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Zhang Z, Li J, Yan B, Tu H, Huang C, Costa M. Loss of MEG3 and upregulation of miR-145 play an important role in the invasion and migration of Cr(VI)-transformed cells. Heliyon 2022; 8:e10086. [PMID: 36046536 PMCID: PMC9421329 DOI: 10.1016/j.heliyon.2022.e10086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/25/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022] Open
Abstract
Chronic exposure of human bronchial epithelial BEAS-2B cells to hexavalent chromium (Cr(VI)) causes malignant cell transformation. These transformed cells exhibit increases in migration and invasion. Neuronal precursor of developmentally downregulated protein 9 (NEDD9) is upregulated in Cr(VI)-transformed cells compared to that of passage-matched normal BEAS-2B cells. Knockdown of NEDD9 by its shRNA reduced invasion and migration of Cr(VI)-transformed cells. Maternally expressed gene 3 (MEG3), a long noncoding RNA, was lost and microRNA 145 (miR-145) was upregulated in Cr(VI)-transformed cells. MEG3 was bound to miR-145 and this binding reduced its activity. Overexpression of MEG3 or inhibition of miR-145 decreased invasion and migration of Cr(VI)-transformed cells. Overexpression of MEG3 was able to decrease miR-145 level and NEDD9 protein level in Cr(VI)-transformed cells. Ectopic expression of MEG3 was also shown to reduce β-catenin activation. Inhibition of miR-145 in Cr(VI)-transformed cells decreased Slug, an important transcription factor that regulates epithelial-to-mesenchymal transition (EMT). Inhibition of miR-145 was found to increase MEG3 in Cr(VI)-transformed cells. Further studies showed that mutation of MEG3 at the binding site for miR-145 did not change NEDD9 and failed to decrease invasion and migration. The present study demonstrated that loss of MEG3 and upregulation of miR-145 elevated NEDD9, resulting in activation of β-catenin and further upregulation of EMT, leading to increased invasion and migration of Cr(VI)-transformed cells.
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Affiliation(s)
- Zhuo Zhang
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25 Street, New York, New York, 10010, USA
| | - Jingxia Li
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25 Street, New York, New York, 10010, USA
| | - Bo Yan
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25 Street, New York, New York, 10010, USA
| | - Huailu Tu
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25 Street, New York, New York, 10010, USA
| | - Chao Huang
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25 Street, New York, New York, 10010, USA
| | - Max Costa
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25 Street, New York, New York, 10010, USA
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2
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Chen W, Ma C, Dong Y, Li S. The bovine Prader-Willi/Angelman imprinted domain has four Sno-lncRNAs types. Anim Genet 2022; 53:685-689. [PMID: 35844032 DOI: 10.1111/age.13244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/14/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
Sno-lncRNAs are intron-derived long noncoding RNAs (lncRNAs) with snoRNA ends. Sno-lncRNAs were first discovered in the human Prader-Willi (PWS)/Angelman (AS) imprinted domain. Here, we report the identification and characterization of four sno-lncRNA types (sno-lncRNA1, sno-lncRNA2, sno-lncRNA3, and sno-lncRNA4) in the bovine PWS/AS imprinted domain. Reverse transcription-PCR first determined the cDNA sequences of the four bovine sno-lncRNAs. A gene structure analysis showed that sno-lncRNA1 lacks introns, but sno-lncRNA2 and sno-lncRNA3 have one and two introns respectively. The three sno-lncRNAs have similar snoRNA ends. Moreover, the three have similar snoRNAs at their 5' and 3' ends. The head-to-tail orientation has six sno-lncRNA copies arranged between bovine SNORD116-6 and SNORD116-12. Moreover, only a copy of sno-lncRNA4 was located between SNORD116-3 and SNORD116-4. The expression of the four sno-lncRNAs was analyzed in the bovine heart, liver, spleen, lung, kidney, muscle, fat, brain, and placenta tissues. The monoallelic expression of sno-lncRNA4 was determined in bovine tissues. The results showed that the four sno-lncRNAs are widely expressed in the nine tissues, although sno-lncRNA3 and sno-lncRNA4 were undetected in the placenta. Moreover, an informative single nucleotide polymorphism (rs448706424) revealed the allelic expression of sno-lncRNA4 in exon 2 of sno-lncRNA4. The bovine genome had six copies of sno-lncRNA1, sno-lncRNA2, and sno-lncRNA3, but their allelic expression was not identified.
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Affiliation(s)
- Weina Chen
- College of Traditional Chinese Medicine, Hebei University, Baoding, China
| | - Chao Ma
- Baoding NO.2 Hospital, Baoding, China
| | - Yanqiu Dong
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, China
| | - Shijie Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, China
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3
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Ishihara T, Griffith OW, Suzuki S, Renfree MB. Presence of H3K4me3 on Paternally Expressed Genes of the Paternal Genome From Sperm to Implantation. Front Cell Dev Biol 2022; 10:838684. [PMID: 35359448 PMCID: PMC8960379 DOI: 10.3389/fcell.2022.838684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting, parent-of-origin-specific gene expression, is controlled by differential epigenetic status of the parental chromosomes. While DNA methylation and suppressive histone modifications established during gametogenesis suppress imprinted genes on the inactive allele, how and when the expressed allele gains its active status is not clear. In this study, we asked whether the active histone-3 lysine-4 trimethylation (H3K4me3) marks remain at paternally expressed genes (PEGs) in sperm and embryos before and after fertilization using published data. Here we show that mouse sperm had the active H3K4me3 at more than half of known PEGs, and these genes were present even after fertilization. Using reciprocal cross data, we identified 13 new transient PEGs during zygotic genome activation. Next, we confirmed that the 12 out of the 13 new transient PEGs were associated with the paternal H3K4me3 in sperm. Nine out of the 12 genes were associated with the paternal H3K4me3 in zygotes. Our results show that paternal H3K4me3 marks escape inactivation during the histone-to-protamine transition that occurs during sperm maturation and are present in embryos from early zygotic stages up to implantation.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Oliver W. Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Marilyn B. Renfree,
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4
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Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol 2021; 9:735527. [PMID: 34722514 PMCID: PMC8552494 DOI: 10.3389/fcell.2021.735527] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
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Affiliation(s)
| | | | - Andrea Cerase
- Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
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5
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Cunningham AM, Walker DM, Ramakrishnan A, Doyle MA, Bagot RC, Cates HM, Peña CJ, Issler O, Lardner CK, Browne C, Russo SJ, Shen L, Nestler EJ. Sperm Transcriptional State Associated with Paternal Transmission of Stress Phenotypes. J Neurosci 2021; 41:6202-6216. [PMID: 34099514 PMCID: PMC8287983 DOI: 10.1523/jneurosci.3192-20.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 01/03/2023] Open
Abstract
Paternal stress can induce long-lasting changes in germ cells potentially propagating heritable changes across generations. To date, no studies have investigated differences in transmission patterns between stress-resilient and stress-susceptible mice. We tested the hypothesis that transcriptional alterations in sperm during chronic social defeat stress (CSDS) transmit increased susceptibility to stress phenotypes to the next generation. We demonstrate differences in offspring from stressed fathers that depend on paternal category (resilient vs susceptible) and offspring sex. Importantly, artificial insemination (AI) reveals that sperm mediates some of the behavioral phenotypes seen in offspring. Using RNA-sequencing (RNA-seq), we report substantial and distinct changes in the transcriptomic profiles of sperm following CSDS in susceptible versus resilient fathers, with alterations in long noncoding RNAs (lncRNAs) predominating especially in susceptibility. Correlation analysis revealed that these alterations were accompanied by a loss of regulation of protein-coding genes by lncRNAs in sperm of susceptible males. We also identify several co-expression gene modules that are enriched in differentially expressed genes (DEGs) in sperm from either resilient or susceptible fathers. Taken together, these studies advance our understanding of intergenerational epigenetic transmission of behavioral experience.SIGNIFICANCE STATEMENT This manuscript contributes to the complex factors that influence the paternal transmission of stress phenotypes. By leveraging the segregation of males exposed to chronic social defeat stress (CSDS) into either resilient or susceptible categories we were able to identify the phenotypic differences in the paternal transmission of stress phenotypes across generations between the two lineages. Importantly, this work also alludes to the significance of both long noncoding RNAs (lncRNAs) and protein coding genes (PCGs) mediating the paternal transmission of stress. The knowledge gained from these data are of particular interest in understanding the risk for the development of psychiatric disorders such as anxiety and depression.
