1
|
Sindhu P, Magotra A, Sindhu V, Chaudhary P. Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility. ZYGOTE 2024:1-17. [PMID: 39291610 DOI: 10.1017/s0967199424000224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.
Collapse
Affiliation(s)
- Pushpa Sindhu
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Vikas Sindhu
- Department of Animal Nutrition, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Pradeep Chaudhary
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| |
Collapse
|
2
|
Li G, Yang X, Li J, Zhang B. Genome-Wide Analysis of lncRNA and mRNA Expression in the Uterus of Laying Hens during Aging. Genes (Basel) 2023; 14:genes14030639. [PMID: 36980911 PMCID: PMC10048286 DOI: 10.3390/genes14030639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Eggshell plays an essential role in preventing physical damage and microbial invasions. Therefore, the analysis of genetic regulatory mechanisms of eggshell quality deterioration during aging in laying hens is important for the biosecurity and economic performance of poultry egg production worldwide. This study aimed to compare the differences in the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs between old and young laying hens by the method of high-throughput RNA sequencing to identify candidate genes associated with aging in the uterus of laying hens. Overall, we detected 176 and 383 differentially expressed (DE) lncRNAs and mRNAs, respectively. Moreover, functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases revealed that DE-lncRNAs and DE-mRNAs were significantly enriched in “phosphate-containing compound metabolic process”, “mitochondrial proton-transporting ATP synthase complex”, “inorganic anion transport”, and other terms related to eggshell calcification and cuticularization. Through integrated analysis, we found that some important genes such as FGF14, COL25A1, GPX8, and GRXCR1 and their corresponding lncRNAs were expressed differentially between two groups, and the results of quantitative real-time polymerase chain reaction (qPCR) among these genes were also in excellent agreement with the sequencing data. In addition, our study found that TCONS_00181492, TCONS_03234147, and TCONS_03123639 in the uterus of laying hens caused deterioration of eggshell quality in the late laying period by up-regulating their corresponding target genes FGF14, COL25A1, and GRXCR1 as well as down-regulating the target gene GPX8 by TCONS_01464392. Our findings will provide a valuable reference for the development of breeding programs aimed at breeding excellent poultry with high eggshell quality or regulating dietary nutrient levels to improve eggshell quality.
Collapse
Affiliation(s)
- Guang Li
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China
| | - Xinyue Yang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China
| | - Junyou Li
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 319-0206, Japan
| | - Bingkun Zhang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-6273-4978
| |
Collapse
|
3
|
Guan X, Sun Y, Zhang C. LncRNAs in blood cells: Roles in cell development and potential pathogenesis in hematological malignancies. Crit Rev Oncol Hematol 2022; 180:103849. [DOI: 10.1016/j.critrevonc.2022.103849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 09/11/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
|
4
|
Exploring the crosstalk between long non-coding RNAs and microRNAs to unravel potential prognostic and therapeutic biomarkers in β-thalassemia. Mol Biol Rep 2022; 49:7057-7068. [PMID: 35717472 DOI: 10.1007/s11033-022-07629-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
β-thalassemia is a prevalent monogenic disorder characterized by reduced or absent synthesis of the β-globin chain. Although great effort has been made to ameliorate the disease severity of β-thalassemic patients, progress has been stymied due to limited understanding of the detailed molecular mechanism of disease pathogenesis. Recently, non-coding RNAs have been established as key players in regulating various physiological and pathological processes. Many ncRNAs are involved in hematopoiesis and erythroid development. Furthermore, various studies have also reported the complex interplay between different ncRNAs, such as miRNA, lncRNAs, etc. in regulating disease progression and pathogenesis. Both lncRNAs and miRNAs have been identified as independent regulators of globin gene expression and are intricately involved in disease pathogenesis; yet accumulating evidence suggests that the cross-talk between lncRNAs and miRNAs is intricately involved in the underlying globin gene expression, fine-tuning the effect of their independent regulation. In this review, we summarize the current progress of research on the roles of lncRNAs and miRNAs implicated in β-thalassemia disease, including their interactions and regulatory networks. This can provide important insights into the detailed epigenetic regulation of globin gene switching and has the potential to develop novel therapeutic approaches against β-thalassemia.
