pathways associated with inter alia the extracellular matrix disassembly and cancer pathways. Furthermore, methylation data from the same samples were integrated into the analysis, and 12 DElncRNAs were described as potentially disturbed by aberrant methylation. In conclusion, this study presents novel data about lncRNA's role in the pathogenesis of equine sarcoids.
Collapse
Affiliation(s)
- Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083, Krakow, Balice, Poland.
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083, Krakow, Balice, Poland
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
| |
Collapse
|
3
|
Zhang B, Yan Z, Wang P, Yang Q, Huang X, Shi H, Tang Y, Ji Y, Zhang J, Gun S. Identification and Characterization of lncRNA and mRNA in Testes of Landrace and Hezuo Boars. Animals (Basel) 2021; 11:ani11082263. [PMID: 34438721 PMCID: PMC8388364 DOI: 10.3390/ani11082263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Precocious puberty is an excellent reproductive trait in domestic animals, which can generate higher breeding benefits in livestock production. However, regulators associated with this sexual maturation process remain largely unknown. Chinese Hezuo (HZ) boars are known for their early sexual maturity. In this work, the characteristics of precocious puberty in HZ pigs were confirmed by histological analysis, and some important long noncoding RNA (lncRNA) and mRNA were identified in the testes of immature (30-day-old) and mature (120-day-old) HZ boars, which could play a key role in precocious puberty. These results will provide a theoretical basis for further research on the regulatory mechanism of precocious puberty, which is important for accelerating the breeding process of highly fertile animals. Abstract Chinese HZ boars are typical plateau miniature boars characterized by precocious puberty, which is closely related to testicular development and spermatogenesis. Accumulating evidence indicates that lncRNA is involved in the testicular development and regulation of spermatogenesis. However, little is known about the lncRNA precocious regulation in testicular development and spermatogenesis on early sexual maturity of HZ boars. Thus, we investigated the expression and characterization of lncRNA and mRNA in 30-day-old and 120-day-old HZ boar testes using transcriptome to explore precocious puberty. Landrace (LC) boar was treated as the control. Histological analyses indicated that HZ boar underwent puberty development at an earlier stage than LC boar and had achieved sexual maturity at 120 days old. RNA-Seq yielded a total of 187 lncRNAs and 984 mRNAs; these molecules were identified as possible candidates for precocious puberty. GO terms and KEGG pathways enrichment analyses revealed that the differentially expressed lncRNA and their targeted genes were involved in metabolic pathways regulating testis development and spermatogenesis, such as the PI3K-Akt, TGF-beta and Wnt pathways. Further screening, some lncRNA (such as LOC102166140, LOC110259451, and MSTRG.15011.2), and mRNA (such as PDCL2, HSD17B4, SHCBP1L, CYP21A2, and SPATA3) were found to be possibly associated with precocious puberty, which would add to our understanding of the molecular regulatory mechanisms of precocious puberty. This study provided valuable information for further study of the role of lncRNA and mRNA in the process of precocious puberty.
Collapse
Affiliation(s)
- Bo Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Haixia Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Yuran Tang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Yanan Ji
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Juanli Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (B.Z.); (Z.Y.); (P.W.); (Q.Y.); (X.H.); (H.S.); (Y.T.); (Y.J.); (J.Z.)
- Gansu Research Center for Swine Production Engineering and Technology, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-931-763-1804
| |
Collapse
|
4
|
Transcriptomic and ChIP-seq Integrative Analysis Reveals Important Roles of Epigenetically Regulated lncRNAs in Placental Development in Meishan Pigs. Genes (Basel) 2020; 11:genes11040397. [PMID: 32268606 PMCID: PMC7230623 DOI: 10.3390/genes11040397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 11/22/2022] Open
Abstract
The development of the placental fold, which increases the maternal–fetal interacting surface area, is of primary importance for the growth of the fetus throughout the whole pregnancy. However, the mechanisms involved remain to be fully elucidated. Increasing evidence has revealed that long non-coding RNAs (lncRNAs) are a new class of RNAs with regulatory functions and could be epigenetically regulated by histone modifications. In this study, 141 lncRNAs (including 73 up-regulated and 68 down-regulated lncRNAs) were identified to be differentially expressed in the placentas of pigs during the establishment and expanding stages of placental fold development. The differentially expressed lncRNAs and genes (DElncRNA-DEgene) co-expression network analysis revealed that these differentially expressed lncRNAs (DElncRNAs) were mainly enriched in pathways of cell adhesion, cytoskeleton organization, epithelial cell differentiation and angiogenesis, indicating that the DElncRNAs are related to the major events that occur during placental fold development. In addition, we integrated the RNA-seq (RNA sequencing) data with the ChIP-seq (chromatin immunoprecipitation sequencing) data of H3K4me3/H3K27ac produced from the placental samples of pigs from the two stages (gestational days 50 and 95). The analysis revealed that the changes in H3K4me3 and/or H3K27ac levels were significantly associated with the changes in the expression levels of 37 DElncRNAs. Furthermore, several H3K4me3/H3K27ac-lncRNAs were characterized to be significantly correlated with genes functionally related to placental development. Thus, this study provides new insights into understanding the mechanisms for the placental development of pigs.