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Affiliation(s)
- Ashley M Cunningham
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Deena M Walker
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Aarthi Ramakrishnan
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Marie A Doyle
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Rosemary C Bagot
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Hannah M Cates
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Catherine J Peña
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Orna Issler
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Casey K Lardner
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Caleb Browne
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Scott J Russo
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Li Shen
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Eric J Nestler
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
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6
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Loss of Selenoprotein Iodothyronine Deiodinase 3 Expression Correlates with Progression of Complete Hydatidiform Mole to Gestational Trophoblastic Neoplasia. Reprod Sci 2021; 28:3200-3211. [PMID: 34129219 DOI: 10.1007/s43032-021-00634-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
To investigate if differences in imprinting at tropho-microRNA (miRNA) genomic clusters can distinguish between pre-gestational trophoblastic neoplasia cases (pre-GTN) and benign complete hydatidiform mole (CHM) cases at the time of initial uterine evacuation. miRNA sequencing was performed on frozen tissue from 39 CHM cases including 9 GTN cases. DIO3, DLK1, RTL1, and MEG 3 mRNA levels were assessed by qRT-PCR. Protein abundance was assessed by Western blot for DIO3, DLK1, and RTL1. qRT-PCR and Western blot were performed for selenoproteins and markers of oxidative stress. Immunohistochemistry (IHC) was performed for DIO3 on an independent validation set of clinical samples (n = 42) and compared to normal placenta controls across gestational ages. Relative expression of the 14q32 miRNA cluster was lower in pre-GTN cases. There were no differences in protein abundance of DLK1 or RTL1. Notably, there was lower protein expression of DIO3 in pre-GTN cases (5-fold, p < 0.03). There were no differences in mRNA levels of DIO3, DLK1, RTL1 or MEG 3. mRNA levels were higher in all CHM cases compared to normal placenta. IHC showed syncytiotrophoblast-specific DIO3 immunostaining in benign CHM cases and normal placenta, while pre-GTN cases of CHM lacked DIO3 expression. We describe two new biomarkers of pre-GTN CHM cases: decreased 14q32 miRNA expression and loss of DIO3 expression by IHC. Differences in imprinting between benign CHM and pre-GTN cases may provide insight into the fundamental development of CHM.
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7
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Essential Role of the 14q32 Encoded miRNAs in Endocrine Tumors. Genes (Basel) 2021; 12:genes12050698. [PMID: 34066712 PMCID: PMC8151414 DOI: 10.3390/genes12050698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The 14q32 cluster is among the largest polycistronic miRNA clusters. miRNAs encoded here have been implicated in tumorigenesis of multiple organs including endocrine glands. METHODS Critical review of miRNA studies performed in endocrine tumors have been performed. The potential relevance of 14q32 miRNAs through investigating their targets, and integrating the knowledge provided by literature data and bioinformatics predictions have been indicated. RESULTS Pituitary adenoma, papillary thyroid cancer and a particular subset of pheochromocytoma and adrenocortical cancer are characterized by the downregulation of miRNAs encoded by the 14q32 cluster. Pancreas neuroendocrine tumors, most of the adrenocortical cancer and medullary thyroid cancer are particularly distinct, as 14q32 miRNAs were overexpressed. In pheochromocytoma and growth-hormone producing pituitary adenoma, however, both increased and decreased expression of 14q32 miRNAs cluster members were observed. In the background of this phenomenon methodological, technical and biological factors are hypothesized and discussed. The functions of 14q32 miRNAs were also revealed by bioinformatics and literature data mining. CONCLUSIONS 14q32 miRNAs have a significant role in the tumorigenesis of endocrine organs. Regarding their stable expression in the circulation of healthy individuals, further investigation of 14q32 miRNAs could provide a potential for use as biomarkers (diagnostic or prognostic) in endocrine neoplasms.
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8
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Oveisi A, Vahdati A, Shahhoseini M, Favaedi R, Maroufizadeh S, Movaghar B. Ovulation Induction Changes Epigenetic Marks of Imprinting Genes in Mice Fetus Organs. CELL JOURNAL 2021; 23:99-108. [PMID: 33650826 PMCID: PMC7944133 DOI: 10.22074/cellj.2021.6953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/03/2019] [Indexed: 11/26/2022]
Abstract
Objective Genomic imprinting is an epigenetic phenomenon that plays a critical role in normal development of embryo.
Using exogenous hormones during assisted reproductive technology (ART) can change an organism hormonal profile
and subsequently affect epigenetic events. Ovarian stimulation changes gene expression and epigenetic pattern of
imprinted genes in the organs of mouse fetus.
Materials and Methods For this experimental study, expression of three imprinted genes H19, Igf2 (Insulin-like growth
factor 2) and Cdkn1c (Cyclin-dependent kinase inhibitor 1C), which have important roles in development of placenta
and embryo, and the epigenetic profile of their regulatory region in some tissues of 19-days-old female fetuses, from
female mice subjected to ovarian stimulation, were evaluated by quantitative reverse-transcription PCR (qRT-PCR)
and Chromatin immunoprecipitation (ChIP) methods.
Results H19 gene was significantly lower in heart (P<0.05), liver (P<0.05), lung (P<0.01), placenta (P<0.01) and ovary
(P<0.01). It was significantly higher in kidney of ovarian stimulation group compared to control fetuses (P<0.05). Igf2
expression was significantly higher in brain (P<0.05) and kidney (P<0.05), while it was significantly lower in lung of
experimental group fetuses in comparison with control fetuses (P<0.05). Cdkn1c expression was significantly higher in
lung (P<0.05). It was significantly decreased in placenta of experimental group fetuses rather than the control fetuses
(P<0.05). Histone modification data and DNA methylation data were in accordance to the gene expression profiles.
Conclusion Results showed altered gene expressions in line with changes in epigenetic pattern of their promoters in
the ovarian stimulation group, compared to normal cycle.
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Affiliation(s)
- Anahita Oveisi
- Department of Biology, Fars Science and Research Branch, Islamic Azad University, Fars, Iran.,Department of Biology, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Akbar Vahdati
- Department of Biology, Fars Science and Research Branch, Islamic Azad University, Fars, Iran.,Department of Biology, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Iran
| | - Raha Favaedi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Saman Maroufizadeh
- School of Nursing and Midwifery, Guilan University of Medical Sciences, Rasht, Iran
| | - Bahar Movaghar
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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9
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Quilter CR, Harvey KM, Bauer J, Skinner BM, Gomez M, Shrivastava M, Doel AM, Drammeh S, Dunger DB, Moore SE, Ong KK, Prentice AM, Bernstein RM, Sargent CA, Affara NA. Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA. FASEB Bioadv 2021; 3:205-230. [PMID: 33842847 PMCID: PMC8019263 DOI: 10.1096/fba.2020-00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/25/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Low birthweight and reduced height gain during infancy (stunting) may arise at least in part from adverse early life environments that trigger epigenetic reprogramming that may favor survival. We examined differential DNA methylation patterns using targeted methyl sequencing of regions regulating gene activity in groups of rural Gambian infants: (a) low and high birthweight (DNA from cord blood (n = 16 and n = 20, respectively), from placental trophoblast tissue (n = 21 and n = 20, respectively), and DNA from peripheral blood collected from infants at 12 months of age (n = 23 and n = 17, respectively)), and, (b) the top 10% showing rapid postnatal length gain (high, n = 20) and the bottom 10% showing slow postnatal length gain (low, n = 20) based on z score change between birth and 12 months of age (LAZ) (DNA from peripheral blood collected from infants at 12 months of age). Using BiSeq analysis to identify significant methylation marks, for birthweight, four differentially methylated regions (DMRs) were identified in trophoblast DNA, compared to 68 DMRs in cord blood DNA, and 54 DMRs in 12‐month peripheral blood DNA. Twenty‐five DMRs were observed to be associated with high and low length for age (LAZ) at 12 months. With the exception of five loci (associated with two different genes), there was no overlap between these groups of methylation marks. Of the 194 CpG methylation marks contained within DMRs, 106 were located to defined gene regulatory elements (promoters, CTCF‐binding sites, transcription factor‐binding sites, and enhancers), 58 to gene bodies (introns or exons), and 30 to intergenic DNA. Distinct methylation patterns associated with birthweight between comparison groups were observed in DNA collected at birth (at the end of intrauterine growth window) compared to those established by 12 months (near the infancy/childhood growth transition). The longitudinal differences in methylation patterns may arise from methylation adjustments, changes in cellular composition of blood or both that continue during the critical postnatal growth period, and in response to early nutritional and infectious environmental exposures with impacts on growth and longer‐term health outcomes.