Collapse
|
5
|
Yang S, Sun G, Wu P, Chen C, Kuang Y, Liu L, Zheng Z, He Y, Gu Q, Lu T, Zhu C, Wang F, Gou F, Yang Z, Zhao X, Yuan S, Yang L, Lu S, Li Y, Lv X, Dong F, Ma Y, Yu J, Ng LG, Shi L, Liu J, Shi L, Cheng T, Cheng H. WDR82-binding long noncoding RNA lncEry controls mouse erythroid differentiation and maturation. J Exp Med 2022; 219:213079. [PMID: 35315911 PMCID: PMC8943841 DOI: 10.1084/jem.20211688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/18/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic differentiation is controlled by both genetic and epigenetic regulators. Long noncoding RNAs (lncRNAs) have been demonstrated to be important for normal hematopoiesis, but their function in erythropoiesis needs to be further explored. We profiled the transcriptomes of 16 murine hematopoietic cell populations by deep RNA sequencing and identified a novel lncRNA, Gm15915, that was highly expressed in erythroid-related progenitors and erythrocytes. For this reason, we named it lncEry. We also identified a novel lncEry isoform, which was the principal transcript that has not been reported before. lncEry depletion impaired erythropoiesis, indicating the important role of the lncRNA in regulating erythroid differentiation and maturation. Mechanistically, we found that lncEry interacted with WD repeat–containing protein 82 (WDR82) to promote the transcription of Klf1 and globin genes and thus control the early and late stages of erythropoiesis, respectively. These findings identified lncEry as an important player in the transcriptional regulation of erythropoiesis.
Collapse
Affiliation(s)
- Shangda Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Peng Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Cong Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yijin Kuang
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Ling Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhaofeng Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Yicheng He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Quan Gu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Fengjiao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Fanglin Gou
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zining Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiangnan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Shiru Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Liu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Shihong Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Xue Lv
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Lai Guan Ng
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Jing Liu
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Lei Shi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| |
Collapse
|
6
|
Ghafouri-Fard S, Niazi V, Taheri M. Role of miRNAs and lncRNAs in hematopoietic stem cell differentiation. Noncoding RNA Res 2021; 6:8-14. [PMID: 33385102 PMCID: PMC7770514 DOI: 10.1016/j.ncrna.2020.12.002] [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: 11/04/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have diverse roles in the differentiation of hematopoietic cells. Among these transcripts, long ncRNAs (lncRNAs) and microRNAs (miRNAs) have especial contribution in this regard particularly by affecting levels of transcription factors that define differentiation of each linage. miR-222, miR-10a, miR-126, miR-106, miR-10b, miR-17, miR-20, miR-146, miR-155, miR-223, miR-221, miR-92, miR-150, miR-126 and miR-142 are among miRNAs that partake in the differentiation of hematopoietic stem cells. Meanwhile, this process is controlled by a number of lncRNAs such as PU.1-AS, AlncRNA-EC7, EGO, HOTAIRM1, Fas-AS1, LincRNA-EPS and lncRNA-CSR. Manipulation of expression of these transcripts has functional significance in the treatment of cancers and in cell therapy. In this paper, we have provided a brief summary of the role of miRNAs and lncRNAs in the regulation of hematopoietic stem cells.
Collapse
Affiliation(s)
- Soudeh Ghafouri-Fard
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Niazi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
7
|
Zhang D, Xia T, Li H, Li Z, Sun G, Li G, Tian Y, Liu X, Xu D, Kang X. Estrogen enhances the expression of a growth-associated long noncoding RNA in chicken liver via ERα. Br Poult Sci 2021; 62:336-345. [PMID: 33390024 DOI: 10.1080/00071668.2020.1868405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. The long noncoding RNA lncGLM is significantly differentially expressed in the livers of peak-laying hens compared with that in the livers of pre-laying hens, but its potential biological role and expression regulation are unclear.2. To explore the potential biological function of lncGLM, single nucleotide polymorphism (SNP) detection and association analysis were carried out in the Gushi×Anka F2 resource population.3. The tissues and spatiotemporal expression characteristics of lncGLM were analysed by real-time quantitative PCR. The effects of 17β-oestradiol on the expression of lncGLM expression were analysed through in vitro and in vivo experiments.4. The results showed that a g.19069338 T > C SNP was present in lncGLM. Association analysis revealed that lncGLM was significantly associated with body slanting length at 12 weeks, body weight at 12 weeks, shank length at four weeks, chest depth at eight weeks, pelvic width at 12 weeks, eviscerated weight, head weight, pancreas weight, pectoralis weight, leg muscle weight, muscular stomach weight rate, pancreas weight rate, carcase weight, aspartate aminotransferase, creatinine and pectoral muscle water loss rate.5. The expression of lncGLM in the liver was higher than that in other sampled tissues. In addition, the expression of lncGLM in the liver was significantly higher in the peak-laying period than at the pre-laying period. Both in vitro and in vivo experiments showed that lncGLM expression was regulated by 17β-oestradiol via oestrogen receptor alpha (ER-α). These results demonstrated that the chicken lncGLM gene is highly expressed in liver tissue and regulated by oestrogen through ER-α.
Collapse
Affiliation(s)
- D Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - T Xia
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - H Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - Z Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - G Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - G Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - Y Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - X Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - D Xu
- Henan Liujiang Ecological Animal Husbandry Co., Ltd, Hebi, China
| | - X Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
8
|
Li WJ, Song YJ, Han HL, Xu HQ, Wei D, Smagghe G, Wang JJ. Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). BMC Genomics 2020; 21:600. [PMID: 32867696 PMCID: PMC7457495 DOI: 10.1186/s12864-020-07014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited. Results We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process. Conclusions This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.
