1
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Zhou J, Tian G, Quan Y, Kong Q, Huang F, Li J, Wu W, Tang Y, Zhou Z, Liu X. The long noncoding RNA THBS1-AS1 promotes cardiac fibroblast activation in cardiac fibrosis by regulating TGFBR1. JCI Insight 2023; 8:160745. [PMID: 36787190 PMCID: PMC10070117 DOI: 10.1172/jci.insight.160745] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Cardiac fibrosis is associated with an adverse prognosis in cardiovascular disease that results in a decreased cardiac compliance and, ultimately, heart failure. Recent studies have identified the role of long noncoding RNA (lncRNA) in cardiac fibrosis. However, the functions of many lncRNAs in cardiac fibrosis remain to be characterized. Through a whole-transcriptome sequencing and bioinformatics analysis on a mouse model of pressure overload-induced cardiac fibrosis, we screened a key lncRNA termed thrombospondin 1 antisense 1 (THBS1-AS1), which was positively associated with cardiac fibrosis. In vitro functional studies demonstrated that the silencing of THBS1-AS1 ameliorated TGF-β1 effects on cardiac fibroblast (CF) activation, and the overexpression of THBS1-AS1 displayed the opposite effect. A mechanistic study revealed that THBS1-AS1 could sponge miR-221/222 to regulate the expression of TGFBR1. Moreover, under TGF-β1 stimulation, the forced expression of miR-221/222 or the knockdown TGFBR1 significantly reversed the THBS1-AS1 overexpression induced by further CF activation. In vivo, specific knockdown of THBS1-AS1 in activated CFs significantly alleviated transverse aorta constriction-induced (TAC-induced) cardiac fibrosis in mice. Finally, we demonstrated that the human THBS1-AS1 can also affect the activation of CFs by regulating TGFBR1. In conclusion, this study reveals that lncRNA THBS1-AS1 is a potentially novel regulator of cardiac fibrosis and may serve as a target for the treatment of cardiac fibrosis.
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Affiliation(s)
- Junteng Zhou
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
- Health Management Center, General Practice Medical Center, and
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
| | - Geer Tian
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Yue Quan
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Qihang Kong
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Fangyang Huang
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
| | - Junli Li
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Wenchao Wu
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
| | - Yong Tang
- International Joint Research Centre on Purinergic Signaling, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhichao Zhou
- Division of Cardiology, Department of Medicine Solna, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Xiaojing Liu
- Laboratory of Cardiovascular Diseases, Regenerative Medicine Research Center
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, China
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2
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Sun KY, Oreper D, Schoenrock SA, McMullan R, Giusti-Rodríguez P, Zhabotynsky V, Miller DR, Tarantino LM, Pardo-Manuel de Villena F, Valdar W. Bayesian modeling of skewed X inactivation in genetically diverse mice identifies a novel Xce allele associated with copy number changes. Genetics 2021; 218:6162162. [PMID: 33693696 DOI: 10.1093/genetics/iyab034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Female mammals are functional mosaics of their parental X-linked gene expression due to X chromosome inactivation (XCI). This process inactivates one copy of the X chromosome in each cell during embryogenesis and that state is maintained clonally through mitosis. In mice, the choice of which parental X chromosome remains active is determined by the X chromosome controlling element (Xce), which has been mapped to a 176-kb candidate interval. A series of functional Xce alleles has been characterized or inferred for classical inbred strains based on biased, or skewed, inactivation of the parental X chromosomes in crosses between strains. To further explore the function structure basis and location of the Xce, we measured allele-specific expression of X-linked genes in a large population of F1 females generated from Collaborative Cross (CC) strains. Using published sequence data and applying a Bayesian "Pólya urn" model of XCI skew, we report two major findings. First, inter-individual variability in XCI suggests mouse epiblasts contain on average 20-30 cells contributing to brain. Second, CC founder strain NOD/ShiLtJ has a novel and unique functional allele, Xceg, that is the weakest in the Xce allelic series. Despite phylogenetic analysis confirming that NOD/ShiLtJ carries a haplotype almost identical to the well-characterized C57BL/6J (Xceb), we observed unexpected patterns of XCI skewing in females carrying the NOD/ShiLtJ haplotype within the Xce. Copy number variation is common at the Xce locus and we conclude that the observed allelic series is a product of independent and recurring duplications shared between weak Xce alleles.
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Affiliation(s)
- Kathie Y Sun
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Computational Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel Oreper
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Computational Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Neuroscience Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel McMullan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Genetics and Molecular Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paola Giusti-Rodríguez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vasyl Zhabotynsky
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa M Tarantino
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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3
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Ji X, Li P, Fuscoe JC, Chen G, Xiao W, Shi L, Ning B, Liu Z, Hong H, Wu J, Liu J, Guo L, Kreil DP, Łabaj PP, Zhong L, Bao W, Huang Y, He J, Zhao Y, Tong W, Shi T. A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. Nucleic Acids Res 2020; 48:8320-8331. [PMID: 32749457 PMCID: PMC7470976 DOI: 10.1093/nar/gkaa638] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.
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Affiliation(s)
- Xiangjun Ji
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peng Li
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA
| | - James C Fuscoe
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wenzhong Xiao
- Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA
| | - Leming Shi
- Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, 200438, China
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Zhichao Liu
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jinghua Liu
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lei Guo
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - David P Kreil
- Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria
| | - Paweł P Łabaj
- Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria.,Małopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
| | - Liping Zhong
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Wenjun Bao
- SAS Institute Inc., Cary, NC, 27513, USA
| | - Yong Huang
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Jian He
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China
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4
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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5
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Chen Z, Zhang Y. Maternal H3K27me3-dependent autosomal and X chromosome imprinting. Nat Rev Genet 2020; 21:555-571. [PMID: 32514155 DOI: 10.1038/s41576-020-0245-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Genomic imprinting and X-chromosome inactivation (XCI) are classic epigenetic phenomena that involve transcriptional silencing of one parental allele. Germline-derived differential DNA methylation is the best-studied epigenetic mark that initiates imprinting, but evidence indicates that other mechanisms exist. Recent studies have revealed that maternal trimethylation of H3 on lysine 27 (H3K27me3) mediates autosomal maternal allele-specific gene silencing and has an important role in imprinted XCI through repression of maternal Xist. Furthermore, loss of H3K27me3-mediated imprinting contributes to the developmental defects observed in cloned embryos. This novel maternal H3K27me3-mediated non-canonical imprinting mechanism further emphasizes the important role of parental chromatin in development and could provide the basis for improving the efficiency of embryo cloning.
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Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Boston, MA, USA.
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6
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Han CL, Liu YP, Sui YP, Chen N, Du TT, Jiang Y, Guo CJ, Wang KL, Wang Q, Fan SY, Shimabukuro M, Meng FG, Yuan F, Zhang JG. Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson's disease. Aging (Albany NY) 2020; 12:718-739. [PMID: 31929116 PMCID: PMC6977703 DOI: 10.18632/aging.102652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/24/2019] [Indexed: 01/08/2023]
Abstract
Levodopa-induced dyskinesia (LID) is a common complication of chronic dopamine replacement therapy in the treatment of Parkinson's disease (PD). Long noncoding RNAs regulate gene expression and participate in many biological processes. However, the role of long noncoding RNAs in LID is not well understood. In the present study, we examined the lncRNA transcriptome profile of a rat model of PD and LID by RNA sequence and got a subset of lncRNAs, which were gradually decreased during the development of PD and LID. We further identified a previously uncharacterized long noncoding RNA, NONRATT023402.2, and its target genes glutathione S-transferase omega (Gsto)2 and prostaglandin E receptor (Ptger)3. All of them were decreased in the PD and LID rats as shown by quantitative real-time PCR, fluorescence in situ hybridization and western blotting. Pearson's correlation analysis showed that their expression was positively correlated with the dyskinesia score of LID rats. In vitro experiments by small interfering RNA confirmed that slicing NONRATT023402 inhibited Gsto2 and Ptger3 and promoted the inflammatory response. These results demonstrate that NONRATT023402.2 may have inhibitive effects on the development of PD and LID.
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Affiliation(s)
- Chun-Lei Han
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yun-Peng Liu
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Yun-Peng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Ning Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ting-Ting Du
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Ying Jiang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Chen-Jia Guo
- Department of Pathology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Kai-Liang Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Qiao Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Shi-Ying Fan
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Michitomo Shimabukuro
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Fan-Gang Meng
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fang Yuan
- Department of Pathophysiology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jian-Guo Zhang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Neurostimulation, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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7
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Zou H, Yu D, Du X, Wang J, Chen L, Wang Y, Xu H, Zhao Y, Zhao S, Pang Y, Liu Y, Hao H, Zhao X, Du W, Dai Y, Li N, Wu S, Zhu H. No imprinted XIST expression in pigs: biallelic XIST expression in early embryos and random X inactivation in placentas. Cell Mol Life Sci 2019; 76:4525-4538. [PMID: 31139846 PMCID: PMC11105601 DOI: 10.1007/s00018-019-03123-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
Dosage compensation, which is achieved by X-chromosome inactivation (XCI) in female mammals, ensures balanced X-linked gene expression levels between the sexes. Although eutherian mammals commonly display random XCI in embryonic and adult tissues, imprinted XCI has also been identified in extraembryonic tissues of mouse, rat, and cow. Little is known about XCI in pigs. Here, we sequenced the porcine XIST gene and identified an insertion/deletion mutation between Asian- and Western-origin pig breeds. Allele-specific analysis revealed biallelic XIST expression in porcine ICSI blastocysts. To investigate the XCI pattern in porcine placentas, we performed allele-specific RNA sequencing analysis on individuals from reciprocal crosses between Duroc and Rongchang pigs. Our results were the first to reveal that random XCI occurs in the placentas of pigs. Next, we investigated the H3K27me3 histone pattern in porcine blastocysts, showing that only 17-31.8% cells have attained XCI. The hypomethylation status of an important XIST DMR (differentially methylated region) in gametes and early embryos demonstrated that no methylation is pre-deposited on XIST in pigs. Our findings reveal that the XCI regulation mechanism in pigs is different from that in mice and highlight the importance of further study of the mechanisms regulating XCI during early porcine embryo development.