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Affiliation(s)
- Claire R Quilter
- Department of Pathology University of Cambridge Cambridge UK.,Present address: East Midlands & East of England NHS Genomic Laboratory Hub, Genomics Laboratories Cambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Kerry M Harvey
- Department of Pathology University of Cambridge Cambridge UK
| | - Julien Bauer
- Department of Pathology University of Cambridge Cambridge UK
| | - Benjamin M Skinner
- Department of Pathology University of Cambridge Cambridge UK.,School of Life Sciences University of Essex Colchester UK
| | - Maria Gomez
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Kennedy Institute of Rheumatology University of Oxford Oxford UK
| | - Manu Shrivastava
- Department of Pathology University of Cambridge Cambridge UK.,Present address: Oxford University Hospitals Oxford UK
| | - Andrew M Doel
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Saikou Drammeh
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - David B Dunger
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK
| | - Sophie E Moore
- Department of Women and Children's Health King's College London London UK.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Ken K Ong
- MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK.,Department of Paediatrics University of Cambridge School of Clinical Medicine Cambridge UK.,Institute of Metabolic Science Cambridge Biomedical Campus Cambridge Cambridge UK
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine Banjul The Gambia
| | - Robin M Bernstein
- Growth and Development Lab Department of Anthropology University of Colorado Boulder CO USA.,Institute of Behavioural Science University of Colorado Boulder CO USA
| | | | - Nabeel A Affara
- Department of Pathology University of Cambridge Cambridge UK
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10
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Baulina N, Kiselev I, Favorova O. Imprinted Genes and Multiple Sclerosis: What Do We Know? Int J Mol Sci 2021; 22:1346. [PMID: 33572862 PMCID: PMC7866243 DOI: 10.3390/ijms22031346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disease of the central nervous system that arises from interplay between non-genetic and genetic risk factors. The epigenetics functions as a link between these factors, affecting gene expression in response to external influence, and therefore should be extensively studied to improve the knowledge of MS molecular mechanisms. Among others, the epigenetic mechanisms underlie the establishment of parent-of-origin effects that appear as phenotypic differences depending on whether the allele was inherited from the mother or father. The most well described manifestation of parent-of-origin effects is genomic imprinting that causes monoallelic gene expression. It becomes more obvious that disturbances in imprinted genes at the least affecting their expression do occur in MS and may be involved in its pathogenesis. In this review we will focus on the potential role of imprinted genes in MS pathogenesis.
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Affiliation(s)
- Natalia Baulina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
| | - Olga Favorova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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11
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Zhu D, Xiao Z, Wang Z, Hu B, Duan C, Zhu Z, Gao N, Zhu Y, Wang H. MEG3/MIR-376B-3P/HMGA2 axis is involved in pituitary tumor invasiveness. J Neurosurg 2020; 134:499-511. [PMID: 31899875 DOI: 10.3171/2019.10.jns191959] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/22/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To date, long noncoding RNAs (lncRNAs) have proven to function as key regulators in tumorigenesis. Among these lncRNAs, MEG3 displays low levels in various neoplasms and tumor cell lines. However, the regulatory mechanism of MEG3 and MIR-376B-3P, one of the microRNAs from downstream gene clusters of the DLK1-MEG3 locus, remains insufficiently defined. METHODS The authors used quantitative real-time polymerase chain reaction analysis to analyze whether decreased MEG3 and MIR-376B-3P expression levels were associated with the invasiveness of clinical nonfunctioning pituitary adenomas (CNFPAs) in 30 patients. Furthermore, functional experiments unveiled the pathophysiological role of MEG3, MIR-376B-3P, and HMGA2 in pituitary-derived folliculostellate (PDFS) cell lines. Moreover, dual-luciferase reporter assay, Western blot analysis, and immunofluorescence were applied to reveal the correlations among MEG3, MIR-376B-3P, and HMGA2. RESULTS MEG3 and MIR-376B-3P were decreased in patients with CNFPA, and their transcriptional levels were highly associated with invasive CNFPAs. Moreover, excessive expression of MEG3 and MIR-376B-3P inhibited tumorigenesis and promoted apoptosis in PDFS cells. Importantly, the authors found that MEG3 acted as an enhancer of MIR-376B-3P expression. Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. CONCLUSIONS This study offers a novel mechanism of an MEG3/MIR-376B-3P/HMGA2 regulatory network in CNFPAs, which may become a breakthrough for anticancer treatments.
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Affiliation(s)
- Dimin Zhu
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Zheng Xiao
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Zongming Wang
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Bin Hu
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Chengbin Duan
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Ziyan Zhu
- 2Department of Histology and Embryology, Medical School of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Nailin Gao
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Yonghong Zhu
- 2Department of Histology and Embryology, Medical School of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haijun Wang
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
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12
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Wang X, Fang Y, Zhou Y, Guo X, Xu K, Li C, Zhang J, Hong Y. SDF-1α/MicroRNA-134 Axis Regulates Nonfunctioning Pituitary Neuroendocrine Tumor Growth via Targeting VEGFA. Front Endocrinol (Lausanne) 2020; 11:566761. [PMID: 33362712 PMCID: PMC7756115 DOI: 10.3389/fendo.2020.566761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Nonfunctioning pituitary neuroendocrine tumor (NF-PitNET) is difficult to resect. Except for surgery, there is no effective treatment for NF-PitNET. MicroRNA-134 (miR-134) has been reported to inhibit proliferation and invasion ability of tumor cells. Herein, the mechanism underlying the effect of miR-134 on alleviating NF-PitNET tumor cells growth is explored. METHODS Mouse pituitary αT3-1 cells were transfected with miR-134 mimics and inhibitor, followed by treatment with stromal cell-derived factor-1α (SDF-1α) in vitro. MiR-134 expression level: we used quantitative real-time PCR (qRT-PCR) to detect the expression of miR-134. Cell behavior level: cell viability and invasion ability were assessed using a cell counting kit-8 (CCK8) assay and Transwell invasion assay respectively. Cytomolecular level: tumor cell proliferation was evaluated by Ki-67 staining; propidium iodide (PI) staining analyzed the effect of miR-134 on cell cycle arrest; western blot analysis and immunofluorescence staining evaluated tumor migration and invasive ability. Additionally, we collected 27 NF-PitNET tumor specimens and related clinical data. The specimens were subjected to qRT-PCR to obtain the relative miR-134 expression level of each specimen; linear regression analysis was used to analyze the miR-134 expression level in tumor specimens and the age of the NF-PitNET population, gender, tumor invasion, prognosis, and other indicators. RESULTS In vitro experiment, miR-134 was observed to significantly inhibit αT3-1 cells proliferation characterized by inhibited cell viability and expressions of vascular endothelial growth factor A (VEGFA) and cell cycle transition from G1 to S phase (P < 0.01). VEGFA was verified as a target of miR-134. Additionally, miR-134-induced inhibition of αT3-1 cell proliferation and invasion was attenuated by SDF-1α and VEGFA overexpression (P < 0.01). In primary NF-PitNET tumor analysis, miR-134 expression level was negatively correlated with tumor invasion (P = 0.003). CONCLUSION The regulation of the SDF-1α/miR-134/VEGFA axis represents a novel mechanism in the pathogenesis of NF-PitNETs and may serve as a potential therapeutic target for the treatment of NF-PitNETs.
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Affiliation(s)
- Xiaoyu Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuanjian Fang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yunxiang Zhou
- Department of Surgical Oncology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoming Guo
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ke Xu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chenguang Li
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianmin Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Brain Research Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, Zhejiang, China
- *Correspondence: Jianmin Zhang, ; Yuan Hong,
| | - Yuan Hong
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- *Correspondence: Jianmin Zhang, ; Yuan Hong,
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13
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Chen Z, Gao Y, Gao S, Song D, Feng Y. MiR-135b-5p promotes viability, proliferation, migration and invasion of gastric cancer cells by targeting Krüppel-like factor 4 (KLF4). Arch Med Sci 2020; 16:167-176. [PMID: 32051721 PMCID: PMC6963155 DOI: 10.5114/aoms.2019.87761] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/23/2017] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION The expression of MiR-135b-5p was up-regulated while Krüppel-like factor 4 (KLF4) expression was extremely low in human gastric carcinoma (GC) tissues. This study aimed to explore the role of miR-135b-5p in GC cells and its influence on various cell capacity and viability by targeting KLF4. MATERIAL AND METHODS The dual-luciferase reporter assay was first performed and the target relationship between miR-135b-5p and KLF4 was confirmed. Then three GC cell lines and the human normal gastric epithelial cell line (GES1) were analyzed for the expression level of miR-135b-5p and KLF4 mRNA by RT-qPCR. The BGC-823 GC cell line was chosen for subsequent assays. RESULTS The expression of miR-135b-5p and KLF4 was manipulated via transfection. The changes of proliferation, invasion, migration, viability, cycle and apoptosis of GC cells were evaluated by MTS, colony formation assay, transwell assay, wound healing assay and flow cytometry assay, respectively. Overexpression of MiR-135b-5p enhanced viability, proliferation, invasion and migration of GC cells, increased cell viability and reduced cell apoptosis. Replenishing of KLF4 functioned oppositely. CONCLUSIONS The inhibitory effects of ectopic KLF4 could be attenuated by co-transfection of miR-135b-5p. Collective data suggested that miR-135b-5p has a tumor-promoting role in GC cells via downregulating KLF4. Hence, inhibition of miR-135b-5p could be valuable for treatment of gastric cancer.