Collapse
Affiliation(s)
- Wei-Jun Li
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yu-Jia Song
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hong-Liang Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hui-Qian Xu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guy Smagghe
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China. .,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. .,Department of Plants and Crops, Ghent University, 9000, Ghent, Belgium.
| | - Jin-Jun Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China. .,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
9
|
Sawaengdee W, Cui K, Zhao K, Hongeng S, Fucharoen S, Wongtrakoongate P. Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts. Front Genet 2020; 11:850. [PMID: 32849830 PMCID: PMC7431964 DOI: 10.3389/fgene.2020.00850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/13/2020] [Indexed: 01/21/2023] Open
Abstract
Erythropoiesis of human hematopoietic stem cells (HSCs) maintains generation of red blood cells throughout life. However, little is known how human erythropoiesis is regulated by long non-coding RNAs (lncRNAs). By using ChIRP-seq, we report here that the lncRNA steroid receptor RNA activator (SRA) occupies chromatin, and co-localizes with CTCF, H3K4me3, and H3K27me3 genome-wide in human erythroblast cell line K562. CTCF binding sites that are also occupied by SRA are enriched for either H3K4me3 or H3K27me3. Transcriptome-wide analyses reveal that SRA facilitates expression of erythroid-associated genes, while repressing leukocyte-associated genes in both K562 and CD36-positive primary human proerythroblasts derived from HSCs. We find that SRA-regulated genes are enriched by both CTCF and SRA bindings. Further, silencing of SRA decreases expression of the erythroid-specific markers TFRC and GYPA, and down-regulates expression of globin genes in both K562 and human proerythroblast cells. Taken together, our findings establish that the lncRNA SRA occupies chromatin, and promotes transcription of erythroid genes, therefore facilitating human erythroid transcriptional program.
Collapse
Affiliation(s)
- Waritta Sawaengdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, Thailand
| |
Collapse
|
10
|
Sun B, Liu C, Li H, Zhang L, Luo G, Liang S, Lü M. Research progress on the interactions between long non-coding RNAs and microRNAs in human cancer. Oncol Lett 2019; 19:595-605. [PMID: 31897175 PMCID: PMC6923957 DOI: 10.3892/ol.2019.11182] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022] Open
Abstract
Numerous types of molecular mechanisms mediate the development of cancer. Non-coding RNAs (ncRNAs) are being increasingly recognized to play important role in mediating the development of diseases, including cancer. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are the two most widely studied ncRNAs. Thus far, lncRNAs are known to have biological roles through a variety of mechanisms, including genetic imprinting, chromatin remodeling, cell cycle control, splicing regulation, mRNA decay and translational regulation, and miRNAs regulate gene expression through the degradation of mRNAs and lncRNAs. Although ncRNAs account for a major proportion of the total RNA, the mechanisms underlying the physiological or pathological processes mediated by various types of ncRNAs, and the specific interaction mechanisms between miRNAs and lncRNAs in various physiological and pathological processes, remain largely unknown. Thus, further research in this field is required. In general, the interaction mechanisms between miRNAs and lncRNAs in human cancer have become important research topics, and the study thereof has led to the recent development of related technologies. By providing examples and descriptions, and performing chart analysis, the present study aimed to review the interaction mechanisms and research approaches for these two types of ncRNAs, as well as their roles in the occurrence and development of cancer. These details have far-reaching significance for the utilization of these molecules in the diagnosis and treatment of cancer.
Collapse
Affiliation(s)
- Binyu Sun
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chunxia Liu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Hao Li
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Lu Zhang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Gang Luo
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Sicheng Liang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Muhan Lü
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| |
Collapse
|
11
|
Jahan S, Beacon TH, He S, Gonzalez C, Xu W, Delcuve GP, Jia S, Hu P, Davie JR. Chromatin organization of transcribed genes in chicken polychromatic erythrocytes. Gene 2019; 699:80-87. [DOI: 10.1016/j.gene.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
|
12
|
LncRNA SNHG20 predicts a poor prognosis and promotes cell progression in epithelial ovarian cancer. Biosci Rep 2019; 39:BSR20182186. [PMID: 30846486 PMCID: PMC6443951 DOI: 10.1042/bsr20182186] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/19/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
The long noncoding RNA small nucleolar RNA host gene 20 (SNHG20) has been demonstrated to play a crucial role in cancer progression. However, the functions of SNHG20 in epithelial ovarian cancer (EOC) are not well established. The aim of the present study was to investigate SNHG20 clinical significance and its underlying mechanism in proliferation and metastasis in EOC. The expression level of SNHG20 was identified via in situ hybridization (ISH) and quantitative RT-PCR (qRT-PCR). The proliferative and metastatic capacities by silencing SNHG20 expression in A2780 and CAOV-3 cells were measured by cell counting kit-8 (CCK-8) and transwell assays. The molecular mRNA and protein expressions were examined using qRT-PCR, Western blot, and double immunofluorescent staining. SNHG20 expression was markedly higher in serous EOC tissues than that in adjacent tissues and closely correlated with histological grade and lymph node (LN) status. Patients with high SNHG20 showed a shorter overall survival (OS) and SNHG20 was an independent risk factor for the prognosis of serous EOC. Knockdown of SNHG20 remarkably inhibited EOC cell proliferation, migration, and invasion, which was associated with dysregulation of P21, Cyclin D1, E-cadherin, and Vimentin. These results suggest that SNHG20 may serve as an independent prognostic predictor and function as a noncoding oncogene in EOC progression, which might be a possible novel diagnostic marker and treatment target.