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Affiliation(s)
- Huiying Zou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Dawei Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jing Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Chen
- Chongqing Academy of Animal Science, Chongqing, 402460, China
| | - Yangyang Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huitao Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunxuan Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanjiang Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunwei Pang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yan Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haisheng Hao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueming Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weihua Du
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunping Dai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China.
| | - Huabin Zhu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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8
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Shi X, Wang X, Hua Y. LncRNA GACAT1 Promotes Gastric Cancer Cell Growth, Invasion And Migration By Regulating MiR-149-mediated Of ZBTB2 And SP1. J Cancer 2018; 9:3715-3722. [PMID: 30405842 PMCID: PMC6216017 DOI: 10.7150/jca.27546] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) were involved in the progression of gastric cancer (GC). In our study, we have determined that GACAT1 expression was upregulated in GC. Overexpression of GACAT1 promoted GC cell proliferation, invasion and migration. We also determined that miR-149 directly interacts with the target site on GACAT1. Furthermore, we investigated that miR-149 downregulated ZBTB2 and SP1 expressions which were induced by GACAT1, miR-149 inhibited GC cell growth and invasion mediated by GACAT1. In conclusion, we found that miR-149 downregulated ZBTB2 and SP1 expressions, and inhibited GC cell progression mediated by GACAT1. Therefore, we indicated that GACAT1 and miR-149 may be potential therapeutic targets for GC.
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Affiliation(s)
- Xiaoqing Shi
- West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaoqin Wang
- West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yimin Hua
- West China Second University Hospital, Sichuan University, Chengdu, China
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9
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Chen X, Zhu Z, Yu F, Huang J, Jia R, Pan J. Effect of shRNA-mediated Xist knockdown on the quality of porcine parthenogenetic embryos. Dev Dyn 2018; 248:140-148. [PMID: 30055068 DOI: 10.1002/dvdy.24660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 06/27/2018] [Accepted: 07/13/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Parthenogenetically activated oocytes exhibit poor embryo development and lower total numbers of cells per blastocyst accompanied by abnormally increased expression of Xist, a long noncoding RNA that plays an important role in triggering X chromosome inactivation during embryogenesis. RESULTS To investigate whether knockdown of Xist influences parthenogenetic development in pigs. We developed an anti-Xist short hairpin RNA (shRNA) vector, which can significantly inhibit Xist expression for at least seven days when injected at 12-13 hr after parthenogenetic activation. Embryonic cleavage, blastocyst formation, and total blastocyst cell numbers were compared during the blastocyst stage, as well as the expression of an X-linked gene and three pluripotent transcription factors. Knockdown of Xist significantly increases the total blastocyst cell number, but does not influence the rate of embryo cleavage and blastocyst formation. The expressions of Sox2, Nanog, and Oct4 were also significantly improved in the injected embryos compared with the control at the blastocyst stage, but the Foxp3 expression level was not increased significantly. CONCLUSIONS The present study provides valuable information for understanding the role of Xist in parthenogenesis and presents a new approach for improving the quality of porcine parthenogenetic embryos. Developmental Dynamics 248:140-148, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaoyu Chen
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, P.R. China
| | - Zhiwei Zhu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, P.R. China
| | - Fuxian Yu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, P.R. China
| | - Jing Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, P.R. China
| | - Ruoxin Jia
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, P.R. China
| | - Jianzhi Pan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, P.R. China
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10
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Sado T. What makes the maternal X chromosome resistant to undergoing imprinted X inactivation? Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0365. [PMID: 28947661 DOI: 10.1098/rstb.2016.0365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 11/12/2022] Open
Abstract
In the mouse, while either X chromosome is chosen for inactivation in a random fashion in the embryonic tissue, the paternally derived X chromosome is preferentially inactivated in the extraembryonic tissues. It has been shown that the maternal X chromosome is imprinted so as not to undergo inactivation in the extraembryonic tissues. X-linked noncoding Xist RNA becomes upregulated on the X chromosome that is to be inactivated. An antisense noncoding RNA, Tsix, which occurs at the Xist locus and has been shown to negatively regulate Xist expression in cis, is imprinted to be expressed from the maternal X in the extraembryonic tissues. Although Tsix appears to be responsible for the imprint laid on the maternal X, those who disagree with this idea would point out the fact that Tsix has not yet been expressed from the maternal X when Xist becomes upregulated on the paternal but not the maternal X at the onset of imprinted X-inactivation in preimplantation embryos. Recent studies have demonstrated, however, that there is a prominent difference in the chromatin structure at the Xist locus depending on the parental origin, which I suggest might account for the repression of maternal Xist in the absence of maternal Tsix at the preimplantation stages.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Takashi Sado
- Department of Bioscience, Graduate School of Agriculture, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan
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11
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Inoue A, Jiang L, Lu F, Zhang Y. Genomic imprinting of Xist by maternal H3K27me3. Genes Dev 2017; 31:1927-1932. [PMID: 29089420 PMCID: PMC5710138 DOI: 10.1101/gad.304113.117] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/28/2017] [Indexed: 11/25/2022]
Abstract
In this study, Inoue et al. investigated the mechanism underlying Xist imprinting in female mammals. They demonstrate that the Xist locus is coated with a broad H3K27me3 domain that is established during oocyte growth and persists through preimplantation development in mice, thus identifying maternal H3K27me3 as the imprinting mark of Xist. Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X-chromosome inactivation (XCI) in female mammals. However, the mechanism underlying Xist imprinting is unclear. Here we show that the Xist locus is coated with a broad H3K27me3 domain that is established during oocyte growth and persists through preimplantation development in mice. Loss of maternal H3K27me3 induces maternal Xist expression and maternal XCI in preimplantation embryos. Our study thus identifies maternal H3K27me3 as the imprinting mark of Xist.
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Affiliation(s)
- Azusa Inoue
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Lan Jiang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Falong Lu
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
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12
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Kaneda M, Takahashi M, Yamanaka KI, Saito K, Taniguchi M, Akagi S, Watanabe S, Nagai T. Epigenetic analysis of bovine parthenogenetic embryonic fibroblasts. J Reprod Dev 2017; 63:365-375. [PMID: 28484201 PMCID: PMC5593088 DOI: 10.1262/jrd.2017-040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although more than 100 imprinted genes have already been identified in the mouse and human genomes, little is known about genomic imprinting in cattle. For a better understanding of these genes in cattle, parthenogenetically activated bovine blastocysts were transferred to recipient cows to obtain parthenotes, and fibroblasts derived from a Day 40 (Day 0 being the day of parthenogenetic activation) parthenogenetic embryo (BpEFs) were successfully obtained. Bovine embryonic fibroblasts (BEFs) were also isolated from a normal fertilized embryo obtained from an artificially inseminated cow. The expression of imprinted genes was analyzed by RT-PCR. Paternally expressed genes (PEGs) in mouse (viz., IGF2, PEG3, ZAC1, NDN, DLK1, SGCE, and PEG10) were expressed in BEFs, but not in BpEFs, suggesting that these genes are also imprinted in cattle. However, other PEGs in mouse (viz., IMPACT, MAGEL2, SNRPN, and PEG1/MEST) were expressed in both BEFs and BpEFs. These genes may not be imprinted in BEFs. The expression of seven maternally expressed genes in mouse was also analyzed, and only CDKN1C was not expressed in BpEFs. The DNA methylation patterns of repetitive elements (Satellite I, Satellite II, alpha-satellite, and Art2) were not different between the BEFs and BpEFs; however, the differentially methylated region (DMR) of paternally methylated H19 was hypomethylated, whereas those of maternally methylated PEG3 and PEG10 were hypermethylated in BpEFs, as expected. The methylation of the SNRPN DMR was not different between the BEFs and BpEFs, in accordance with the SNRPN expression levels in both cell types. The XIST gene, which is essential for X chromosome inactivation in females, was expressed in BpEFs, whereas its DMR was half-methylated, suggesting that X chromosome inactivation is normal in these cells. Microarray analysis was also applied to identify novel PEGs that should be expressed only in BEFs but not in BpEFs. More than 300 PEG candidate genes, including IGF2, PEG3, and PEG10, were obtained. These results illustrate the epigenetic characteristic of bovine parthenogenetic embryos and contribute to the identification of novel imprinted genes in cattle.