Collapse
|
5
|
Zou H, Yu D, Du X, Wang J, Chen L, Wang Y, Xu H, Zhao Y, Zhao S, Pang Y, Liu Y, Hao H, Zhao X, Du W, Dai Y, Li N, Wu S, Zhu H. No imprinted XIST expression in pigs: biallelic XIST expression in early embryos and random X inactivation in placentas. Cell Mol Life Sci 2019; 76:4525-4538. [PMID: 31139846 PMCID: PMC11105601 DOI: 10.1007/s00018-019-03123-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
Dosage compensation, which is achieved by X-chromosome inactivation (XCI) in female mammals, ensures balanced X-linked gene expression levels between the sexes. Although eutherian mammals commonly display random XCI in embryonic and adult tissues, imprinted XCI has also been identified in extraembryonic tissues of mouse, rat, and cow. Little is known about XCI in pigs. Here, we sequenced the porcine XIST gene and identified an insertion/deletion mutation between Asian- and Western-origin pig breeds. Allele-specific analysis revealed biallelic XIST expression in porcine ICSI blastocysts. To investigate the XCI pattern in porcine placentas, we performed allele-specific RNA sequencing analysis on individuals from reciprocal crosses between Duroc and Rongchang pigs. Our results were the first to reveal that random XCI occurs in the placentas of pigs. Next, we investigated the H3K27me3 histone pattern in porcine blastocysts, showing that only 17-31.8% cells have attained XCI. The hypomethylation status of an important XIST DMR (differentially methylated region) in gametes and early embryos demonstrated that no methylation is pre-deposited on XIST in pigs. Our findings reveal that the XCI regulation mechanism in pigs is different from that in mice and highlight the importance of further study of the mechanisms regulating XCI during early porcine embryo development.
Collapse
Affiliation(s)
- Huiying Zou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Dawei Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jing Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Chen
- Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Yangyang Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huitao Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunxuan Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanjiang Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunwei Pang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yan Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haisheng Hao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueming Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weihua Du
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunping Dai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China.
| | - Huabin Zhu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
6
|
Gao Y, Li S, Lai Z, Zhou Z, Wu F, Huang Y, Lan X, Lei C, Chen H, Dang R. Analysis of Long Non-Coding RNA and mRNA Expression Profiling in Immature and Mature Bovine ( Bos taurus) Testes. Front Genet 2019; 10:646. [PMID: 31333723 PMCID: PMC6624472 DOI: 10.3389/fgene.2019.00646] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/18/2019] [Indexed: 01/08/2023] Open
Abstract
Testis development and spermatogenesis are strictly regulated by numbers of genes and non-coding genes. However, long non-coding RNAs (lncRNAs) as key regulators in multitudinous biological processes have not been systematically identified in bovine testes during sexual maturation. In this study, we comprehensively analyzed lncRNA and mRNA expression profiling of six bovine testes at 3 days after birth and 13 months by RNA sequencing. 23,735 lncRNAs and 22,118 mRNAs were identified, in which 540 lncRNAs (P-value < 0.05) and 3,525 mRNAs (P-adjust < 0.05) were significantly differentially expressed (DE) between two stages. Correspondingly, the results of RT-qPCR analysis showed well correlation with the transcriptome data. Moreover, GO and KEGG enrichment analyses showed that DE genes and target genes of DE lncRNAs were enriched in spermatogenesis. Furthermore, we constructed lncRNA–gene interaction networks; consequently, 15 DE lncRNAs and 12 cis-target genes were involved. The target genes (SPATA16, TCF21, ZPBP, PACRG, ATP8B3, COMP, ACE, and OSBP2) were found associated with bovine sexual maturation. In addition, the expression of lncRNAs and cis-target genes was detected in bovine Leydig cells, Sertoli cells, and spermatogonia. Our study identified and analyzed lncRNAs and mRNAs in testis tissues, suggesting that lncRNAs may regulate testis development and spermatogenesis. Our findings provided new insights for further investigation of biological function in bovine lncRNA.