Collapse
|
13
|
Wang GZ, Du K, Hu SQ, Chen SY, Jia XB, Cai MC, Shi Y, Wang J, Lai SJ. Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue. Lipids Health Dis 2018; 17:271. [PMID: 30486837 PMCID: PMC6263043 DOI: 10.1186/s12944-018-0915-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023] Open
Abstract
Background The rabbit is widely used as an important experimental model for biomedical research, and shows low adipose tissue deposition during growth. Long non-coding RNAs (lncRNAs) are associated with adipose growth, but little is known about the function of lncRNAs in the rabbit adipose tissue. Methods Deep RNA-sequencing and comprehensive bioinformatics analyses were used to characterize the lncRNAs of rabbit visceral adipose tissue (VAT) at 35, 85 and 120 days after birth. Differentially expressed (DE) lncRNAs were identified at the three growth stages by DESeq. The cis and trans prediction ways predicted the target genes of the DE lncRNAs. To explore the function of lncRNAs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the candidate genes. Results A total of 991,157,544 clean reads were generated after RNA-Seq of the three growth stages, of which, 30,353 and 107 differentially expressed (DE) lncRNAs were identified. Compared to the protein-coding transcripts, the rabbit lncRNAs shared some characteristics such as shorter length and fewer exons. Cis and trans target gene prediction revealed, 43 and 64 DE lncRNAs respectively, corresponding to 72 and 20 protein-coding genes. GO enrichment and KEGG pathway analyses revealed that the candidate DE lncRNA target genes were involved in oxidative phosphorylation, glyoxylate and dicarboxylate metabolism, and other adipose growth-related pathways. Six DE lncRNAs were randomly selected and validated by q-PCR. Conclusions This study is the first to profile the potentially functional lncRNAs in the adipose tissue growth in rabbits, and contributes to our understanding of mammalian adipogenesis. Electronic supplementary material The online version of this article (10.1186/s12944-018-0915-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Guo-Ze Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.,College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Kun Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shen-Qiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xian-Bo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming-Cheng Cai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
14
|
Liu J, Li Y, Tong J, Gao J, Guo Q, Zhang L, Wang B, Zhao H, Wang H, Jiang E, Kurita R, Nakamura Y, Tanabe O, Engel JD, Bresnick EH, Zhou J, Shi L. Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development. Nat Commun 2018; 9:4386. [PMID: 30349036 PMCID: PMC6197277 DOI: 10.1038/s41467-018-06883-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 10/02/2018] [Indexed: 01/19/2023] Open
Abstract
In addition to serving as a prosthetic group for enzymes and a hemoglobin structural component, heme is a crucial homeostatic regulator of erythroid cell development and function. While lncRNAs modulate diverse physiological and pathological cellular processes, their involvement in heme-dependent mechanisms is largely unexplored. In this study, we elucidated a lncRNA (UCA1)-mediated mechanism that regulates heme metabolism in human erythroid cells. We discovered that UCA1 expression is dynamically regulated during human erythroid maturation, with a maximal expression in proerythroblasts. UCA1 depletion predominantly impairs heme biosynthesis and arrests erythroid differentiation at the proerythroblast stage. Mechanistic analysis revealed that UCA1 physically interacts with the RNA-binding protein PTBP1, and UCA1 functions as an RNA scaffold to recruit PTBP1 to ALAS2 mRNA, which stabilizes ALAS2 mRNA. These results define a lncRNA-mediated posttranscriptional mechanism that provides a new dimension into how the fundamental heme biosynthetic process is regulated as a determinant of erythrocyte development. LncRNAs modulate diverse physiological cellular processes, however, their involvement in heme-dependent processes are not yet clear. Here the authors reveal the role of lncRNA UCA1 in erythroid cell development.