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Affiliation(s)
- Zhi Chen
- Department of Nephrology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yongjian Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Shuohui Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Defeng Song
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Ye Feng
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
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14
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Being in a loop: how long non-coding RNAs organise genome architecture. Essays Biochem 2019; 63:177-186. [DOI: 10.1042/ebc20180057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
Chromatin architecture has a significant impact on gene expression. Evidence in the last two decades support RNA as an important component of chromatin structure [Genes Dev. (2005) 19, 1635–1655; PLoS ONE (2007) 2, e1182; Nat. Genet. (2002) 30, 329–334]. Long non-coding RNAs (lncRNAs) are able to control chromatin structure through nucleosome positioning, interaction with chromatin re-modellers and chromosome looping. These functions are carried out in cis at the site of lncRNAs transcription or in trans at distant loci. While the evidence for a role in lncRNAs in regulating gene expression through chromatin interactions is increasing, there is still very little conclusive evidence for a potential role in looping organisation. Here, we review models for the involvement of lncRNAs in genome architecture and the experimental evidence to support them.
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15
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Nacher JC, Akutsu T. Controllability Methods for Identifying Associations Between Critical Control ncRNAs and Human Diseases. Methods Mol Biol 2019; 1912:289-300. [PMID: 30635898 DOI: 10.1007/978-1-4939-8982-9_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human diseases are not only associated to mutations in protein-coding genes. Contrary to what was thought decades ago, the human genome is largely transcribed which generates a large amount of nonprotein-coding RNAs (ncRNAs). Interestingly, these ncRNAs are not only able to perform biological functions and interact with other molecules such as proteins, but also have been reported involved in human diseases. In this book chapter, we review the recent research done on controllability methods related to associations between ncRNAs and human diseases. First, we introduce the bipartite complex network resulting from the interactions of ncRNAs and proteins. We then explain the theoretical background of controllability algorithms and apply these methods to the problem of identifying ncRNAs with critical roles in network control. Then, by performing statistical analyses we can answer the question on whether the subset of critical control ncRNAs is also enriched by human diseases. In addition, we review three-layer network models for prediction of ncRNA-disease associations.
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Affiliation(s)
- Jose C Nacher
- Faculty of Science, Department of Information Science, Toho University, Chiba, Japan.
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.
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16
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Wong WKM, Sørensen AE, Joglekar MV, Hardikar AA, Dalgaard LT. Non-Coding RNA in Pancreas and β-Cell Development. Noncoding RNA 2018; 4:E41. [PMID: 30551650 PMCID: PMC6315983 DOI: 10.3390/ncrna4040041] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
In this review, we provide an overview of the current knowledge on the role of different classes of non-coding RNAs for islet and β-cell development, maturation and function. MicroRNAs (miRNAs), a prominent class of small RNAs, have been investigated for more than two decades and patterns of the roles of different miRNAs in pancreatic fetal development, islet and β-cell maturation and function are now emerging. Specific miRNAs are dynamically regulated throughout the period of pancreas development, during islet and β-cell differentiation as well as in the perinatal period, where a burst of β-cell replication takes place. The role of long non-coding RNAs (lncRNA) in islet and β-cells is less investigated than for miRNAs, but knowledge is increasing rapidly. The advent of ultra-deep RNA sequencing has enabled the identification of highly islet- or β-cell-selective lncRNA transcripts expressed at low levels. Their roles in islet cells are currently only characterized for a few of these lncRNAs, and these are often associated with β-cell super-enhancers and regulate neighboring gene activity. Moreover, ncRNAs present in imprinted regions are involved in pancreas development and β-cell function. Altogether, these observations support significant and important actions of ncRNAs in β-cell development and function.
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Affiliation(s)
- Wilson K M Wong
- NHMRC Clinical Trials Center, University of Sydney, Camperdown NSW 2050, Sydney, Australia.
| | - Anja E Sørensen
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark.
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Center, University of Sydney, Camperdown NSW 2050, Sydney, Australia.
| | - Anand A Hardikar
- NHMRC Clinical Trials Center, University of Sydney, Camperdown NSW 2050, Sydney, Australia.
| | - Louise T Dalgaard
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark.
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17
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Stelzer Y, Wu H, Song Y, Shivalila CS, Markoulaki S, Jaenisch R. Parent-of-Origin DNA Methylation Dynamics during Mouse Development. Cell Rep 2018; 16:3167-3180. [PMID: 27653683 PMCID: PMC5119552 DOI: 10.1016/j.celrep.2016.08.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/08/2016] [Accepted: 08/19/2016] [Indexed: 12/13/2022] Open
Abstract
Parent-specific differentially methylated regions (DMRs) are established during gametogenesis and regulate parent-specific expression of imprinted genes. Monoallelic expression of imprinted genes is essential for development, suggesting that imprints are faithfully maintained in embryos and adults. To test this hypothesis, we targeted a reporter for genomic methylation to the imprinted Dlk1-Dio3 intergenic DMR (IG-DMR) to assess the methylation of both parental alleles at single-cell resolution. Biallelic gain or loss of IG-DMR methylation occurred in a small fraction of mouse embryonic stem cells, significantly affecting developmental potency. Mice carrying the reporter in either parental allele showed striking parent-specific changes in IG-DMR methylation, causing substantial and consistent tissue- and cell-type-dependent signatures in embryos and postnatal animals. Furthermore, dynamics in DNA methylation persisted during adult neurogenesis, resulting in inter-individual diversity. This substantial cell-cell DNA methylation heterogeneity implies that dynamic DNA methylation variations in the adult may be of functional importance.
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Affiliation(s)
- Yonatan Stelzer
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Hao Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yuelin Song
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Chikdu S Shivalila
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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18
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Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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19
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Abraham JM, Meltzer SJ. Long Noncoding RNAs in the Pathogenesis of Barrett's Esophagus and Esophageal Carcinoma. Gastroenterology 2017; 153:27-34. [PMID: 28528706 PMCID: PMC5515484 DOI: 10.1053/j.gastro.2017.04.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/13/2022]
Abstract
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development. As anticipated, alterations in this large control system can contribute to disease pathogenesis and carcinogenesis. We review the involvement of noncoding RNAs, lncRNAs in particular, in development of Barrett's esophagus and esophageal carcinoma.
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20
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Elhamamsy AR. Role of DNA methylation in imprinting disorders: an updated review. J Assist Reprod Genet 2017; 34:549-562. [PMID: 28281142 PMCID: PMC5427654 DOI: 10.1007/s10815-017-0895-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic imprinting is a complex epigenetic process that contributes substantially to embryogenesis, reproduction, and gametogenesis. Only small fraction of genes within the whole genome undergoes imprinting. Imprinted genes are expressed in a monoallelic parent-of-origin-specific manner, which means that only one of the two inherited alleles is expressed either from the paternal or maternal side. Imprinted genes are typically arranged in clusters controlled by differentially methylated regions or imprinting control regions. Any defect or relaxation in imprinting process can cause loss of imprinting in the key imprinted loci. Loss of imprinting in most cases has a harmful effect on fetal development and can result in neurological, developmental, and metabolic disorders. Since DNA methylation and histone modifications play a key role in the process of imprinting. This review focuses on the role of DNA methylation in imprinting process and describes DNA methylation aberrations in different imprinting disorders.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Department of Clinical Pharmacy, School of Pharmacy, Tanta University, Tanta, 31512, Gharbia, Egypt.