Collapse
Affiliation(s)
- Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhenyu Lai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zihui Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| |
Collapse
|
7
|
Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development. Sci Rep 2019; 9:8501. [PMID: 31186438 PMCID: PMC6559957 DOI: 10.1038/s41598-019-44600-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/03/2019] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), >200 nt in length, are transcribed from mammalian genomes. They play important regulatory roles in various biological processes; However, the function and expression profile of lncRNAs involved in the development of hair follicles in the fetus, have been relatively under-explored area. To investigate the specific role of lncRNAs and mRNAs that regulate hair follicle development, we herein performed a comprehensive study on the lncRNA and mRNA expression profiles of sheep at multiple embryonic days (E65, E85, E105, and E135) and six lambs aged one week (D7) and one month (D30) using RNA-seq technology. The number of genes (471 lncRNAs and 12,812 mRNAs) differentially expressed and potential targets of differentially expressed lncRNAs were predicted. Differentially expressed lncRNAs were grouped into 10 clusters based on their expression pattern by K-means clustering. Moreover, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that some differentially expressed mRNAs, such as DKK1, DSG4, FOXE1, Hoxc13, SFRP1, SFRP2, and Wnt10A overlapped with lncRNAs targets, and enriched in important hair follicle developmental pathways, including Wnt, TNF, and MAPK signaling pathways. In addition, 9 differentially expressed lncRNAs and 4 differentially expressed mRNAs were validated using quantitative real-time PCR (qRT-PCR). This study helps enrich the Ovis lncRNA databases and provides a comprehensive lncRNA transcriptome profile of fetal and postnatal skin of sheep. Additionally, it provides a foundation for further experiments on the role of lncRNAs in the regulation of hair growth in sheep.
Collapse
|
8
|
Han K, Ren R, Cao J, Zhao S, Yu M. Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs. Front Genet 2019; 10:277. [PMID: 30984246 PMCID: PMC6449610 DOI: 10.3389/fgene.2019.00277] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Development of placental folds is a critical event affecting placental function in pigs because it can increase surface area for improvement in capillary density as gestation advances. However, the molecular mechanisms of the event are not well defined. Histone modifications have important roles in gene regulation. To investigate their effects on regulation of genes controlling porcine placental development, RNA-seq and ChIP-seq of porcine placental tissues from gestational days 50 (establishment stage of placental folds) and 95 (expanding stage of placental folds) were carried out in this study. The differentially expressed genes were identified and of which the down- and up-regulated genes are related to endoplasmic reticulum (ER) stress and angiogenesis, respectively. In addition, we mapped the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), which are associated with transcriptional activation. A number of differential modification regions between the 2 gestational stages were identified and majority of them are those with increased signals of H3K4me3 (14,576 out of 16,931). Furthermore, we observed that the increase of H3K4me3 is significantly correlated with the elevated expression levels of the neighboring genes, and notably, these genes were enriched in pathways related to blood vessel formation and microvascular permeability. Taken together, the findings suggest important roles of histone modifications on placental remolding in response to developmental changes.
Collapse
Affiliation(s)
- Kun Han
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruimin Ren
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianhua Cao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mei Yu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
9
|
Improved analysis of anthocyanins and vitamin C in blue-purple potato cultivars. Food Chem 2017; 242:217-224. [PMID: 29037681 DOI: 10.1016/j.foodchem.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/16/2017] [Accepted: 09/01/2017] [Indexed: 01/08/2023]
Abstract
Methods were optimized for extraction and quantification of anthocyanins (ACY) and vitamin C in potatoes. Acidified aqueous methanol (70%) was the optimal extraction solvent and freeze-drying significantly improved the extraction yield of ACY. The content of ACY varied widely in five potato cultivars from 0.42 to 3.18mg/g dry weight, with the latter being the highest value found in the Finnish cultivar 'Synkeä Sakari'. Compared with dithiothreitol (DTT), tris(2-carboxyethyl) phosphine hydrochloride (TCEP) was more efficient in reducing dehydroascorbic acid (DHA) to ascorbic acid (AA) and for quantifying the content of total ascorbic acid (TAA). For raw potatoes, quantification of TAA after treatment with TCEP was more reliable than a direct analysis of AA, whereas AA can be analyzed directly in steam-cooked samples. The TAA contents in the three potato cultivars were around 0.30-0.35mg/g dry weight. The loss of AA in steam cooking was 24%.