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Affiliation(s)
- Masahiro Kaneda
- Division of Animal Life Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Masashi Takahashi
- Department of Animal Science, Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | | | - Koji Saito
- Kumamoto Prefectural Agriculture Research Center, Kumamoto 861-1113, Japan
| | - Masanori Taniguchi
- Kumamoto Prefectural Agriculture Research Center, Kumamoto 861-1113, Japan
| | - Satoshi Akagi
- Animal Breeding and Reproduction Research Division, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Ibaraki 305-0901, Japan
| | - Shinya Watanabe
- Animal Breeding and Reproduction Research Division, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Ibaraki 305-0901, Japan
| | - Takashi Nagai
- Headquarters, National Agriculture and Food Research Organization, Ibaraki 305-8517, Japan
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13
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Wu BJ, Zhao LX, Zhu CC, Chen YL, Wei MY, Bao SQ, Sun SC, Li XH. Altered apoptosis/autophagy and epigenetic modifications cause the impaired postimplantation octaploid embryonic development in mice. Cell Cycle 2016; 16:82-90. [PMID: 27830977 DOI: 10.1080/15384101.2016.1252884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Polyploids are pervasive in plants and have large impacts on crop breeding, but natural polyploids are rare in animals. Mouse diploid embryos can be induced to become tetraploid by blastomere fusion at the 2-cell stage and tetraploid embryos can develop to the blastocyst stage in vitro. However, there is little information regarding mouse octaploid embryonic development and precise mechanisms contributing to octaploid embryonic developmental limitations are unknown. To investigate the genetic and epigenetic mechanisms underlying octaploid embryonic development, we generated mouse octaploid embryos and evaluated the in vitro/in vivo developmental potential. Here we show that octaploid embryos can develop to the blastocyst stage in vitro, but all fetus impaired immediately after implantation. Our results indicate that cell lineage specification of octaploid embryo was disorganized. Furthermore, these octaploid embryos showed increased apoptosis as well as alterations in epigenetic modifications when compared with diploid embryos. Thus, our cumulative data provide cues for why mouse octaploid embryonic development is limited and its failed postimplantation development.
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Affiliation(s)
- Bao-Jiang Wu
- a College of Animal Science and Technology, Nanjing Agricultural University , Nanjing , China.,b Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University , Huhhot , China.,c Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal , Huhhot , China
| | - Li-Xia Zhao
- b Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University , Huhhot , China.,c Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal , Huhhot , China
| | - Cheng-Cheng Zhu
- a College of Animal Science and Technology, Nanjing Agricultural University , Nanjing , China
| | - Yang-Lin Chen
- b Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University , Huhhot , China
| | - Meng-Yi Wei
- b Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University , Huhhot , China
| | - Si-Qin Bao
- b Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University , Huhhot , China.,c Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal , Huhhot , China
| | - Shao-Chen Sun
- a College of Animal Science and Technology, Nanjing Agricultural University , Nanjing , China
| | - Xi-He Li
- b Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University , Huhhot , China.,c Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal , Huhhot , China
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14
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Fukuda A, Mitani A, Miyashita T, Sado T, Umezawa A, Akutsu H. Maintenance of Xist Imprinting Depends on Chromatin Condensation State and Rnf12 Dosage in Mice. PLoS Genet 2016; 12:e1006375. [PMID: 27788132 PMCID: PMC5082930 DOI: 10.1371/journal.pgen.1006375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022] Open
Abstract
In female mammals, activation of Xist (X-inactive specific transcript) is essential for establishment of X chromosome inactivation. During early embryonic development in mice, paternal Xist is preferentially expressed whereas maternal Xist (Xm-Xist) is silenced. Unlike autosomal imprinted genes, Xist imprinting for Xm-Xist silencing was erased in cloned or parthenogenetic but not fertilized embryos. However, the molecular mechanism underlying the variable nature of Xm-Xist imprinting is poorly understood. Here, we revealed that Xm-Xist silencing depends on chromatin condensation states at the Xist/Tsix genomic region and on Rnf12 expression levels. In early preimplantation, chromatin decondensation via H3K9me3 loss and histone acetylation gain caused Xm-Xist derepression irrespective of embryo type. Although the presence of the paternal genome during pronuclear formation impeded Xm-Xist derepression, Xm-Xist was robustly derepressed when the maternal genome was decondensed before fertilization. Once Xm-Xist was derepressed by chromatin alterations, the derepression was stably maintained and rescued XmXpΔ lethality, indicating that loss of Xm-Xist imprinting was irreversible. In late preimplantation, Oct4 served as a chromatin opener to create transcriptional permissive states at Xm-Xist/Tsix genomic loci. In parthenogenetic embryos, Rnf12 overdose caused Xm-Xist derepression via Xm-Tsix repression; physiological Rnf12 levels were essential for Xm-Xist silencing maintenance in fertilized embryos. Thus, chromatin condensation and fine-tuning of Rnf12 dosage were crucial for Xist imprint maintenance by silencing Xm-Xist. X-inactive specific transcript (Xist) is essential a large non-coding RNA for establishment of X chromosome inactivation in female mammals. The aberrant X chromosome inactivation critically affects cellular viability. Therefore, spatiotemporal regulation of Xist expression is required for proper development. In mice, Xist expression is imprinted in early embryonic development and maternal Xist is never expressed during preimplantation phases irrespective of the presence of Xist activator, maternal Rnf12. Generally, parental origin-specific expression pattern of autosomal imprinted genes is maintained in various types of embryos. However, Xist imprinting for transcriptional silencing of maternal Xist was erased in cloned or parthenogenetic but not fertilized embryos. Here, we dissect the molecular mechanism underlying the variable nature of Xist imprinting. We show that in fertilized embryos, chromatin condensation states are essential maternal Xist repression in early preimplantation phases, whereas at late preimplantation stages, pluripotency factor Oct4 serves as a chromatin opener and the maintenance of Xist silencing depends on Rnf12 expression dosage. Although the Oct4 mediated chromatin decondensation also occurs in parthenogetic embryos, Rnf12 overdose causes maternal Xist derepression at late preimplantation phases. Thus these findings reveal that the chromatin regulation by pluripotency factor and Xist activator dose define Xist imprinting state.
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Affiliation(s)
- Atsushi Fukuda
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Okura, Setagaya, Tokyo, Japan
| | - Atsushi Mitani
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Okura, Setagaya, Tokyo, Japan
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Kitasato, Minami, Sagamihara, Kanagawa, Japan
| | - Toshiyuki Miyashita
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, Kitasato, Minami, Sagamihara, Kanagawa, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nakamachi, Nara, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Okura, Setagaya, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Okura, Setagaya, Tokyo, Japan
- Department of Stem Cell Research, Fukushima Medical University, Hikarigaoka, Fukushima City, Fukushima, Japan
- * E-mail:
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15
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Federici F, Magaraki A, Wassenaar E, van Veen-Buurman CJH, van de Werken C, Baart EB, Laven JSE, Grootegoed JA, Gribnau J, Baarends WM. Round Spermatid Injection Rescues Female Lethality of a Paternally Inherited Xist Deletion in Mouse. PLoS Genet 2016; 12:e1006358. [PMID: 27716834 PMCID: PMC5065126 DOI: 10.1371/journal.pgen.1006358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
In mouse female preimplantation embryos, the paternal X chromosome (Xp) is silenced by imprinted X chromosome inactivation (iXCI). This requires production of the noncoding Xist RNA in cis, from the Xp. The Xist locus on the maternally inherited X chromosome (Xm) is refractory to activation due to the presence of an imprint. Paternal inheritance of an Xist deletion (XpΔXist) is embryonic lethal to female embryos, due to iXCI abolishment. Here, we circumvented the histone-to-protamine and protamine-to-histone transitions of the paternal genome, by fertilization of oocytes via injection of round spermatids (ROSI). This did not affect initiation of XCI in wild type female embryos. Surprisingly, ROSI using ΔXist round spermatids allowed survival of female embryos. This was accompanied by activation of the intact maternal Xist gene, initiated with delayed kinetics, around the morula stage, resulting in Xm silencing. Maternal Xist gene activation was not observed in ROSI-derived males. In addition, no Xist expression was detected in male and female morulas that developed from oocytes fertilized with mature ΔXist sperm. Finally, the expression of the X-encoded XCI-activator RNF12 was enhanced in both male (wild type) and female (wild type as well as XpΔXist) ROSI derived embryos, compared to in vivo fertilized embryos. Thus, high RNF12 levels may contribute to the specific activation of maternal Xist in XpΔXist female ROSI embryos, but upregulation of additional Xp derived factors and/or the specific epigenetic constitution of the round spermatid-derived Xp are expected to be more critical. These results illustrate the profound impact of a dysregulated paternal epigenome on embryo development, and we propose that mouse ROSI can be used as a model to study the effects of intergenerational inheritance of epigenetic marks.