Collapse
Affiliation(s)
- Jinhua Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lingling Zhang
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Bingrui Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Hongtao Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ryo Kurita
- Japanese Red Cross Society, Department of Research and Development, Central Blood Institute, Tokyo, 105-8521, Japan
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Cell Engineering Division, Ibaraki, 305-0074, Japan
| | - Osamu Tanabe
- Department of Integrative Genomics Tohoku Medical Megabank, Tohoku University, Sedai, 980-8573, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emery H Bresnick
- Wisconsin Institutes for Medical Research, Paul Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53562, USA
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| |
Collapse
|
15
|
Li BJ, Jiang DL, Meng ZN, Zhang Y, Zhu ZX, Lin HR, Xia JH. Genome-wide identification and differentially expression analysis of lncRNAs in tilapia. BMC Genomics 2018; 19:729. [PMID: 30286721 PMCID: PMC6172845 DOI: 10.1186/s12864-018-5115-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited. Results Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs. Conclusions This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia. Electronic supplementary material The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| |
Collapse
|
16
|
Peng Y, Chang L, Wang Y, Wang R, Hu L, Zhao Z, Geng L, Liu Z, Gong Y, Li J, Li X, Zhang C. Genome-wide differential expression of long noncoding RNAs and mRNAs in ovarian follicles of two different chicken breeds. Genomics 2018; 111:1395-1403. [PMID: 30268779 DOI: 10.1016/j.ygeno.2018.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 08/23/2018] [Accepted: 09/17/2018] [Indexed: 01/27/2023]
Abstract
Bashang long-tail chickens are an indigenous breed with dual purpose in China (meat and eggs) but have low egg laying performance. To improve the low egg laying performance, a genome-wide analysis of mRNAs and long noncoding RNAs (lncRNAs) from Bashang long-tail chickens and Hy-Line brown layers was performed. A total of 16,354 mRNAs and 8691 lncRNAs were obtained from ovarian follicles. Between the breeds, 160 mRNAs and 550 lncRNAs were found to be significantly differentially expressed. Integrated network analysis suggested some differentially expressed genes were involved in ovarian follicular development through oocyte meiosis, progesterone-mediated oocyte maturation, and cell cycle. The impact of lncRNAs on cis and trans target genes, indicating some lncRNAs may play important roles in ovarian follicular development. The current results provided a catalog of chicken ovarian follicular lncRNAs and genes for further study to understand their roles in regulation of egg laying performance.
Collapse
Affiliation(s)
- Yongdong Peng
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Li Chang
- College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding 071001, Hebei, People's Republic of China; Qinhuangdao Animal Disease Control Center, Qinhuangdao 066001, Hebei, People's Republic of China
| | - Yaqi Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Ruining Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Lulu Hu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Ziya Zhao
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Liying Geng
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Zhengzhu Liu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Yuanfang Gong
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Jingshi Li
- College of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China
| | - Xianglong Li
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China.
| | - Chuansheng Zhang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei, People's Republic of China.
| |
Collapse
|
17
|
Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
Collapse
Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
| |
Collapse
|
18
|
Lin X, Gao Q, Zhu L, Zhou G, Ni S, Han H, Yue Z. Long noncoding RNAs regulate Wnt signaling during feather regeneration. Development 2018; 145:dev.162388. [DOI: 10.1242/dev.162388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 10/04/2018] [Indexed: 02/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are non-protein coding transcripts that are involved in a broad range of biological processes. Here, we examined the functional roles of lncRNAs in feather regeneration. RNA-seq profiling of the regenerating feather blastema revealed that the Wnt signaling is among the most active pathways during feather regeneration, with the Wnt ligands and their inhibitors showing distinct expression patterns. Co-expression analysis identified hundreds of lncRNAs with similar expression patterns to either the Wnt ligands (the Lwnt group) or their downstream target genes (the Twnt group). Among these, we randomly picked two lncRNAs in the Lwnt group, and three lncRNAs in the Twnt group to validate their expression and function. Members in the Twnt group regulated feather regeneration and axis formation, whereas members in the Lwnt group showed no obvious phenotype. Further analysis confirmed that the three Twnt group members inhibit Wnt signal transduction and at the same time are down-stream target genes of this pathway. Our results suggested that the feather regeneration model can be utilized to systematically annotate the functions of lncRNAs in the chicken genome.