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21
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Cavaillé J. Box C/D small nucleolar RNA genes and the Prader-Willi syndrome: a complex interplay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28296064 DOI: 10.1002/wrna.1417] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 12/22/2022]
Abstract
The nucleolus of mammalian cells contains hundreds of box C/D small nucleolar RNAs (SNORDs). Through their ability to base pair with ribosomal RNA precursors, most play important roles in the synthesis and/or activity of ribosomes, either by guiding sequence-specific 2'-O-methylations or by facilitating RNA folding and cleavages. A growing number of SNORD genes with elusive functions have been discovered recently. Intriguingly, the vast majority of them are located in two large, imprinted gene clusters at human chromosome region 15q11q13 (the SNURF-SNRPN domain) and at 14q32 (the DLK1-DIO3 domain) where they are expressed, respectively, only from the paternally and maternally inherited alleles. These placental mammal-specific SNORD genes have many features of the canonical SNORDs that guide 2'-O-methylations, yet they lack obvious complementarity with ribosomal RNAs and, surprisingly, they are processed from large, tandemly repeated genes expressed preferentially in the brain. This review summarizes our understanding of the biology of these peculiar SNORD genes, focusing particularly on SNORD115 and SNORD116 in the SNURF-SNRPN domain. It examines the growing evidence that altered levels of these SNORDs and/or their host-gene transcripts may be a primary cause of Prader-Willi syndrome (PWS; a rare disorder characterized by overeating and obesity) as well as abnormalities in signaling through the 5-HT2C serotonin receptor. Finally, the hypothesis that PWS may be a ribosomopathy (ribosomal disease) is also discussed. WIREs RNA 2017, 8:e1417. doi: 10.1002/wrna.1417 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse; UPS and CNRS, LMBE, Toulouse, France
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22
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Abstract
The regulatory potential of RNA has never ceased to amaze: from RNA catalysis, to RNA-mediated splicing, to RNA-based silencing of an entire chromosome during dosage compensation. More recently, thousands of long noncoding RNA (lncRNA) transcripts have been identified, the majority with unknown function. Thus, it is tempting to think that these lncRNAs represent a cadre of new factors that function through ribonucleic mechanisms. Some evidence points to several lncRNAs with tantalizing physiological contributions and thought-provoking molecular modalities. However, dissecting the RNA biology of lncRNAs has been difficult, and distinguishing the independent contributions of functional RNAs from underlying DNA elements, or the local act of transcription, is challenging. Here, we aim to survey the existing literature and highlight future approaches that will be needed to link the RNA-based biology and mechanisms of lncRNAs in vitro and in vivo.
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Affiliation(s)
- Loyal A Goff
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA; The Broad Institute, Cambridge, Massachusetts 02142, USA
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23
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Hollins SL, Cairns MJ. MicroRNA: Small RNA mediators of the brains genomic response to environmental stress. Prog Neurobiol 2016; 143:61-81. [PMID: 27317386 DOI: 10.1016/j.pneurobio.2016.06.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/24/2016] [Accepted: 06/11/2016] [Indexed: 01/09/2023]
Abstract
The developmental processes that establish the synaptic architecture of the brain while retaining capacity for activity-dependent remodeling, are complex and involve a combination of genetic and epigenetic influences. Dysregulation of these processes can lead to problems with neural circuitry which manifest in humans as a range of neurodevelopmental syndromes, such as schizophrenia, bipolar disorder and fragile X mental retardation. Recent studies suggest that prenatal, postnatal and intergenerational environmental factors play an important role in the aetiology of stress-related psychopathology. A number of these disorders have been shown to display epigenetic changes in the postmortem brain that reflect early life experience. These changes affect the regulation of gene expression though chromatin remodeling (transcriptional) and post-transcriptional influences, especially small noncoding microRNA (miRNA). These dynamic and influential molecules appear to play an important function in both brain development and its adaption to stress. In this review, we examine the role of miRNA in mediating the brain's response to both prenatal and postnatal environmental perturbations and explore how stress- induced alterations in miRNA expression can regulate the stress response via modulation of the immune system. Given the close relationship between environmental stress, miRNA, and brain development/function, we assert that miRNA hold a significant position at the molecular crossroads between neural development and adaptations to environmental stress. A greater understanding of the dynamics that mediate an individual's predisposition to stress-induced neuropathology has major human health benefits and is an important area of research.
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Affiliation(s)
- Sharon L Hollins
- School of Biomedical Sciences and Pharmacy and the Hunter Medical Research Institute, the University of Newcastle, Callaghan, NSW 2308, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy and the Hunter Medical Research Institute, the University of Newcastle, Callaghan, NSW 2308, Australia; Schizophrenia Research Institute, Sydney, NSW, Australia.
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24
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Li Y, Li J, Fang C, Shi L, Tan J, Xiong Y, Bin Fan, Li C. Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages. Sci Rep 2016; 6:26852. [PMID: 27229484 PMCID: PMC4882596 DOI: 10.1038/srep26852] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023] Open
Abstract
Some documented evidences proved small RNAs (sRNA) and targeted genes are involved in mammalian testicular development and spermatogenesis. However, the detailed molecular regulation mechanisms of them remain largely unknown so far. In this study, we obtained a total of 10,716 mRNAs, 67 miRNAs and 16,953 piRNAs which were differentially expressed between LC and LW pig breeds or between the two sexual maturity stages. Of which, we identified 16 miRNAs and 28 targeted genes possibly related to spermatogenesis; 14 miRNA and 18 targeted genes probably associated with cell adhesion related testis development. We also annotated 579 piRNAs which could potentially regulate cell death, nucleosome organization and other basic biology process, which implied that those piRNAs might be involved in sexual maturation difference. The integrated network analysis results suggested that some differentially expressed genes were involved in spermatogenesis through the ECM-receptor interaction, focal adhesion, Wnt and PI3K-Akt signaling pathways, some particular miRNAs have the negative regulation roles and some special piRNAs have the positive and negative regulation roles in testicular development. Our data provide novel insights into the molecular expression and regulation similarities and diversities of spermatogenesis and testicular development in different pig breeds at different stages of sexual maturity.
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Affiliation(s)
- Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jialian Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Guangxi Yangxiang Pig Gene Technology limited Company, Guigang, 537120, People's Republic of China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Liang Shi
- Guangxi Yangxiang Incorporated Company, Guigang, 537100, People's Republic of China
| | - Jiajian Tan
- Guangxi Yangxiang Incorporated Company, Guigang, 537100, People's Republic of China
| | - Yuanzhu Xiong
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bin Fan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Guangxi Yangxiang Pig Gene Technology limited Company, Guigang, 537120, People's Republic of China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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25
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Chen HX, Yan ZH, Long JE, Yan JB, Huang Y. [Computational and experimental identification of novel microRNAs in goat.]. YI CHUAN = HEREDITAS 2016; 30:1326-32. [PMID: 18930894 DOI: 10.3724/sp.j.1005.2008.01326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
microRNA (miRNA) is a class of non-coding small RNA molecules with roughly 22 nucleotides in length, regulating gene expression on post-transcriptional level and playing an important role in cell proliferation, differentiation and apoptosis process. Based on the conservation of miRNAs sequence, we compared the known miRNAs among five mammals, i.e., human, mouse, cattle, pig and dog with the sequence of sheep genome that is highly homologous to goat genome, published on the NCBI, and 11 candidate miRNAs were eventually obtained. RT-PCR analysis showed the expression of the 11 miRNAs in brain and 5 in liver, indicating that they might be novel miRNAs. The methodology provides an alternative approach to the exploration of new miRNAs in goat.
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Affiliation(s)
- Hai-Xuan Chen
- 1. Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai 200040, China; 2. Key Lab of Medical Embryo Molecular Biology, the Ministry of Health; Shanghai Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China E-mail:
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26
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Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of RNAs that engage in numerous biological processes across every branch of life. Although initially discovered as mRNA-like transcripts that do not encode proteins, recent studies have revealed features of lncRNAs that further distinguish them from mRNAs. In this Review, we describe special events in the lifetimes of lncRNAs - before, during and after transcription - and discuss how these events ultimately shape the unique characteristics and functional roles of lncRNAs.