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Affiliation(s)
- Federica Federici
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Aristea Magaraki
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Catherina J. H. van Veen-Buurman
- Division of Reproductive Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Christine van de Werken
- Division of Reproductive Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Esther B Baart
- Division of Reproductive Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Joop S. E. Laven
- Division of Reproductive Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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16
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Deuve JL, Bonnet-Garnier A, Beaujean N, Avner P, Morey C. Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome. Epigenetics 2016; 10:931-42. [PMID: 26267271 PMCID: PMC4844198 DOI: 10.1080/15592294.2015.1081327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
During the first divisions of the female mouse embryo, the paternal X-chromosome is coated by Xist non-coding RNA and gradually silenced. This imprinted X-inactivation principally results from the apposition, during oocyte growth, of an imprint on the X-inactivation master control region: the X-inactivation center (Xic). This maternal imprint of yet unknown nature is thought to prevent Xist upregulation from the maternal X (XM) during early female development. In order to provide further insight into the XM imprinting mechanism, we applied single-cell approaches to oocytes and pre-implantation embryos at different stages of development to analyze the expression of candidate genes within the Xic. We show that, unlike the situation pertaining in most other cellular contexts, in early-growing oocytes, Xist and Tsix sense and antisense transcription occur simultaneously from the same chromosome. Additionally, during early development, Xist appears to be transiently transcribed from the XM in some blastomeres of late 2-cell embryos concomitant with the general activation of the genome indicating that XM imprinting does not completely suppress maternal Xist transcription during embryo cleavage stages. These unexpected transcriptional regulations of the Xist locus call for a re-evaluation of the early functioning of the maternal imprint on the X-chromosome and suggest that Xist/Tsix antagonist transcriptional activities may participate in imprinting the maternal locus as described at other loci subject to parental imprinting.
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Affiliation(s)
- Jane Lynda Deuve
- a Laboratoire de Génétique Moléculaire Murine; Institut Pasteur ; Paris , France
| | | | - Nathalie Beaujean
- b INRA; UMR1198 Biologie du Développement et Reproduction ; Jouy-en-Josas , France
| | - Philip Avner
- a Laboratoire de Génétique Moléculaire Murine; Institut Pasteur ; Paris , France
| | - Céline Morey
- a Laboratoire de Génétique Moléculaire Murine; Institut Pasteur ; Paris , France
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17
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Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
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18
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Pandya-Jones A, Plath K. The "lnc" between 3D chromatin structure and X chromosome inactivation. Semin Cell Dev Biol 2016; 56:35-47. [PMID: 27062886 DOI: 10.1016/j.semcdb.2016.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions.
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Affiliation(s)
- Amy Pandya-Jones
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA.
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19
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Prudhomme J, Morey C. Epigenesis and plasticity of mouse trophoblast stem cells. Cell Mol Life Sci 2016; 73:757-74. [PMID: 26542801 PMCID: PMC11108370 DOI: 10.1007/s00018-015-2086-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 12/28/2022]
Abstract
The critical role of the placenta in supporting a healthy pregnancy is mostly ensured by the extraembryonic trophoblast lineage that acts as the interface between the maternal and the foetal compartments. The diverse trophoblast cell subtypes that form the placenta originate from a single layer of stem cells that emerge from the embryo when the earliest cell fate decisions are occurring. Recent studies show that these trophoblast stem cells exhibit extensive plasticity as they are capable of differentiating down multiple pathways and are easily converted into embryonic stem cells in vitro. In this review, we discuss current knowledge of the mechanisms and control of the epigenesis of mouse trophoblast stem cells through a comparison with the corresponding mechanisms in pluripotent embryonic stem cells. To illustrate some of the more striking manifestations of the epigenetic plasticity of mouse trophoblast stem cells, we discuss them within the context of two paradigms of epigenetic regulation of gene expression: the imprinted gene expression of specific loci and the process of X-chromosome inactivation.
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Affiliation(s)
- Julie Prudhomme
- Laboratoire de Génétique Moléculaire Murine, Institut Pasteur, 75015, Paris, France
| | - Céline Morey
- CNRS, UMR7216 Epigenetics and Cell Fate, 75013, Paris, France.
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20
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Prudhomme J, Dubois A, Navarro P, Arnaud D, Avner P, Morey C. A rapid passage through a two-active-X-chromosome state accompanies the switch of imprinted X-inactivation patterns in mouse trophoblast stem cells. Epigenetics Chromatin 2015; 8:52. [PMID: 26628922 PMCID: PMC4665903 DOI: 10.1186/s13072-015-0044-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/16/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND In female mice, while the presence of two-active X-chromosomes characterises pluripotency, it is not tolerated in most other cellular contexts. In particular, in the trophoblastic lineage, impairment of paternal X (X(P)) inactivation results in placental defects. RESULTS Here, we show that Trophoblast Stem (TS) cells can undergo a complete reversal of imprinted X-inactivation without detectable change in cell-type identity. This reversal occurs through a reactivation of the X(P) leading to TS clones showing two active Xs. Intriguingly, within such clones, all the cells rapidly and homogeneously either re-inactivate the X(P) or inactivate, de novo, the X(M). CONCLUSION This secondary non-random inactivation suggests that the two-active-X states in TS and in pluripotent contexts are epigenetically distinct. These observations also reveal a pronounced plasticity of the TS epigenome allowing TS cells to dramatically and accurately reprogram gene expression profiles. This plasticity may serve as a back-up system when X-linked mono-allelic gene expression is perturbed.
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Affiliation(s)
- Julie Prudhomme
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Agnès Dubois
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Epigenetics of Stem Cells Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Danielle Arnaud
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Philip Avner
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Dynamics of Epigenetic Regulation, EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Céline Morey
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; CNRS, UMR7216 Epigenetics and Cell Fate, 35 rue Hélène Brion, 75013 Paris, France
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21
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Amakawa Y, Sakata Y, Hoki Y, Arata S, Shioda S, Fukagawa T, Sasaki H, Sado T. A new Xist allele driven by a constitutively active promoter is dominated by Xist locus environment and exhibits the parent-of-origin effects. Development 2015; 142:4299-308. [PMID: 26511926 DOI: 10.1242/dev.128819] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/21/2015] [Indexed: 01/09/2023]
Abstract
The dosage difference of X-linked genes between the sexes in mammals is compensated for by genetic inactivation of one of the X chromosomes in XX females. A noncoding RNA transcribed from the Xist gene at the onset of X chromosome inactivation coats the X chromosome in cis and induces chromosome-wide heterochromatinization. Here, we report a new Xist allele (Xist(CAG)) driven by a CAG promoter, which is known to be constitutively active in many types of cells. The paternal transmission of Xist(CAG) resulted in the preferential inactivation of the targeted paternal X (Xp) not only in the extra-embryonic but also the embryonic lineage, whereas maternal transmission ended with embryonic lethality at the early postimplantation stage with a phenotype that resembled mutant embryos carrying a maternal deficiency in Tsix, an antisense negative regulator of Xist, in both sexes. Interestingly, we found that the upregulation of Xist(CAG) in preimplantation embryos temporally differed depending on its parental origin: its expression started at the 4- to 8-cell stages when paternally inherited, and Xist(CAG) was upregulated at the blastocyst stage when maternally inherited. This might indicate that the Xist locus on Xp is permissive to transcription, but the Xist locus on the maternal X (Xm) is not. We extrapolated from these findings that the maternal Xist allele might manifest a chromatin structure inaccessible by transcription factors relative to the paternal allele. This might underlie the mechanism for the maternal repression of Xist at the early cleavage stage when Tsix expression has not yet occurred on Xm.
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Affiliation(s)
- Yuko Amakawa
- Division of Molecular Genetics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Yuka Sakata
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu-University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan Department of Advanced Bioscience, Graduate School of Agriculture, Kinki University, 3327-204, Nakamachi, Nara 631-8505, Japan
| | - Yuko Hoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu-University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Arata
- Department of Anatomy, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Seiji Shioda
- Department of Anatomy, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Tatsuo Fukagawa
- Division of Molecular Genetics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu-University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Sado
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu-University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan Department of Advanced Bioscience, Graduate School of Agriculture, Kinki University, 3327-204, Nakamachi, Nara 631-8505, Japan
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Fukuda A, Mitani A, Miyashita T, Umezawa A, Akutsu H. Chromatin condensation of Xist genomic loci during oogenesis in mice. Development 2015; 142:4049-55. [PMID: 26459223 PMCID: PMC4712840 DOI: 10.1242/dev.127308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/02/2015] [Indexed: 01/29/2023]
Abstract
Repression of maternal Xist (Xm-Xist) during preimplantation in mouse embryos is essential for establishing imprinted X chromosome inactivation. Nuclear transplantation (NT) studies using nuclei derived from non-growing (ng) and full-grown (fg) oocytes have indicated that maternal-specific repressive modifications are imposed on Xm-Xist during oogenesis, as well as on autosomal imprinted genes. Recent studies have revealed that histone H3 lysine 9 trimethylation (H3K9me3) enrichments on Xm-Xist promoter regions are involved in silencing at the preimplantation stages. However, whether H3K9me3 is imposed on Xm-Xist during oogenesis is not known. Here, we dissected the chromatin states in ng and fg oocytes and early preimplantation stage embryos. Chromatin immunoprecipitation experiments against H3K9me3 revealed that there was no significant enrichment within the Xm-Xist region during oogenesis. However, NT embryos with ng nuclei (ngNT) showed extensive Xm-Xist derepression and H3K9me3 hypomethylation of the promoter region at the 4-cell stage, which corresponds to the onset of paternal Xist expression. We also found that the chromatin state at the Xist genomic locus became markedly condensed as oocyte growth proceeded. Although the condensed Xm-Xist genomic locus relaxed during early preimplantation phases, the extent of the relaxation across Xm-Xist loci derived from normally developed oocytes was significantly smaller than those of paternal-Xist and ngNT-Xist genomic loci. Furthermore, Xm-Xist from 2-cell metaphase nuclei became derepressed following NT. We propose that chromatin condensation is associated with imprinted Xist repression and that skipping of the condensation step by NT leads to Xist activation during the early preimplantation phase. Summary: The analysis of chromatin state and H3K9me3 levels in mouse oocytes and early embryos provides insights into the dynamics of Xist repression and activation during early development and reprogramming.