Collapse
Affiliation(s)
- Xiang Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - QingXiang Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - LiYan Zhu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - GuiXuan Zhou
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - ShiWei Ni
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - Hao Han
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - ZhiCao Yue
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| |
Collapse
|
19
|
Ren J, Du X, Zeng T, Chen L, Shen J, Lu L, Hu J. Divergently expressed gene identification and interaction prediction of long noncoding RNA and mRNA involved in duck reproduction. Anim Reprod Sci 2017; 185:8-17. [PMID: 28886878 DOI: 10.1016/j.anireprosci.2017.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 01/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) and divergently expressed genes exist widely in different tissues of mammals and birds, in which they are involved in various biological processes. However, there is limited information on their role in the regulation of normal biological processes during differentiation, development, and reproduction in birds. In this study, whole transcriptome strand-specific RNA sequencing of the ovary from young ducks (60days), first-laying ducks (160days), and old ducks, i.e., ducks that stopped laying eggs (490days) was performed. The lncRNAs and mRNAs from these ducks were systematically analyzed and identified by duck genome sequencing in the three study groups. The transcriptome from the duck ovary comprised 15,011 protein-coding genes and 2905 lncRNAs; all the lncRNAs were identified as novel long noncoding transcripts. The comparison of transcriptome data from different study groups identified 2240 divergent transcription genes and 135 divergently expressed lncRNAs, which differed among the groups; most of them were significantly downregulated with age. Among the divergent genes, 38 genes were related to the reproductive process and 6 genes were upregulated. Further prediction analysis revealed that 52 lncRNAs were closely correlated with divergent reproductive mRNAs. More importantly, 6 remarkable lncRNAs were correlated significantly with the conversion of the ovary in different phases. Our results aid in the understanding of the divergent transcriptome of duck ovary in different phases and the underlying mechanisms that drive the specificity of protein-coding genes and lncRNAs in duck ovary.
Collapse
Affiliation(s)
- Jindong Ren
- College of Animal Science and Technology, Northwest A & F University, No. 21 Xinong Road, Yangling, Shaanxi 712100, PR China; Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Xue Du
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Tao Zeng
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Li Chen
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Junda Shen
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Lizhi Lu
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Jianhong Hu
- College of Animal Science and Technology, Northwest A & F University, No. 21 Xinong Road, Yangling, Shaanxi 712100, PR China.
| |
Collapse
|
20
|
Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Epigenetics Chromatin 2017; 10:35. [PMID: 28693562 PMCID: PMC5504709 DOI: 10.1186/s13072-017-0142-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation. RESULTS We found that, similarly to mammalian genome, the chicken genomes is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream major regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation. CONCLUSIONS Our findings demonstrate that the effects of tissue-specific transcription activation are not restricted to the host genomic locus but affect the overall chromatin structure and transcriptional output of the encompassing topologically associating domain.
Collapse
Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| | - Aleksandra A Galitsyna
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051
| | - Ilya M Flyamer
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Arkadiy K Golov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334
| | - Ekaterina E Khrameeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia 143026.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Nezar A Abdennur
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Mikhail S Gelfand
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,Skolkovo Institute of Science and Technology, Skolkovo, Russia 143026.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia 125319
| | - Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334
| | - Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| |
Collapse
|
21
|
Cai B, Li Z, Ma M, Wang Z, Han P, Abdalla BA, Nie Q, Zhang X. LncRNA-Six1 Encodes a Micropeptide to Activate Six1 in Cis and Is Involved in Cell Proliferation and Muscle Growth. Front Physiol 2017; 8:230. [PMID: 28473774 PMCID: PMC5397475 DOI: 10.3389/fphys.2017.00230] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/31/2017] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in epigenetic regulation of skeletal muscle development. In our previous RNA-seq study (accession number GSE58755), we found that lncRNA-Six1 is an lncRNA that is differentially expressed between White Recessive Rock (WRR) and Xinghua (XH) chicken. In this study, we have further demonstrated that lncRNA-Six1 is located 432 bp upstream of the gene encoding the protein Six homeobox 1 (Six1). A dual-luciferase reporter assay identified that lncRNA-Six1 overlaps the Six1 proximal promoter. In lncRNA-Six1, a micropeptide of about 7.26 kDa was found to play an important role in the lncRNA-Six1 in cis activity. Overexpression of lncRNA-Six1 promoted the mRNA and protein expression level of the Six1 gene, while knockdown of lncRNA-Six1 inhibited Six1 expression. Moreover, tissue expression profiles showed that both the lncRNA-Six1 and the Six1 mRNA were highly expressed in chicken breast tissue. LncRNA-Six1 overexpression promoted cell proliferation and induced cell division. Conversely, its loss of function inhibited cell proliferation and reduced cell viability. Similar effects were observed after overexpression or knockdown of the Six1 gene. In addition, overexpression or knockdown of Six1 promoted or inhibited, respectively, the expression levels of muscle-growth-related genes, such as MYOG, MYHC, MYOD, IGF1R, and INSR. Taken together, these data demonstrate that lncRNA-Six1 carries out cis-acting regulation of the protein-encoding Six1 gene, and encodes a micropeptide to activate Six1 gene, thus promoting cell proliferation and being involved in muscle growth.