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Affiliation(s)
- Jeffrey J Quinn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
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Grothaus K, Kanber D, Gellhaus A, Mikat B, Kolarova J, Siebert R, Wieczorek D, Horsthemke B. Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment. Epigenetics 2016; 11:216-26. [PMID: 26890210 DOI: 10.1080/15592294.2016.1145330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Gene duplication by retrotransposition, i.e., the reverse transcription of an mRNA and integration of the cDNA into the genome, is an important mechanism in evolution. Based on whole-genome bisulfite sequencing of monocyte DNA, we have investigated the methylation state of all CpG islands (CGIs) associated with a retrocopy (n = 1,319), their genomic environment, as well as the CGIs associated with the ancestral genes. Approximately 10% of retrocopies are associated with a CGI. Whereas almost all CGIs of the human genome are unmethylated, 68% of the CGIs associated with a retrocopy are methylated. In retrocopies resulting from multiple retrotranspositions of the same ancestral gene, the methylation state of the CGI often differs. There is a strong positive correlation between the methylation state of the CGI/retrocopy and their genomic environment, suggesting that the methylation state of the integration site determined the methylation state of the CGI/retrocopy, or that methylation of the retrocopy by a host defense mechanism has spread into the adjacent regions. Only a minor fraction of CGI/retrocopies (n = 195) has intermediate methylation levels. Among these, the previously reported CGI/retrocopy in intron 2 of the RB1 gene (PPP1R26P1) as well as the CGI associated with the retrocopy RPS2P32 identified in this study carry a maternal methylation imprint. In conclusion, these findings shed light on the evolutionary dynamics and constraints of DNA methylation.
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Affiliation(s)
- Katrin Grothaus
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Deniz Kanber
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Alexandra Gellhaus
- b Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Essen , Essen , Germany
| | - Barbara Mikat
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Julia Kolarova
- c Institut für Humangenetik, Christian-Albrechts-Universität Kiel & Universitätsklinikum Schleswig-Holstein , Campus Kiel, Kiel , Germany
| | - Reiner Siebert
- c Institut für Humangenetik, Christian-Albrechts-Universität Kiel & Universitätsklinikum Schleswig-Holstein , Campus Kiel, Kiel , Germany
| | - Dagmar Wieczorek
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Bernhard Horsthemke
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
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Ma J, Chen X, Liu Y, Xie Q, Sun Y, Chen J, Leng L, Yan H, Zhao B, Tang N. Ancestral TCDD exposure promotes epigenetic transgenerational inheritance of imprinted gene Igf2: Methylation status and DNMTs. Toxicol Appl Pharmacol 2015; 289:193-202. [PMID: 26455773 DOI: 10.1016/j.taap.2015.09.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 11/22/2022]
Abstract
Ancestral TCDD exposure could induce epigenetic transgenerational phenotypes, which may be mediated in part by imprinted gene inheritance. The aim of our study was to evaluate the transgenerational effects of ancestral TCDD exposure on the imprinted gene insulin-like growth factor-2 (Igf2) in rat somatic tissue. TCDD was administered daily by oral gavage to groups of F0 pregnant SD rats at dose levels of 0 (control), 200 or 800 ng/kg bw during gestation day 8-14. Animal transgenerational model of ancestral exposure to TCDD was carefully built, avoiding sibling inbreeding. Hepatic Igf2 expression of the TCDD male progeny was decreased concomitantly with hepatic damage and increased activities of serum hepatic enzymes both in the F1 and F3 generation. Imprinted Control Region (ICR) of Igf2 manifested a hypermethylated pattern, whereas methylation status in the Differentially Methylated Region 2 (DMR2) showed a hypomethylated manner in the F1 generation. These epigenetic alterations in these two regions maintained similar trends in the F3 generation. Meanwhile, the expressions of DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) changed in a non-monotonic manner both in the F1 and F3 generation. This study provides evidence that ancestral TCDD exposure may promote epigenetic transgenerational alterations of imprinted gene Igf2 in adult somatic tissue.
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Affiliation(s)
- Jing Ma
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Xi Chen
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Yanan Liu
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yawen Sun
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Jingshan Chen
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Ling Leng
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Huan Yan
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Naijun Tang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China.
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miR-300 mediates Bmi1 function and regulates differentiation in primitive cardiac progenitors. Cell Death Dis 2015; 6:e1953. [PMID: 26512961 PMCID: PMC4632286 DOI: 10.1038/cddis.2015.255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 07/11/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022]
Abstract
B lymphoma Mo-MLV insertion region 1 (Bmi1) is a polycomb-family transcriptional factor critical for self-renewal in many adult stem cells and human neoplasia. We sought to identify microRNAs regulated by Bmi1 that could play a role in multipotent cardiac progenitor cell (CPC) decisions. We found that miR-300, a poorly characterized microRNA mapping in the Dlk1-Dio3 microRNA cluster, was positively regulated by Bmi1 in CPCs. Forced expression of miR-300 in CPCs promoted an improved stemness signature with a significant increase in Oct4 levels, a reduction in senescence progression and an enhanced proliferative status via p19 activation and inhibition of p16 accumulation. Endothelial and cardiogenic differentiation were clearly compromised by sustained miR-300 expression. Additionally, RNA and protein analysis revealed a significant reduction in key cardiac transcription factors, including Nkx2.5 and Tbx5. Collectively, these results suggest that some functions attributed to Bmi1 are due to induction of miR-300, which decreases the cardiogenic differentiation potential of multipotent CPCs in vitro and promotes self-renewal.
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Geaghan M, Cairns MJ. MicroRNA and Posttranscriptional Dysregulation in Psychiatry. Biol Psychiatry 2015; 78:231-9. [PMID: 25636176 DOI: 10.1016/j.biopsych.2014.12.009] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 11/11/2014] [Accepted: 12/03/2014] [Indexed: 11/27/2022]
Abstract
Psychiatric syndromes, including schizophrenia, mood disorders, and autism spectrum disorders, are characterized by a complex range of symptoms, including psychosis, depression, mania, and cognitive deficits. Although the mechanisms driving pathophysiology are complex and remain largely unknown, advances in the understanding of gene association and gene networks are providing significant clues to their etiology. In recent years, small noncoding RNA molecules known as microRNA (miRNA) have emerged as potential players in the pathophysiology of mental illness. These small RNAs regulate hundreds of target transcripts by modifying their stability and translation on a broad scale, influencing entire gene networks in the process. There is evidence to suggest that numerous miRNAs are dysregulated in postmortem neuropathology of neuropsychiatric disorders, and there is strong genetic support for association of miRNA genes and their targets with these conditions. This review presents the accumulated evidence linking miRNA dysregulation and dysfunction with schizophrenia, bipolar disorder, major depressive disorder, and autism spectrum disorders and the potential of miRNAs as biomarkers or therapeutics for these disorders. We further assess the functional roles of some outstanding miRNAs associated with these conditions and how they may be influencing the development of psychiatric symptoms.
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Affiliation(s)
- Michael Geaghan
- School of Biomedical Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, Australia.; Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Murray J Cairns
- School of Biomedical Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, Australia.; Schizophrenia Research Institute, Sydney, Australia.; Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, New South Wales, Australia..
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31
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Crea F, Clermont PL, Parolia A, Wang Y, Helgason CD. The non-coding transcriptome as a dynamic regulator of cancer metastasis. Cancer Metastasis Rev 2015; 33:1-16. [PMID: 24346158 PMCID: PMC3988524 DOI: 10.1007/s10555-013-9455-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the discovery of microRNAs, non-coding RNAs (NC-RNAs) have increasingly attracted the attention of cancer investigators. Two classes of NC-RNAs are emerging as putative metastasis-related genes: long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs). LncRNAs orchestrate metastatic progression through several mechanisms, including the interaction with epigenetic effectors, splicing control and generation of microRNA-like molecules. In contrast, snoRNAs have been long considered “housekeeping” genes with no relevant function in cancer. However, recent evidence challenges this assumption, indicating that some snoRNAs are deregulated in cancer cells and may play a specific role in metastasis. Interestingly, snoRNAs and lncRNAs share several mechanisms of action, and might synergize with protein-coding genes to generate a specific cellular phenotype. This evidence suggests that the current paradigm of metastatic progression is incomplete. We propose that NC-RNAs are organized in complex interactive networks which orchestrate cellular phenotypic plasticity. Since plasticity is critical for cancer cell metastasis, we suggest that a molecular interactome composed by both NC-RNAs and proteins orchestrates cancer metastasis. Interestingly, expression of lncRNAs and snoRNAs can be detected in biological fluids, making them potentially useful biomarkers. NC-RNA expression profiles in human neoplasms have been associated with patients’ prognosis. SnoRNA and lncRNA silencing in pre-clinical models leads to cancer cell death and/or metastasis prevention, suggesting they can be investigated as novel therapeutic targets. Based on the literature to date, we critically discuss how the NC-RNA interactome can be explored and manipulated to generate more effective diagnostic, prognostic, and therapeutic strategies for metastatic neoplasms.