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Affiliation(s)
- Atsushi Fukuda
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Atsushi Mitani
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - Toshiyuki Miyashita
- Department of Molecular Genetics, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan Department of Stem Cell Research, Fukushima Medical University, 1 Hikarigaoka, Fukushima City, Fukushima 960-1295, Japan
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23
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Mizutani E, Oikawa M, Kassai H, Inoue K, Shiura H, Hirasawa R, Kamimura S, Matoba S, Ogonuki N, Nagatomo H, Abe K, Wakayama T, Aiba A, Ogura A. Generation of Cloned Mice from Adult Neurons by Direct Nuclear Transfer1. Biol Reprod 2015; 92:81. [DOI: 10.1095/biolreprod.114.123455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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24
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Chen YH, Yu J. Epigenetic disruptions of histone signatures for the trophectoderm and inner cell mass in mouse parthenogenetic embryos. Stem Cells Dev 2014; 24:550-64. [PMID: 25315067 DOI: 10.1089/scd.2014.0310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epigenetic asymmetry has been shown to be associated with the first lineage allocation event in preimplantation development, that is, the formation of the trophectoderm (TE) and inner cell mass (ICM) lineages in the blastocyst. Since parthenogenesis causes aberrant segregation between the TE and ICM lineages, we examined several development-associated histone modifications in parthenotes, including those involved in (i) transcriptional activation [acetylated histone H3 lysine 9 (H3K9Ac) and lysine 14 (H3K14Ac), trimethylated histone H3 lysine 4 (H3K4Me3), and dimethylated histone H3 arginine 26 (H3R26Me2)] and (ii) transcriptional repression [trimethylated histone H3 lysine 9 (H3K9Me3) and lysine 27 (H3K27Me3), and mono-ubiquitinated histone H2A lysine 119 (H2AK119u1)]. Here, we report that in parthenotes, H3R26Me2 expression decreased from the morula stage, while expression patterns and levels of H3K9Ac, H3K27Me3, and H2AK119u1 were unchanged until the blastocyst stage; whereas H3K14Ac, H3K4Me3, and H3K9Me3 showed normal patterns and levels of expressions. Relative to the decrease of H3K9Ac in the ICM and increase in the TE of parthenotes, we detected reduced expression of TAT-interactive protein 60 acetyltransferase and histone deacetylase 1 deacetylase in the ICM and TE of parthenotes, respectively. Relative to the decrease of H3R26Me2, we also observed decreased expression of coactivator-associated arginine methyltransferase 1 methyltransferase and increased expression of the Wnt effector transcription factor 7L2 and miR-181c microRNA in parthenotes. Furthermore, relative to the decrease in H3K27Me3 and H2AK119u1, we found increased phosphorylation of Akt1 and enhancer of zeste homolog 2 in parthenogenetic TE. Therefore, our findings that histone signatures are impaired in parthenotes provide a mechanistic explanation for aberrant lineage segregation and TE defects.
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Affiliation(s)
- Yi-Hui Chen
- 1 Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center , Taipei, Taiwan
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25
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The role of maternal-specific H3K9me3 modification in establishing imprinted X-chromosome inactivation and embryogenesis in mice. Nat Commun 2014; 5:5464. [PMID: 25394724 PMCID: PMC4243243 DOI: 10.1038/ncomms6464] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 10/02/2014] [Indexed: 12/22/2022] Open
Abstract
Maintaining a single active X-chromosome by repressing Xist is crucial for embryonic development in mice. Although the Xist activator RNF12/RLIM is present as a maternal factor, maternal Xist (Xm-Xist) is repressed during preimplantation phases to establish imprinted X-chromosome inactivation (XCI). Here we show, using a highly reproducible chromatin immunoprecipitation method that facilitates chromatin analysis of preimplantation embryos, that H3K9me3 is enriched at the Xist promoter region, preventing Xm-Xist activation by RNF12. The high levels of H3K9me3 at the Xist promoter region are lost in embryonic stem (ES) cells, and ES-cloned embryos show RNF12-dependent Xist expression. Moreover, lack of Xm-XCI in the trophectoderm, rather than loss of paternally expressed imprinted genes, is the primary cause of embryonic lethality in 70–80% of parthenogenotes immediately after implantation. This study reveals that H3K9me3 is involved in the imprinting that silences Xm-Xist. Our findings highlight the role of maternal-specific H3K9me3 modification in embryo development. During mouse preimplantation phases, a repressive imprint is imposed on the maternal allele of Xist, which encodes a large non-coding RNA required for X-chromosome inactivation. Here the authors show that trimethylation of histone H3 at lysine 9 on Xist promoter chromatin is responsible for the maternally determined Xist repression.
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26
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Merzouk S, Deuve JL, Dubois A, Navarro P, Avner P, Morey C. Lineage-specific regulation of imprinted X inactivation in extraembryonic endoderm stem cells. Epigenetics Chromatin 2014; 7:11. [PMID: 25053977 PMCID: PMC4105886 DOI: 10.1186/1756-8935-7-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/02/2014] [Indexed: 01/09/2023] Open
Abstract
Background Silencing of the paternal X chromosome (Xp), a phenomenon known as imprinted X-chromosome inactivation (I-XCI), characterises, amongst mouse extraembryonic lineages, the primitive endoderm and the extraembryonic endoderm (XEN) stem cells derived from it. Results Using a combination of chromatin immunoprecipitation characterisation of histone modifications and single-cell expression studies, we show that whilst the Xp in XEN cells, like the inactive X chromosome in other cell types, globally accumulates the repressive histone mark H3K27me3, a large number of Xp genes locally lack H3K27me3 and escape from I-XCI. In most cases this escape is specific to the XEN cell lineage. Importantly, the degree of escape and the genes concerned remain unchanged upon XEN conversion into visceral endoderm, suggesting stringent control of I-XCI in XEN derivatives. Surprisingly, chemical inhibition of EZH2, a member of the Polycomb repressive complex 2 (PRC2), and subsequent loss of H3K27me3 on the Xp, do not drastically perturb the pattern of silencing of Xp genes in XEN cells. Conclusions The observations that we report here suggest that the maintenance of gene expression profiles of the inactive Xp in XEN cells involves a tissue-specific mechanism that acts partly independently of PRC2 catalytic activity.
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Affiliation(s)
- Sarra Merzouk
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Pasteur Cell, Pierre and Marie Curie University (UPMC), 25 rue du Dr Roux, 75015 Paris, France
| | - Jane Lynda Deuve
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Present address: Pierre and Marie Curie University (UPMC), UMR7622, Institute of Biology of Paris-Seine (IBPS), 75005 Paris, France
| | - Agnès Dubois
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Present address: Epigenetics of Stem Cells Laboratory', Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Pablo Navarro
- Present address: Epigenetics of Stem Cells Laboratory', Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
| | - Philip Avner
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France ; Present address: Dynamics of Epigenetic Regulation, EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Céline Morey
- Mouse Molecular Genetics Laboratory, Pasteur Institute, 25 rue du Dr Roux, 75015 Paris, France
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27
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TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data. BIOMED RESEARCH INTERNATIONAL 2014; 2014:317642. [PMID: 24729968 PMCID: PMC3960524 DOI: 10.1155/2014/317642] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/14/2014] [Accepted: 01/27/2014] [Indexed: 11/17/2022]
Abstract
High-throughput genomic technologies like lncRNA microarray and RNA-Seq often generate a set of lncRNAs of interest, yet little is known about the transcriptional regulation of the set of lncRNA genes. Here, based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and annotated human lncRNAs from GENCODE, we developed a web-based interface titled “TF2lncRNA,” where TF peaks from each ChIP-Seq experiment are crossed with the genomic coordinates of a set of input lncRNAs, to identify which TFs present a statistically significant number of binding sites (peaks) within the regulatory region of the input lncRNA genes. The input can be a set of coexpressed lncRNA genes or any other cluster of lncRNA genes. Users can thus infer which TFs are likely to be common transcription regulators of the set of lncRNAs. In addition, users can retrieve all lncRNAs potentially regulated by a specific TF in a specific cell line of interest or retrieve all TFs that have one or more binding sites in the regulatory region of a given lncRNA in the specific cell line. TF2LncRNA is an efficient and easy-to-use web-based tool.