Collapse
Affiliation(s)
- Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Manting Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Zhijun Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Peigong Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Bahareldin A Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| |
Collapse
|
22
|
Wang B, Huang Z, Gao R, Zeng Z, Yang W, Sun Y, Wei W, Wu Z, Yu L, Li Q, Zhang S, Li F, Liu G, Liu B, Leng L, Zhan W, Yu Y, Yang G, Zhou S. Expression of Long Noncoding RNA Urothelial Cancer Associated 1 Promotes Cisplatin Resistance in Cervical Cancer. Cancer Biother Radiopharm 2017; 32:101-110. [PMID: 28414550 DOI: 10.1089/cbr.2016.2156] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bi Wang
- Department of Gynecology, Maternal and Child Health Hospital of Guiyang City, Guiyang, China
- School of Medical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Zhi Huang
- Department of Interventional Radiology, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Rui Gao
- Guizhou Entry-exit Inspection and Quarantine Bureau, Guiyang, China
| | - Zhu Zeng
- School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Weiming Yang
- Department of Gynecology, Maternal and Child Health Hospital of Guiyang City, Guiyang, China
| | - Yuan Sun
- Department of Gynecology, Maternal and Child Health Hospital of Guiyang City, Guiyang, China
| | - Wei Wei
- Department of Gynecology, Maternal and Child Health Hospital of Guiyang City, Guiyang, China
| | - Zhongqing Wu
- Department of Gynecology, Maternal and Child Health Hospital of Guiyang City, Guiyang, China
| | - Lei Yu
- School of Medical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Qinshan Li
- School of Medical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Shuai Zhang
- Department of Interventional Radiology, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Fenghu Li
- Department of Interventional Radiology, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| | - Guoli Liu
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Bingjie Liu
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Li Leng
- Department of Pediatrics, The Second Affiliated Hospital of Guiyang College of Traditional Chinese Medicine, Guiyang, China
| | - Wei Zhan
- Department of Pediatrics, The Second Affiliated Hospital of Guiyang College of Traditional Chinese Medicine, Guiyang, China
| | - Yanlong Yu
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Guozhen Yang
- School of Medical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Shi Zhou
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Department of Interventional Radiology, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China
| |
Collapse
|
23
|
Qian Y, Liu D, Cao S, Tao Y, Wei D, Li W, Li G, Pan X, Lei D. Upregulation of the long noncoding RNA UCA1 affects the proliferation, invasion, and survival of hypopharyngeal carcinoma. Mol Cancer 2017; 16:68. [PMID: 28327194 PMCID: PMC5361721 DOI: 10.1186/s12943-017-0635-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/08/2017] [Indexed: 11/10/2022] Open
Abstract
Background Several long noncoding RNAs (lncRNAs) are involved in oncogenesis. Methods and Results Our microarray analysis showed that numerous lncRNAs are dysregulated in hypopharyngeal squamous cell carcinoma (HSCC) tumor tissues as compared with normal tissues. Among those lncRNAs, urothelial carcinoma-associated 1 (UCA1) has been found to have an oncogenic role in HSCC. We confirmed the upregulation of UCA1 in HSCC by assessing its expression levels in a cohort of 53 patient tumors and paired non-tumor samples. In addition, we found that high UCA1 expression was significantly associated with advanced T category, late clinical stage, greater lymphatic invasion, and worse prognosis. Furthermore, in vitro experiments demonstrated that UCA1 functioned as an oncogene by promoting the proliferation and invasion and preventing the apoptosis of HSCC cells. Conclusions Taken together, our findings for the first time identify the role of UCA1 as a tumor promoter and a pro-metastatic factor in HSCC, demonstrating that UCA1 is a potential prognostic biomarker and therapeutic target in HSCC.
Collapse
Affiliation(s)
- Ye Qian
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Dayu Liu
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Shengda Cao
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Ye Tao
- Department of Otolaryngology & Head and Neck Surgery, 2nd Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dongmin Wei
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Wenming Li
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xinliang Pan
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China.
| | - Dapeng Lei
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University; Key Laboratory of Otolaryngology, NHFPC (Shandong University), 107 West Wenhua Road, Jinan, Shandong, 250012, People's Republic of China.