Collapse
|
10
|
Kim JG, Nonneman D, Kim DW, Shin S, Rohrer GA. Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1086-1092. [PMID: 28669142 PMCID: PMC5494481 DOI: 10.5713/ajas.17.0143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 11/27/2022]
Abstract
Objective O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) catalyzes the addition of O-GlcNAc and GlcNAcylation has extensive crosstalk with phosphorylation to regulate signaling and transcription. Pig OGT is located near the region of chromosome X that affects follicle stimulating hormone level and testes size. The objective of this study was to find the variations of OGT between European and Chinese pigs. Methods Pigs were tested initially for polymorphism in OGT among European and Chinese pigs by polymerase chain reaction and sequencing at the U.S. Meat Animal Research Center (USMARC). The polymorphism was also determined in an independent population of pigs including European and Chinese Meishan (ME) breeds at the National Institute of Animal Science (NIAS, RDA, Korea). Results The intron 20 of OGT from European and Chinese pigs was 514 and 233 bp, respectively, in the pigs tested initially. They included 1 White composite (WC) boar and 7 sows (2 Minzu×WC, 2 Duroc [DU]×WC, 2 ME×WC, 1 Fengzing×WC) at USMARC. The 281-bp difference was due to an inserted 276-bp element and GACTT in European pigs. When additional WC and ME boars, the grandparents that were used to generate the 1/2ME×1/2WC parents, and the 84 boars of 16 litters from mating of 1/2ME×1/2WC parents were analyzed, the breeds of origin of X chromosome quantitative trait locus (QTL) were confirmed. The polymorphism was determined in an independent population of pigs including DU, Landrace, Yorkshire, and ME breeds at NIAS. OGT was placed at position 67 cM on the chromosome X of the USMARC swine linkage map. Conclusion There was complete concordance with the insertion in European pigs at USMARC and NIAS. This polymorphism could be a useful marker to identify the breed of origin of X chromosome QTL in pigs produced by crossbreeding Chinese and European pigs.
Collapse
Affiliation(s)
- Jong Gug Kim
- Department of Animal Sciences, College of Agriculture and Life Science, and Institute of Molecular Biology and Genetics, Chonbuk National University, Jeonju 54896, Korea
| | - Dan Nonneman
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Doo-Wan Kim
- Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Sangsu Shin
- Department of Animal Biotechnology, Kyungpook National University, Sangju 37224, Korea
| | - Gary A Rohrer
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| |
Collapse
|
11
|
Tian L, Dong SS, Hu J, Yao JJ, Yan PS. The effect of maternal obesity on fatty acid transporter expression and lipid metabolism in the full-term placenta of lean breed swine. J Anim Physiol Anim Nutr (Berl) 2017; 102:e242-e253. [PMID: 28508539 DOI: 10.1111/jpn.12735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/31/2017] [Indexed: 12/30/2022]
Abstract
This study was conducted to evaluate the influence of back-fat thickness (BF), at mating of sows, on the maternal and newborn circulating lipids, expression of placental fatty acids (FA) transporters and lipid accumulation in placenta. Full-term placentas were obtained by vaginal delivery from BFI (9-14 mm; n = 37), BFII (15-19 mm; n = 43) and BFIII (20-27 mm; n = 38) sows according to BF at mating, and frozen placental sections were analysed for fat accumulation. Blood samples were collected from the sows of day 105 pregnancy and from cord blood at delivery. mRNA and protein expression levels were evaluated with real-time RT-PCR and Western blotting. Our results demonstrated that BFII females had significantly increased litter weight and placental efficiency, decreased maternal triglyceride (TG) and non-esterified fatty acids (NEFA) levels, decreased maternal IL-6, TNFα and leptin levels compared to BFIII females (p < .05). BFIII sows were associated with significantly decreased newborn TG levels, increased newborn glucose, IL-6 and TNFα levels compared to BFI or BFII sows (p < .05). BFI and BFII females had significantly decreased placental TG, NEFA and cholesterol (CHOL) contents compared to BFIII females (p < .05). Moreover, decreased CD36, FATP1, FABP4, and FABP1 mRNA and protein and FATP4 protein expression, and increased LPL activity were also observed in BFIII group compared with BFII group (p < .05). PPARγ mRNA and protein and lipogenic genes such as SREBP-1c, ACSL1, ACCα, FAS and SCD mRNA expression were downregulated or upregulated, respectively, in the placentas of BFIII sows compared to BFI or BFII sows (p < .05). Overall, this study demonstrated that there is no advantage, in terms of litter live size, litter weight and placental FA transport and metabolism, in performing the mating of sows with BF>19 mm.