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28
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Zhang J, Zhang P, Wang L, Piao HL, Ma L. Long non-coding RNA HOTAIR in carcinogenesis and metastasis. Acta Biochim Biophys Sin (Shanghai) 2014; 46:1-5. [PMID: 24165275 DOI: 10.1093/abbs/gmt117] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have gained massive attention in recent years as a potentially new and crucial layer of gene regulation. LncRNAs are prevalently transcribed in the genome, but their roles in gene regulation and disease development are largely unknown. HOX antisense intergenic RNA (HOTAIR), a lncRNA located in the HOXC locus, has been shown to repress HOXD gene expression and promote breast cancer metastasis. Mechanistically, HOTAIR interacts with and recruits polycomb repressive complex 2 (PRC2) and regulates chromosome occupancy by EZH2 (a subunit of PRC2), which leads to histone H3 lysine 27 trimethylation of the HOXD locus. Moreover, HOTAIR is pervasively overexpressed in most human cancers compared with noncancerous adjacent tissues. This review summarizes the studies on the HOTAIR lncRNA over the past 6 years.
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Affiliation(s)
- Jinsong Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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29
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Leeb M, Wutz A. Haploid genomes illustrate epigenetic constraints and gene dosage effects in mammals. Epigenetics Chromatin 2013; 6:41. [PMID: 24305551 PMCID: PMC4175507 DOI: 10.1186/1756-8935-6-41] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022] Open
Abstract
Sequencing projects have revealed the information of many animal genomes and thereby enabled the exploration of genome evolution. Insights into how genomes have been repeatedly modified provide a basis for understanding evolutionary innovation and the ever increasing complexity of animal developmental programs. Animal genomes are diploid in most cases, suggesting that redundant information in two copies of the genome increases evolutionary fitness. Genomes are well adapted to a diploid state. Changes of ploidy can be accommodated early in development but they rarely permit successful development into adulthood. In mammals, epigenetic mechanisms including imprinting and X inactivation restrict haploid development. These restrictions are relaxed in an early phase of development suggesting that dosage regulation appears less critical. Here we review the recent literature on haploid genomes and dosage effects and try to embed recent findings in an evolutionary perspective.
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Affiliation(s)
- Martin Leeb
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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30
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Miri K, Latham K, Panning B, Zhong Z, Andersen A, Varmuza S. The imprinted polycomb group gene Sfmbt2 is required for trophoblast maintenance and placenta development. Development 2013; 140:4480-9. [PMID: 24154523 PMCID: PMC3817938 DOI: 10.1242/dev.096511] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/19/2013] [Indexed: 12/27/2022]
Abstract
Imprinted genes play important roles in placenta development and function. Parthenogenetic embryos, deficient in paternally expressed imprinted genes, lack extra-embryonic tissues of the trophoblast lineage. Parthenogenetic trophoblast stem cells (TSCs) are extremely difficult to derive, suggesting that an imprinted gene(s) is necessary for TSC establishment or maintenance. In a candidate study, we were able to narrow the list to one known paternally expressed gene, Sfmbt2. We show that mouse embryos inheriting a paternal Sfmbt2 gene trap null allele have severely reduced placentae and die before E12.5 due to reduction of all trophoblast cell types. We infected early embryos with lentivirus vectors expressing anti-Sfmbt2 shRNAs and found that TSC derivation was significantly reduced. Together, these observations support the hypothesis that loss of SFMBT2 results in defects in maintenance of trophoblast cell types necessary for development of the extra-embryonic tissues, the placenta in particular.
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Affiliation(s)
- Kamelia Miri
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Sreet, Toronto, Ontario M5S 3G5, Canada
| | - Keith Latham
- The Fels Institute of Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, PA 19140, USA
| | - Barbara Panning
- Biochemistry and Biophysics Department, University of California at San Francisco, Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517, USA
| | - Zhisheng Zhong
- The Fels Institute of Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, PA 19140, USA
| | - Angela Andersen
- Biochemistry and Biophysics Department, University of California at San Francisco, Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517, USA
| | - Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Sreet, Toronto, Ontario M5S 3G5, Canada
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31
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Kohda T, Ishino F. Embryo manipulation via assisted reproductive technology and epigenetic asymmetry in mammalian early development. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120353. [PMID: 23166403 PMCID: PMC3539368 DOI: 10.1098/rstb.2012.0353] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The early stage of mammalian development from fertilization to implantation is a period when global and differential changes in the epigenetic landscape occur in paternally and maternally derived genomes, respectively. The sperm and egg DNA methylation profiles are very different from each other, and just after fertilization, only the paternally derived genome is subjected to genome-wide hydroxylation of 5-methylcytosine, resulting in an epigenetic asymmetry in parentally derived genomes. Although most of these differences are not present by the blastocyst stage, presumably due to passive demethylation, the maintenance of genomic imprinting memory and X chromosome inactivation in this stage are of critical importance for post-implantation development. Zygotic gene activation from paternally or maternally derived genomes also starts around the two-cell stage, presumably in a different manner in each of them. It is during this period that embryo manipulation, including assisted reproductive technology, is normally performed; so it is critically important to determine whether embryo manipulation procedures increase developmental risks by disturbing subsequent gene expression during the embryonic and/or neonatal development stages. In this review, we discuss the effects of various embryo manipulation procedures applied at the fertilization stage in relation to the epigenetic asymmetry in pre-implantation development. In particular, we focus on the effects of intracytoplasmic sperm injection that can result in long-lasting transcriptome disturbances, at least in mice.
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Affiliation(s)
- Takashi Kohda
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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32
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Dupont C, Gribnau J. Different flavors of X-chromosome inactivation in mammals. Curr Opin Cell Biol 2013; 25:314-21. [PMID: 23578369 DOI: 10.1016/j.ceb.2013.03.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/27/2013] [Accepted: 03/13/2013] [Indexed: 12/22/2022]
Abstract
Dosage compensation of X-linked gene products between the sexes in therians has culminated in the inactivation of one of the two X chromosomes in female cells. Over the years, the mouse has been the preferred animal model to study this X-chromosome inactivation (XCI) process in placental mammals (eutherians). Similar to the imprinted inactivation of the paternally inherited X chromosome (Xp) in marsupials (methatherians), the Xp is inactivated during early mouse development. In this eutherian model, cell derivatives of the primitive endoderm (PE) and trophectoderm (TE) will continue to display this imprinted form of XCI. Cells developing from the mouse epiblast will reactivate the Xp, and subsequently initiate XCI of either the Xp or the maternally inherited Xm, in a random manner. Examination of XCI in other eutherians and in metatherians, however, indicates clear differences in the form and timing of XCI. This review highlights and discusses imprinted and random XCI from such a comparative viewpoint.
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Affiliation(s)
- Cathérine Dupont
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3015GE Rotterdam, The Netherlands
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33
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Abstract
A plethora of noncoding (nc) RNAs has been revealed through the application of high-throughput analysis of the transcriptome, and this has led to an intensive search for possible biological functions attributable to these transcripts. A major category of functional ncRNAs that has emerged is for those that are implicated in coordinate gene silencing, either in cis or in trans. The archetype for this class is the well-studied long ncRNA Xist which functions in cis to bring about transcriptional silencing of an entire X chromosome in female mammals. An important step in X chromosome inactivation is the recruitment of the Polycomb repressive complex PRC2 that mediates histone H3 lysine 27 methylation, a hallmark of the inactive X chromosome, and recent studies have suggested that this occurs as a consequence of PRC2 interacting directly with Xist RNA. Accordingly, other ncRNAs have been linked to PRC2 targeting either in cis or in trans, and here also the mechanism has been proposed to involve direct interaction between PRC2 proteins and the different ncRNAs. In this review, I discuss the evidence for and against this hypothesis, in the process highlighting alternative models and discussing experiments that, in the future, will help to resolve existing discrepancies.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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34
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Yan B, Wang Z. Long noncoding RNA: its physiological and pathological roles. DNA Cell Biol 2012; 31 Suppl 1:S34-41. [PMID: 22612272 DOI: 10.1089/dna.2011.1544] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length. They comprise a diverse class of transcripts that structurally resemble mRNAs, but do not encode proteins. The characterization of lncRNAs and their acceptance as crucial regulators of numerous developmental and biological pathways have suggested that the lncRNA study has gradually become one of the hot topics in the field of RNA biology. In this article, we will highlight recent progress regarding lncRNAs studies, including their classification, biological functional characterization, and their potential roles in disease development.
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Affiliation(s)
- Biao Yan
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China.