| |
Collapse
|
24
|
Lin J, Xia J, Zhang K, Yang Q. Genome-wide profiling of chicken dendritic cell response to infectious bursal disease. BMC Genomics 2016; 17:878. [PMID: 27816055 PMCID: PMC5097849 DOI: 10.1186/s12864-016-3157-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Avian infectious bursal disease virus (IBDV) is a highly contagious, immunosuppressive disease of young chickens, which causes high mortality rates and large economic losses in the poultry industry. Dendritic cells (DCs), which are antigen-presenting cells, have the unique ability to induce both innate and acquired immune responses and may significantly influence virus pathogenicity. To understand the interaction between IBDV and DCs, a microarray was used to analyse the response of DCs infected by IBDV. RESULTS IBDV infection induced 479 upregulated and 466 downregulated mRNAs in chicken DCs. Analysis of Gene Ontology suggested that transcription from the RNA polymerase II promoter and the RNA biosynthetic process were enriched, and pathway analyses suggested that oxidative phosphorylation, as well as the T cell receptor and Interleukin-17 (IL-17) signalling pathways might be activated by IBDV infection. Moreover, microRNA (miRNA) and long non-coding RNA (lncRNA) alterations in IBDV-infected chicken DCs were observed. A total of 18 significantly upregulated or downregulated miRNAs and 441 significantly upregulated or downregulated lncRNAs were identified in IBDV-stimulated DCs. We constructed 42 transcription factor (TF)-miRNA-mRNA interactions involving 1 TF, 3 miRNAs, and 42 mRNAs in IBDV-stimulated DCs. Finally, we predicted the target genes of differentially expressed lncRNAs, and constructed lncRNA-mRNA regulatory networks. CONCLUSIONS The results of this study suggest a mechanism to explain how IBDV infection triggers an effective immune response in chicken DCs.
Collapse
Affiliation(s)
- Jian Lin
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| | - Jing Xia
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| | - Keyun Zhang
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| | - Qian Yang
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| |
Collapse
|
25
|
Weikard R, Demasius W, Kuehn C. Mining long noncoding RNA in livestock. Anim Genet 2016; 48:3-18. [DOI: 10.1111/age.12493] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- R. Weikard
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - W. Demasius
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - C. Kuehn
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
- Faculty of Agricultural and Environmental Sciences; University Rostock; 18059 Rostock Germany
| |
Collapse
|
26
|
Long non-coding RNA UCA1 promotes the tumorigenesis in pancreatic cancer. Biomed Pharmacother 2016; 83:1220-1226. [PMID: 27562722 DOI: 10.1016/j.biopha.2016.08.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/05/2016] [Accepted: 08/15/2016] [Indexed: 02/01/2023] Open
Abstract
The contribution of long non-coding RNAs (lncRNAs) to tumorigenesis and metastasis of pancreatic cancer (PC) remains largely unknown. Urothelial cancer-associated 1 (UCA1), which is an originally identified lncRNA in bladder cancer, has be proved to play a pivotal role in bladder cancer progression and embryonic development. In this study, we detected the mRNA expression of UCA1 in 128 PC patients by qRT-PCR, and found that UCA1 expression was significantly, up-regulated in tumor tissues than that in matched adjacent non-tumor tissues (p<0.05). Clinicopathological analysis demonstrated that UCA1 expression in PC significantly correlated with malignant potential factors such as tumor size (p=0.021), depth of invasion (p=0.033), CA19-9 level (p=0.034) and tumor stage (p=0.013). Cox proportional hazards regression analysis also confirmed that high UCA1 expression was an independent prognostic biomarker of PC (p=0.046), which led to an obviously shorter 5-year overall survival (OS) compared to those patients with low UCA1 expressions (p=0.018). Furthermore, we effectively down-regulated UCA1 mRNA expression by transfecting RNA interfere fragments into SW-1990 cells, and our results in vitro indicated that down-regulation of UCA1 could effectively inhibit the cell proliferative activities, induce apoptotic rate and cause cell cycle arrest in PC cells (p<0.05). Meanwhile, UCA1 expression negative-correlated with p27 in PC tissues (r2=0.46, p<0.01), and knockdown of p27 partly abrogated the cell proliferative activities caused by UCA1 (p<0.05). Our results raised the possibility of using UCA1 as a potential prognostic biomarker and therapy target of PC, and down-regulation of UCA1 might be considered to be a novel molecular treatment strategy for patients with PC.
Collapse
|
27
|
Achawanantakun R, Chen J, Sun Y, Zhang Y. LncRNA-ID: Long non-coding RNA IDentification using balanced random forests. Bioinformatics 2015; 31:3897-905. [PMID: 26315901 DOI: 10.1093/bioinformatics/btv480] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 08/07/2015] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Long non-coding RNAs (lncRNAs), which are non-coding RNAs of length above 200 nucleotides, play important biological functions such as gene expression regulation. To fully reveal the functions of lncRNAs, a fundamental step is to annotate them in various species. However, as lncRNAs tend to encode one or multiple open reading frames, it is not trivial to distinguish these long non-coding transcripts from protein-coding genes in transcriptomic data. RESULTS In this work, we design a new tool that calculates the coding potential of a transcript using a machine learning model (random forest) based on multiple features including sequence characteristics of putative open reading frames, translation scores based on ribosomal coverage, and conservation against characterized protein families. The experimental results show that our tool competes favorably with existing coding potential computation tools in lncRNA identification. AVAILABILITY AND IMPLEMENTATION The scripts and data can be downloaded at https://github.com/zhangy72/LncRNA-ID.
Collapse
Affiliation(s)
- Rujira Achawanantakun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jiao Chen
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yanni Sun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yuan Zhang
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|