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Affiliation(s)
- Francesco Crea
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada,
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32
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Lee B, Mazar J, Aftab MN, Qi F, Shelley J, Li JL, Govindarajan S, Valerio F, Rivera I, Thurn T, Tran TA, Kameh D, Patel V, Perera RJ. Long noncoding RNAs as putative biomarkers for prostate cancer detection. J Mol Diagn 2015; 16:615-26. [PMID: 25307116 DOI: 10.1016/j.jmoldx.2014.06.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer is one of the leading causes of mortality among US males. There is an urgent unmet need to develop sensitive and specific biomarkers for the early detection of prostate cancer to reduce overtreatment and accompanying morbidity. We identified a group of differentially expressed long noncoding RNAs in prostate cancer cell lines and patient samples and further characterized six long noncoding RNAs (AK024556, XLOC_007697, LOC100287482, XLOC_005327, XLOC_008559, and XLOC_009911) in prostatic adenocarcinoma tissue samples (Gleason score >6.0) and compared them with matched normal (healthy) tissues. Interestingly, these markers were also successfully detected in patient urine samples and were found to be up-regulated when compared with normal (healthy) urine. AK024556 (SPRY4-IT1) was highly up-regulated in human prostate cancer cell line PC3 but not in LNCaP, and siRNA knockdown of SPRY4-IT1 in PC3 cells inhibited cell proliferation and invasion and increased cell apoptosis. Chromogenic in situ hybridization assay was developed to detect long noncoding RNAs in primary prostatic adenocarcinoma tissue samples, paving the way for clinical diagnostics. We believe that these results will set the stage for more extensive studies to develop novel long noncoding RNA-based diagnostic assays for early prostate cancer detection and will help to distinguish benign prostate cancer from precancerous lesions.
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33
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Angrisani A, Tafer H, Stadler PF, Furia M. Developmentally regulated expression and expression strategies of Drosophila snoRNAs. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 61:69-78. [PMID: 25641266 DOI: 10.1016/j.ibmb.2015.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
Small nucleolar RNAs constitute a significant portion of the eukaryotic small ncRNA transcriptome and guide site-specific methylation or pseudouridylation of target RNAs. In addition, they can play diverse regulatory roles on gene expression, acting as precursors of smaller fragments able to modulate alternative splicing or operate as microRNAs. Defining their expression strategies and the full repertory of their biological functions is a critical, but still ongoing, process in most organisms. Considering that Drosophila melanogaster is one of the most advantageous model organism for genetic, functional and developmental studies, we analysed the whole genomic organization of its annotated snoRNAs - whose vast majority is known to be embedded in an intronic context - and show by GO term enrichment analysis that protein-coding genes involved in cell division and cytoskeleton organization are those mostly preferred as hosts. This finding was unexpected, and delineates an unpredicted link between snoRNA host genes and cell proliferation that might be of general relevance. We also defined by quantitative RT-PCR the expression of a representative subset of annotated specimens throughout the life cycle, providing a first overview on developmental profiling of the fly snoRNA transcriptome. We found that most of the tested specimens, rather than acting as housekeeping genes with uniform expression, exhibit dynamic developmental expression patterns; moreover, intronic snoRNAs harboured by the same host gene often exhibit distinct temporal profiles, indicating that they can be expressed uncoordinatedly. In addition to provide an updated outline of the fly snoRNA transcriptome, our data highlight that expression of these versatile ncRNAs can be finely regulated.
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Affiliation(s)
- Alberto Angrisani
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy
| | - Hakim Tafer
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Maria Furia
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy.
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Kanduri C. Long noncoding RNAs: Lessons from genomic imprinting. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:102-11. [PMID: 26004516 DOI: 10.1016/j.bbagrm.2015.05.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/17/2022]
Abstract
Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding RNAs (lncRNAs). In this article, I overview the functional role of intergenic lncRNAs (H19, IPW, and MEG3), antisense lncRNAs (Kcnq1ot1, Airn, Nespas, Ube3a-ATS), and enhancer lncRNAs (IG-DMR eRNAs) to understand the diverse mechanisms being employed by them in cis and/or trans to regulate the parent-of-origin-specific expression of target genes. Recent evidence suggests that some of the lncRNAs regulate imprinting by promoting intra-chromosomal higher-order chromatin compartmentalization, affecting replication timing and subnuclear positioning. Whereas others act via transcriptional occlusion or transcriptional collision-based mechanisms. By establishing genomic imprinting of target genes, the lncRNAs play a critical role in important biological functions, such as placental and embryonic growth, pluripotency maintenance, cell differentiation, and neural-related functions such as synaptic development and plasticity. An emerging consensus from the recent evidence is that the imprinted lncRNAs fine-tune gene expression of the protein-coding genes to maintain their dosage in cell. Hence, lncRNAs from imprinted clusters offer insights into their mode of action, and these mechanisms have been the basis for uncovering the mode of action of lncRNAs in several other biological contexts. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.
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Ruhrmann S, Stridh P, Kular L, Jagodic M. Genomic imprinting: A missing piece of the Multiple Sclerosis puzzle? Int J Biochem Cell Biol 2015; 67:49-57. [PMID: 26002250 DOI: 10.1016/j.biocel.2015.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 12/14/2022]
Abstract
Evidence for parent-of-origin effects in complex diseases such as Multiple Sclerosis (MS) strongly suggests a role for epigenetic mechanisms in their pathogenesis. In this review, we describe the importance of accounting for parent-of-origin when identifying new risk variants for complex diseases and discuss how genomic imprinting, one of the best-characterized epigenetic mechanisms causing parent-of-origin effects, may impact etiology of complex diseases. While the role of imprinted genes in growth and development is well established, the contribution and molecular mechanisms underlying the impact of genomic imprinting in immune functions and inflammatory diseases are still largely unknown. Here we discuss emerging roles of imprinted genes in the regulation of inflammatory responses with a particular focus on the Dlk1 cluster that has been implicated in etiology of experimental MS-like disease and Type 1 Diabetes. Moreover, we speculate on the potential wider impact of imprinting via the action of imprinted microRNAs, which are abundantly present in the Dlk1 locus and predicted to fine-tune important immune functions. Finally, we reflect on how unrelated imprinted genes or imprinted genes together with non-imprinted genes can interact in so-called imprinted gene networks (IGN) and suggest that IGNs could partly explain observed parent-of-origin effects in complex diseases. Unveiling the mechanisms of parent-of-origin effects is therefore likely to teach us not only about the etiology of complex diseases but also about the unknown roles of this fascinating phenomenon underlying uneven genetic contribution from our parents. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Stridh
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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36
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Varmuza S, Miri K. What does genetics tell us about imprinting and the placenta connection? Cell Mol Life Sci 2015; 72:51-72. [PMID: 25194419 PMCID: PMC11114082 DOI: 10.1007/s00018-014-1714-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/07/2023]
Abstract
Genomic imprinting is an epigenetic gene silencing phenomenon that is specific to eutherians in the vertebrate lineage. The acquisition of both placentation and genomic imprinting has spurred interest in the possible evolutionary link for many years. In this review we examine the genetic evidence and find that while many imprinted domains are anchored by genes required for proper placenta development in a parent of origin fashion, an equal number of imprinted genes have no apparent function that depends on imprinting. Examination of recent data from studies of molecular and genetic mechanisms points to a maternal control of the selection and maintenance of imprint marks, reinforcing the importance of the oocyte in the healthy development of the placenta and fetus.