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35
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Maccani MA, Knopik VS. Cigarette smoke exposure-associated alterations to non-coding RNA. Front Genet 2012; 3:53. [PMID: 22509180 PMCID: PMC3321413 DOI: 10.3389/fgene.2012.00053] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/20/2012] [Indexed: 11/19/2022] Open
Abstract
Environmental exposures vary by timing, severity, and frequency and may have a number of deleterious effects throughout the life course. The period of in utero development, for example, is one of the most crucial stages of development during which adverse environmental exposures can both alter the growth and development of the fetus as well as lead to aberrant fetal programming, increasing disease risk. During fetal development and beyond, the plethora of exposures, including nutrients, drugs, stress, and trauma, influence health, development, and survival. Recent research in environmental epigenetics has investigated the roles of environmental exposures in influencing epigenetic modes of gene regulation during pregnancy and at various stages of life. Many relatively common environmental exposures, such as cigarette smoking, alcohol consumption, and drug use, may have consequences for the expression and function of non-coding RNA (ncRNA), important post-transcriptional regulators of gene expression. A number of ncRNA have been discovered, including microRNA (miRNA), Piwi-interacting RNA (piRNA), and long non-coding RNA (long ncRNA). The best-characterized species of ncRNA are miRNA, the mature forms of which are ∼22 nucleotides in length and capable of post-transcriptionally regulating target mRNA utilizing mechanisms based largely on the degree of complementarity between miRNA and target mRNA. Because miRNA can still negatively regulate gene expression when imperfectly base-paired with a target mRNA, a single miRNA can have a large number of potential mRNA targets and can regulate many different biological processes critical for health and development. The following review analyzes the current literature detailing links between cigarette smoke exposure and aberrant expression and function of ncRNA, assesses how such alterations may have consequences throughout the life course, and proposes future directions for this intriguing field of research.
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Affiliation(s)
- Matthew A Maccani
- Division of Behavioral Genetics, Rhode Island Hospital Providence, RI, USA
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36
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Brockdorff N. Chromosome silencing mechanisms in X-chromosome inactivation: unknown unknowns. Development 2012; 138:5057-65. [PMID: 22069184 DOI: 10.1242/dev.065276] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fifty years ago, Mary Lyon hypothesised that one of the two X chromosomes in female mammalian cells is inactivated at random during early embryogenesis and that the inactive X is then stably maintained through all subsequent cell divisions. Although Lyon's hypothesis is now widely regarded as fact, we should not forget that her conceptual leap met with considerable resistance from the scientific establishment at the time - a common response to new ideas. Taking this point as a theme, I discuss our current understanding of the molecular mechanism of chromosome silencing in X-chromosome inactivation and focus on topics where new findings are challenging the prevailing view.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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37
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RNAi-mediated knockdown of Xist can rescue the impaired postimplantation development of cloned mouse embryos. Proc Natl Acad Sci U S A 2011; 108:20621-6. [PMID: 22065773 DOI: 10.1073/pnas.1112664108] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cloning mammals by somatic cell nuclear transfer (SCNT) is highly inefficient. Most SCNT-generated embryos die after implantation because of unidentified, complex epigenetic errors in the process of postimplantation embryonic development. Here we identify the most upstream level of dysfunction leading to impaired development of clones by using RNAi against Xist, a gene responsible for X chromosome inactivation (XCI). A prior injection of Xist-specific siRNA into reconstructed oocytes efficiently corrected SCNT-specific aberrant Xist expression at the morula stage, but failed to do so thereafter at the blastocyst stage. However, we found that shortly after implantation, this aberrant XCI status in cloned embryos had been corrected autonomously in both embryonic and extraembryonic tissues, probably through a newly established XCI control for postimplantation embryos. Embryo transfer experiments revealed that siRNA-treated embryos showed 10 times higher survival than controls as early as embryonic day 5.5 and this high survival persisted until term, resulting in a remarkable improvement in cloning efficiency (12% vs. 1% in controls). Importantly, unlike control clones, these Xist-siRNA clones at birth showed only a limited dysregulation of their gene expression, indicating that correction of Xist expression in preimplantation embryos had a long-term effect on their postnatal normality. Thus, contrary to the general assumption, our results suggest that the fate of cloned embryos is determined almost exclusively before implantation by their XCI status. Furthermore, our strategy provides a promising breakthrough for mammalian SCNT cloning, because RNAi treatment of oocytes is readily applicable to most mammal species.
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38
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Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 2011; 12:429-42. [PMID: 21587299 DOI: 10.1038/nrg2987] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
X-chromosome inactivation (XCI) ensures dosage compensation in mammals and is a paradigm for allele-specific gene expression on a chromosome-wide scale. Important insights have been made into the developmental dynamics of this process. Recent studies have identified several cis- and trans-acting factors that regulate the initiation of XCI via the X-inactivation centre. Such studies have shed light on the relationship between XCI and pluripotency. They have also revealed the existence of dosage-dependent activators that trigger XCI when more than one X chromosome is present, as well as possible mechanisms underlying the monoallelic regulation of this process. The recent discovery of the plasticity of the inactive state during early development, or during cloning, and induced pluripotency have also contributed to the X chromosome becoming a gold standard in reprogramming studies.
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39
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XCI in preimplantation mouse and human embryos: first there is remodelling…. Hum Genet 2011; 130:203-15. [PMID: 21647603 PMCID: PMC3132436 DOI: 10.1007/s00439-011-1014-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/19/2011] [Indexed: 12/21/2022]
Abstract
Female eutherians silence one of their X chromosomes to accomplish an equal dose of X-linked gene expression compared with males. The mouse is the most widely used animal model in XCI research and has proven to be of great significance for understanding the complex mechanism of X-linked dosage compensation. Although the basic principles of XCI are similar in mouse and humans, differences exist in the timing of XCI initiation, the genetic elements involved in XCI regulation and the form of XCI in specific tissues. Therefore, the mouse has its limitations as a model to understand early human XCI and analysis of human tissues is required. In this review, we describe these differences with respect to initiation of XCI in human and mouse preimplantation embryos, the extra-embryonic tissues and the in vitro model of the epiblast: the embryonic stem cells.
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40
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Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, Zhao G, Luo H, Bu D, Zhao H, Skogerbø G, Wu Z, Zhao Y. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res 2011; 39:3864-78. [PMID: 21247874 PMCID: PMC3089475 DOI: 10.1093/nar/gkq1348] [Citation(s) in RCA: 440] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Although accumulating evidence has provided insight into the various functions of long-non-coding RNAs (lncRNAs), the exact functions of the majority of such transcripts are still unknown. Here, we report the first computational annotation of lncRNA functions based on public microarray expression profiles. A coding–non-coding gene co-expression (CNC) network was constructed from re-annotated Affymetrix Mouse Genome Array data. Probable functions for altogether 340 lncRNAs were predicted based on topological or other network characteristics, such as module sharing, association with network hubs and combinations of co-expression and genomic adjacency. The functions annotated to the lncRNAs mainly involve organ or tissue development (e.g. neuron, eye and muscle development), cellular transport (e.g. neuronal transport and sodium ion, acid or lipid transport) or metabolic processes (e.g. involving macromolecules, phosphocreatine and tyrosine).
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Affiliation(s)
- Qi Liao
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China
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41
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Rivera RM. Epigenetic aspects of fertilization and preimplantation development in mammals: lessons from the mouse. Syst Biol Reprod Med 2011; 56:388-404. [PMID: 20849224 DOI: 10.3109/19396368.2010.482726] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
During gametogenesis, the parental genomes are separated and are epigenetically marked by modifications that will direct the expression profile of genes necessary for meiosis as well as for the formation of the oocyte and sperm cell. Immediately after sperm-egg fusion, the parental haploid genomes show great epigenetic asymmetry with differences in the levels of DNA methylation and histone tail modifications. The epigenetic program acquired during oogenesis and spermatogenesis must be reset for the zygote to successfully proceed through preimplantation development and this occurs as the two genomes approach each other in preparation for karyogamy. During preimplantation development, the embryo is vested with the responsibility of maintaining the primary imprints. In addition, female embryos must silence one of the X-chromosomes in order to transcribe equal levels of X-linked genes as their male counterparts. This review is intended as a survey of the epigenetic modifications and mechanisms present in zygotes and preimplantation mouse embryos, namely DNA methylation, histone modifications, dosage compensation, genomic imprinting, and regulation by non-coding RNAs.
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Liu N, Enkemann SA, Liang P, Hersmus R, Zanazzi C, Huang J, Wu C, Chen Z, Looijenga LHJ, Keefe DL, Liu L. Genome-wide gene expression profiling reveals aberrant MAPK and Wnt signaling pathways associated with early parthenogenesis. J Mol Cell Biol 2010; 2:333-44. [PMID: 20926514 DOI: 10.1093/jmcb/mjq029] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mammalian parthenogenesis could not survive but aborted during mid-gestation, presumably because of lack of paternal gene expression. To understand the molecular mechanisms underlying the failure of parthenogenesis at early stages of development, we performed global gene expression profiling and functional analysis of parthenogenetic blastocysts in comparison with those of blastocysts from normally fertilized embryos. Parthenogenetic blastocysts exhibited changes in the expression of 749 genes, of which 214 had lower expression and 535 showed higher expressions than fertilized embryos using a minimal 1.8-fold change as a cutoff. Genes important for placenta development were decreased in their expression in parthenote blastocysts. Some maternally expressed genes were up-regulated and paternal-related genes were down-regulated. Moreover, aberrantly increased Wnt signaling and reduced mitogen-activated protein kinase (MAPK) signaling were associated with early parthenogenesis. The protein level of extracellular signal-regulated kinase 2 (ERK2) was low in parthenogenetic blastocysts compared with that of fertilized blastocysts 120 h after fertilization. 6-Bromoindirubin-3'-oxime, a specific glycogen synthase kinase-3 (GSK-3) inhibitor, significantly decreased embryo hatching. The expression of several imprinted genes was altered in parthenote blastocysts. Gene expression also linked reduced expression of Xist to activation of X chromosome. Our findings suggest that failed X inactivation, aberrant imprinting, decreased ERK/MAPK signaling and possibly elevated Wnt signaling, and reduced expression of genes for placental development collectively may contribute to abnormal placenta formation and failed fetal development in parthenogenetic embryos.