Collapse
Affiliation(s)
- L Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - S S Dong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - J Hu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - J J Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - P S Yan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
12
|
Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e343. [PMID: 27483026 PMCID: PMC5023402 DOI: 10.1038/mtna.2016.57] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/14/2016] [Indexed: 02/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) may play an important role in Alzheimer's disease (AD) pathogenesis. However, despite considerable research in this area, the comprehensive and systematic understanding of lncRNAs in AD is still limited. The emergence of RNA sequencing provides a predictor and has incomparable advantage compared with other methods, including microarray. In this study, we identified lncRNAs in a 7-month-old mouse brain through deep RNA sequencing using the senescence-accelerated mouse prone 8 (SAMP8) and senescence-accelerated mouse resistant 1 (SAMR1) models. A total of 599,985,802 clean reads and 23,334 lncRNA transcripts were obtained. Then, we identified 97 significantly upregulated and 114 significantly downregulated lncRNA transcripts from all cases in SAMP8 mice relative to SAMR1 mice. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these significantly dysregulated lncRNAs were involved in regulating the development of AD from various angles, such as nerve growth factor term (GO: 1990089), mitogen-activated protein kinase signaling pathway, and AD pathway. Furthermore, the most probable AD-associated lncRNAs were predicted and listed in detail. Our study provided the systematic dissection of lncRNA profiling in SAMP8 mouse brain and accelerated the development of lncRNA biomarkers in AD. These attracting biomarkers could provide significant insights into AD therapy in the future.
Collapse
|
13
|
Difference in expression patterns of placental cholesterol transporters, ABCA1 and SR-BI, in Meishan and Yorkshire pigs with different placental efficiency. Sci Rep 2016; 6:20503. [PMID: 26852751 PMCID: PMC4745079 DOI: 10.1038/srep20503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/05/2016] [Indexed: 11/08/2022] Open
Abstract
Cholesterol is a key cell membrane component and precursor of steroid hormones. The maternal cholesterol is an important exogenous cholesterol source for the developing embryos and its transportation is mediated by ABCA1 and SR-BI. Here we reported that during the peri-implantation period in pigs, ABCA1 was expressed by uterine luminal epithelium (LE) and interestingly, its expression was more abundantly in LE on mesometrial side of uterus. However, SR-BI was expressed primarily by LE, glandular epithelial cells (GE) and trophoblast cells (Tr). During the placentation period, the expression levels of ABCA1 and SR-BI proteins at epithelial bilayer and placental areolae were significantly higher in Chinese Meishan pigs compared to Yorkshire pigs. Consisitently, mRNA levels of HMGCR, the rate-limiting enzyme for cholesterol synthesis, were significantly higher in Meishan placentas than in Yorkshire placentas. Our findings revealed the routes of transplacental cholesterol transport mediated by ABCA1 and SR-BI in pigs and indicated that ABCA1 related pathway may participate in anchoring the conceptus to the mesometrial side of uterus. Additionally, an ABCA1 dependent compensatory mechanism related to the placental efficiency in response to the smaller placenta size in Meishan pigs was suggested.
Collapse
|
14
|
Abstract
Background Piglet birth weight variability, a trait also known as the within-litter homogeneity of birth weight, reflects the sow’s prolificacy, because it is positively genetically correlated with preweaning mortality but negatively correlated with the mean growth of piglets during sucking. In addition, the maternal additive genetic variance and heritability has been found exist for this trait, thus, reduction in the variability of piglet birth weight to improve the sow prolificacy is possible by selective breeding. Results We performed a genome wide association study (GWAS) in 82 sows with extreme standard deviation of birth weights within the first parity to identify significant SNPs, and finally 266 genome-wide significant SNPs (p < 0.01) were identified. These SNPs were mainly enriched on chromosome 7, 1, 13, 14, 15 and 18. We further scanned genes of the top 50 SNPs with the lowest p values and found some genes involved in plasma glucose homeostasis (GLP1R) and lipid metabolism as well as maternal-fetal lipid transport (AACS, APOB, OSBPL10 and LRP1B) which may contribute to the birth weight variability trait. Conclusions Birth weight variability trait has a low heritability. It is not easy to get significant signal by GWAS using small sample size. Herein, we identified some candidate chromosome regions especially chromosome 7 and suggested five genes which may provide some information for the further study. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0309-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xuemin Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China. .,Institute of Animal Science, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China.