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Affiliation(s)
- Na Liu
- College of Life Sciences, Nankai University, Tianjin 300071, China
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43
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Marshall H, Bhaumik M, Aviv H, Moore D, Yao M, Dutta J, Rahim H, Gounder M, Ganesan S, Saleem A, Rubin E. Deficiency of the dual ubiquitin/SUMO ligase Topors results in genetic instability and an increased rate of malignancy in mice. BMC Mol Biol 2010; 11:31. [PMID: 20429939 PMCID: PMC2873312 DOI: 10.1186/1471-2199-11-31] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 04/29/2010] [Indexed: 01/07/2023] Open
Abstract
Background Topors is a nuclear protein that co-localizes with promyelocytic leukemia bodies and has both ubiquitin and SUMO E3 ligase activity. Expression studies implicated Topors as a tumor suppressor in various malignancies. To gain insight into the function of Topors, we generated a Topors-deficient mouse strain. Results Mice homozygous for a mutant Topors allele exhibited a high rate of perinatal mortality and decreased lifespan. In addition, heterozygotes were found to have an increased incidence of malignancy, involving a variety of tissues. Consistent with this finding, primary embryonic fibroblasts lacking Topors exhibited an increased rate of malignant transformation, associated with aneuploidy and defective chromosomal segregation. While loss of Topors did not alter sensitivity to DNA-damaging or microtubule-targeting agents, cells lacking Topors exhibited altered pericentric heterochromatin, manifested by mislocalization of HP1α and an increase in transcription from pericentric major satellite DNA. Topors-deficient cells exhibited a transcriptional profile similar to that of cells treated with histone deacetylase inhibitors, and were resistant to the anti-proliferative effects of the histone deacetylase inhibitor trichostatin A. Conclusion These results indicate a unique role for Topors in the maintenance of genomic stability and pericentric heterochromatin, as well as in cellular sensitivity to histone deacetylase inhibitors.
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Affiliation(s)
- Henderson Marshall
- Department of Pharmacology, Cancer Institute of New Jersey, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08901, USA
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Epigenetic regulatory mechanisms during preimplantation development. ACTA ACUST UNITED AC 2009; 87:297-313. [DOI: 10.1002/bdrc.20165] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Kalantry S, Purushothaman S, Bowen RB, Starmer J, Magnuson T. Evidence of Xist RNA-independent initiation of mouse imprinted X-chromosome inactivation. Nature 2009; 460:647-51. [PMID: 19571810 PMCID: PMC2754729 DOI: 10.1038/nature08161] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 05/19/2009] [Indexed: 11/09/2022]
Abstract
XX female mammals undergo transcriptional silencing of most genes on one of their two X-chromosomes to equalize X-linked gene dosage with XY males in a process referred to as X-chromosome inactivation (XCI). XCI is a paradigm of epigenetic regulation1. Once enacted in individual cells of the early female embryo, XCI is stably transmitted such that most descendant cells maintain silencing of that X-chromosome2. In eutherian mammals, XCI is thought to be triggered by the expression of the non-coding Xist RNA from the future inactive-X (Xi)3,4,5; Xist RNA in turn is proposed to recruit protein complexes that bring about heterochromatinization of the Xi6,7. Here we test whether imprinted XCI, which results in preferential inactivation of the paternal X-chromosome (Xp), occurs in mouse embryos inheriting an Xp lacking Xist. We find that silencing of Xp-linked genes can initiate in the absence of paternal Xist; Xist is, however, required to stabilize silencing of the Xp. Xp-linked gene silencing associated with mouse imprinted XCI, therefore, can initiate in the embryo independently of Xist RNA.
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Affiliation(s)
- Sundeep Kalantry
- Department of Genetics, and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
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46
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van den Berg IM, Laven JS, Stevens M, Jonkers I, Galjaard RJ, Gribnau J, Hikke van Doorninck J. X chromosome inactivation is initiated in human preimplantation embryos. Am J Hum Genet 2009; 84:771-9. [PMID: 19481196 DOI: 10.1016/j.ajhg.2009.05.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 04/27/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022] Open
Abstract
X chromosome inactivation (XCI) is the mammalian mechanism that compensates for the difference in gene dosage between XX females and XY males. Genetic and epigenetic regulatory mechanisms induce transcriptional silencing of one X chromosome in female cells. In mouse embryos, XCI is initiated at the preimplantation stage following early whole-genome activation. It is widely thought that human embryos do not employ XCI prior to implantation. Here, we show that female preimplantation embryos have a progressive accumulation of XIST RNA on one of the two X chromosomes, starting around the 8-cell stage. XIST RNA accumulates at the morula and blastocyst stages and is associated with transcriptional silencing of the XIST-coated chromosomal region. These findings indicate that XCI is initiated in female human preimplantation-stage embryos and suggest that preimplantation dosage compensation is evolutionarily conserved in placental mammals.
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47
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Lee TL, Pang ALY, Rennert OM, Chan WY. Genomic landscape of developing male germ cells. BIRTH DEFECTS RESEARCH. PART C, EMBRYO TODAY : REVIEWS 2009; 87:43-63. [PMID: 19306351 PMCID: PMC2939912 DOI: 10.1002/bdrc.20147] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a highly orchestrated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific gene products whose expressions are strictly regulated. In the past decade the advent of high-throughput gene expression analytical techniques has made functional genomic studies of this process, particularly in model animals such as mice and rats, feasible and practical. These studies have just begun to reveal the complexity of the genomic landscape of the developing male germ cells. Over 50% of the mouse and rat genome are expressed during testicular development. Among transcripts present in germ cells, 40% - 60% are uncharacterized. A number of genes, and consequently their associated biological pathways, are differentially expressed at different stages of spermatogenesis. Developing male germ cells present a rich repertoire of genetic processes. Tissue-specific as well as spermatogenesis stage-specific alternative splicing of genes exemplifies the complexity of genome expression. In addition to this layer of control, discoveries of abundant presence of antisense transcripts, expressed psuedogenes, non-coding RNAs (ncRNA) including long ncRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and retrogenes all point to the presence of multiple layers of expression and functional regulation in male germ cells. It is anticipated that application of systems biology approaches will further our understanding of the regulatory mechanism of spermatogenesis.
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Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alan Lap-Yin Pang
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Owen M. Rennert
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Wai-Yee Chan
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Department of Pediatrics, Georgetown University College of Medicine, Washington, DC
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Abstract
The development of genetic sex determination and cytologically distinct sex chromosomes leads to the potential problem of gene dosage imbalances between autosomes and sex chromosomes and also between males and females. To circumvent these imbalances, mammals have developed an elaborate system of dosage compensation that includes both upregulation and repression of the X chromosome. Recent advances have provided insights into the evolutionary history of how both the imprinted and random forms of X chromosome inactivation have come about. Furthermore, our understanding of the epigenetic switch at the X-inactivation center and the molecular aspects of chromosome-wide silencing has greatly improved recently. Here, we review various facets of the ever-expanding field of mammalian dosage compensation and discuss its evolutionary, developmental, and mechanistic components.
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Affiliation(s)
- Bernhard Payer
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
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49
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Vassena R, Dee Schramm R, Latham KE. Species-dependent expression patterns of DNA methyltransferase genes in mammalian oocytes and preimplantation embryos. Mol Reprod Dev 2005; 72:430-6. [PMID: 16155959 DOI: 10.1002/mrd.20375] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA methyltransferases (DNMTs) comprise a family of proteins involved in the establishment and maintenance of DNA methylation patterns in the mammalian genome. DNA methylation involves the transfer of the methyl group of the coenzyme S-adenosyl-L-methionine to the 5 position of cytosine residues within CpG dinucleotides. DNA methylation is implicated in the control of imprinted genes expression, X chromosome silencing, development of certain types of cancer, and embryonic development. DNA methylation is also believed to protect the genome from parasitic elements such as transposons, retrotransposons, and viruses. The aim of this study was to analyze the expression patterns of DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L genes in rhesus macaque (Macaca mulatta) oocytes and preimplantation stage embryos from fertilization to the hatched blastocyst stage, and to compare these results with the expression profiles in the mouse and other mammalian species. We describe species-dependent differences as well as similarities in expression patterns of DNMT genes among mammals.
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Affiliation(s)
- Rita Vassena
- The Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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50
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Huynh KD, Lee JT. A continuity of X-chromosome silence from gamete to zygote. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2005; 69:103-12. [PMID: 16117638 DOI: 10.1101/sqb.2004.69.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- K D Huynh
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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