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China. .,Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Dadong Deng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoping Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
15
|
Liu R, Wang M, Su L, Li X, Zhao S, Yu M. The Expression Pattern of MicroRNAs and the Associated Pathways Involved in the Development of Porcine Placental Folds That Contribute to the Expansion of the Exchange Surface Area. Biol Reprod 2015; 93:62. [PMID: 26157073 DOI: 10.1095/biolreprod.114.126540] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 07/06/2015] [Indexed: 01/12/2023] Open
Abstract
The development of the microscopically folded structure of the diffuse epitheliochorial placenta in pigs is important because it expands the surface area for maternal-fetal exchange, resulting in an increase in placental efficiency. To better understand the regulatory mechanisms involved in this process, we characterized miRNA expression profiles in porcine placentas during the initiation and establishment of placental fold development. A total of 42 miRNAs were found to be differentially expressed, and their putative target genes were predicted using four target prediction programs. Following a comparative analysis with published gene expression pattern data obtained from porcine placentas in the corresponding stages of placental fold development, only those genes that were negatively correlated with miRNA expression were retained for further function and pathway enrichment analysis. The results showed that the up-regulated miRNAs were associated mainly with extracellular matrix remodeling and tissue morphogenesis, while the down-regulated miRNAs were related to cell proliferation and signal transduction. Furthermore, we provide evidence that miR-130b may facilitate the expression of HPSE, which has been reported to be a regulator of the folding of the pig placenta, by suppressing the expression of PPARG. In addition, we also reveal that the miRNA-target pairs expressed in the pig placenta may trigger the degradation of the stromal matrix and basement membrane (miR-29a-COL1A2, COL3A1, and LAMC1) and regulate trophoblast epithelial cell adherens junctions (the miR-200 family and miR-205-ZEB2-CDH1) and proliferation (miR-17-92 cluster-HBP1 and ULK1). Taken together, these results indicate that miRNAs and related pathways may have potential roles in porcine placental fold development.
Collapse
Affiliation(s)
- Ruize Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Min Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Lijie Su
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China College of Public Health, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoping Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Mei Yu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| |
Collapse
|
16
|
Hwang JY, Kim EB, Ka H, Lee CK. Identification of the porcine XIST gene and its differential CpG methylation status in male and female pig cells. PLoS One 2013; 8:e73677. [PMID: 24040022 PMCID: PMC3767593 DOI: 10.1371/journal.pone.0073677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/22/2013] [Indexed: 11/18/2022] Open
Abstract
XIST, a long non-coding RNA, plays an important role in triggering X chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. However, a porcine XIST has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. Here, we present a full-length porcine XIST sequence assembled using known sequences (GenBank), RNA-Seq data (NCBI SRA), and PCR/sequencing. The proposed porcine XIST gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. Transcription covering the entire XIST region was observed specifically in female cells, but not in male cells. We also identified eight transcription starting sites (TSSs) and evaluated CpG methylation patterns in the upstream (+2.0 kb) and downstream (−2.0 kb) regions. Sixty-seven CG di-nucleotides identified in the target region were considered to be candidate CpG sites, and were enriched in the following two regions: −284 to +53 bp (13 sites) and +285 to +1,727 bp (54 sites) from the selected TSS. Male 5` region of XIST (64.5 sites, 96.26%) had a higher level of CpG methylation than female DNA (33.4 sites, 49.85%). Taken together, our results revealed that the porcine XIST gene is expressed exclusively in female cells, which is influenced by the lower level of CpG methylation in the putative promoter region compared with male cells. The porcine XIST presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.
Collapse
Affiliation(s)
- Jae Yeon Hwang
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Eun Bae Kim
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- Department of Animal Products and Food Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Hakhyun Ka
- Division of Biological Science and Technology, Institute of Biomaterials and Institute for Poverty Alleviation and International Development, Yonsei University, Wonju, Kangwon-do, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|