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Affiliation(s)
- Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 611-25 Harbord Street, Toronto, M5S 3G5, Canada,
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Greife A, Knievel J, Ribarska T, Niegisch G, Schulz WA. Concomitant downregulation of the imprinted genes DLK1 and MEG3 at 14q32.2 by epigenetic mechanisms in urothelial carcinoma. Clin Epigenetics 2014; 6:29. [PMID: 25741387 PMCID: PMC4348104 DOI: 10.1186/1868-7083-6-29] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/07/2014] [Indexed: 01/01/2023] Open
Abstract
Background The two oppositely imprinted and expressed genes, DLK1 and MEG3, are located in the same gene cluster at 14q32. Previous studies in bladder cancer have suggested that tumor suppressor genes are located in this region, but these have not been identified. Results We observed that both DLK1 and MEG3 are frequently silenced in urothelial cancer tissues and cell lines. The concomitant downregulation of the two genes is difficult to explain by known mechanisms for inactivating imprinted genes, namely deletion of active alleles or epitype switching. Indeed, quantitative PCR revealed more frequent copy number gains than losses in the gene cluster that were, moreover, consistent within each sample, excluding gene losses as the cause of downregulation. Instead, we observed distinctive epigenetic alterations at the three regions controlling DLK1 and MEG3 expression, namely the DLK1 promoter; the intergenic (IG) and MEG3 differentially methylated regions (DMRs). Bisulfite sequencing and pyrosequencing revealed novel patterns of DNA methylation in tumor cells, which were distinct from that of either paternal allele. Furthermore, chromatin immunoprecipitation demonstrated loss of active and gain of repressive histone modifications at all regulatory sequences. Conclusions Our data support the idea that the main cause of the prevalent downregulation of DLK1 and MEG3 in urothelial carcinoma is epigenetic silencing across the 14q32 imprinted gene cluster, resulting in the unusual concomitant inactivation of oppositely expressed and imprinted genes. Electronic supplementary material The online version of this article (doi:10.1186/1868-7083-6-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annemarie Greife
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Judith Knievel
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Teodora Ribarska
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
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Gao WL, Liu M, Yang Y, Yang H, Liao Q, Bai Y, Li YX, Li D, Peng C, Wang YL. The imprinted H19 gene regulates human placental trophoblast cell proliferation via encoding miR-675 that targets Nodal Modulator 1 (NOMO1). RNA Biol 2014; 9:1002-10. [DOI: 10.4161/rna.20807] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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39
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Galiveti CR, Raabe CA, Konthur Z, Rozhdestvensky TS. Differential regulation of non-protein coding RNAs from Prader-Willi Syndrome locus. Sci Rep 2014; 4:6445. [PMID: 25246219 PMCID: PMC4171697 DOI: 10.1038/srep06445] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/28/2014] [Indexed: 12/22/2022] Open
Abstract
Prader-Willi Syndrome (PWS) is a neurogenetic disorder caused by the deletion of imprinted genes on the paternally inherited human chromosome 15q11-q13. This locus harbours a long non-protein-coding RNA (U-UBE3A-ATS) that contains six intron-encoded snoRNAs, including the SNORD116 and SNORD115 repetitive clusters. The 3′-region of U-UBE3A-ATS is transcribed in the cis-antisense direction to the ubiquitin-protein ligase E3A (UBE3A) gene. Deletion of the SNORD116 region causes key characteristics of PWS. There are few indications that SNORD115 might regulate serotonin receptor (5HT2C) pre-mRNA processing. Here we performed quantitative real-time expression analyses of RNAs from the PWS locus across 20 human tissues and combined it with deep-sequencing data derived from Cap Analysis of Gene Expression (CAGE-seq) libraries. We found that the expression profiles of SNORD64, SNORD107, SNORD108 and SNORD116 are similar across analyzed tissues and correlate well with SNORD116 embedded U-UBE3A-ATS exons (IPW116). Notable differences in expressions between the aforementioned RNAs and SNORD115 together with the host IPW115 and UBE3A cis-antisense exons were observed. CAGE-seq analysis revealed the presence of potential transcriptional start sites originated from the U-UBE3A-ATS spanning region. Our findings indicate novel aspects for the expression regulation in the PWS locus.
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Affiliation(s)
- Chenna R Galiveti
- 1] Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany [2] Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Carsten A Raabe
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
| | - Zoltán Konthur
- 1] Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany [2] Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Timofey S Rozhdestvensky
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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40
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Insulin and insulin-like growth factor 1 receptors are required for normal expression of imprinted genes. Proc Natl Acad Sci U S A 2014; 111:14512-7. [PMID: 25246545 DOI: 10.1073/pnas.1415475111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In addition to signaling through the classical tyrosine kinase pathway, recent studies indicate that insulin receptors (IRs) and insulin-like growth factor 1 (IGF1) receptors (IGF1Rs) can emit signals in the unoccupied state through some yet-to-be-defined noncanonical pathways. Here we show that cells lacking both IRs and IGF1Rs exhibit a major decrease in expression of multiple imprinted genes and microRNAs, which is partially mimicked by inactivation of IR alone in mouse embryonic fibroblasts or in vivo in brown fat in mice. This down-regulation is accompanied by changes in DNA methylation of differentially methylated regions related to these loci. Different from a loss of imprinting pattern, loss of IR and IGF1R causes down-regulated expression of both maternally and paternally expressed imprinted genes and microRNAs, including neighboring reciprocally imprinted genes. Thus, the unoccupied IR and IGF1R generate previously unidentified signals that control expression of imprinted genes and miRNAs through transcriptional mechanisms that are distinct from classical imprinting control.
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LncRBase: an enriched resource for lncRNA information. PLoS One 2014; 9:e108010. [PMID: 25233092 PMCID: PMC4169474 DOI: 10.1371/journal.pone.0108010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/11/2014] [Indexed: 11/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora of cellular regulatory processes. Although several noncoding transcripts have been functionally annotated as lncRNAs within the genome, not all have been proven to fulfill the criteria for a functional regulator and further analyses have to be done in order to include them in a functional cohort. LncRNAs are being classified and reclassified in an ongoing annotation process, and the challenge is fraught with ambiguity, as newer evidences of their biogenesis and functional implication come into light. In our effort to understand the complexity of this still enigmatic biomolecule, we have developed a new database entitled "LncRBase" where we have classified and characterized lncRNAs in human and mouse. It is an extensive resource of human and mouse lncRNA transcripts belonging to fourteen distinct subtypes, with a total of 83,201 entries for mouse and 133,361 entries for human: among these, we have newly annotated 8,507 mouse and 14,813 human non coding RNA transcripts (from UCSC and H-InvDB 8.0) as lncRNAs. We have especially considered protein coding gene loci which act as hosts for non coding transcripts. LncRBase includes different lncRNA transcript variants of protein coding genes within LncRBase. LncRBase provides information about the genomic context of different lncRNA subtypes, their interaction with small non coding RNAs (ncRNAs) viz. piwi interacting RNAs (piRNAs) and microRNAs (miRNAs) and their mode of regulation, via association with diverse other genomic elements. Adequate knowledge about genomic origin and molecular features of lncRNAs is essential to understand their functional and behavioral complexities. Overall, LncRBase provides a thorough study on various aspects of lncRNA origin and function and a user-friendly interface to search for lncRNA information. LncRBase is available at http://bicresources.jcbose.ac.in/zhumur/lncrbase.
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Alteration of imprinted Dlk1-Dio3 miRNA cluster expression in the entorhinal cortex induced by maternal immune activation and adolescent cannabinoid exposure. Transl Psychiatry 2014; 4:e452. [PMID: 25268256 PMCID: PMC4203021 DOI: 10.1038/tp.2014.99] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 07/09/2014] [Accepted: 08/21/2014] [Indexed: 12/19/2022] Open
Abstract
A significant feature of the cortical neuropathology of schizophrenia is a disturbance in the biogenesis of short non-coding microRNA (miRNA) that regulate translation and stability of mRNA. While the biological origin of this phenomenon has not been defined, it is plausible that it relates to major environmental risk factors associated with the disorder such as exposure to maternal immune activation (MIA) and adolescent cannabis use. To explore this hypothesis, we administered the viral mimic poly I:C to pregnant rats and further exposed some of their maturing offsprings to daily injections of the synthetic cannabinoid HU210 for 14 days starting on postnatal day 35. Whole-genome miRNA expression analysis was then performed on the left and right hemispheres of the entorhinal cortex (EC), a region strongly associated with schizophrenia. Animals exposed to either treatment alone or in combination exhibited significant differences in the expression of miRNA in the left hemisphere, whereas the right hemisphere was less responsive. Hemisphere-associated differences in miRNA expression were greatest in the combined treatment and highly over-represented in a single imprinted locus on chromosome 6q32. This observation was significant as the syntenic 14q32 locus in humans encodes a large proportion of miRNAs differentially expressed in peripheral blood lymphocytes from patients with schizophrenia, suggesting that interaction of early and late environmental insults may affect miRNA expression, in a manner that is relevant to schizophrenia.
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Kunej T, Obsteter J, Pogacar Z, Horvat S, Calin GA. The decalog of long non-coding RNA involvement in cancer diagnosis and monitoring. Crit Rev Clin Lab Sci 2014; 51:344-57. [PMID: 25123609 DOI: 10.3109/10408363.2014.944299] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts without protein-coding capacity; initially regarded as "transcriptional noise", lately they have emerged as essential factors in both cell biology and mechanisms of disease. In this article, we present basic knowledge of lncRNA molecular mechanisms, associated physiological processes and cancer association, as well as their diagnostic and therapeutic value in the form of a decalog: (1) Non-coding RNAs (ncRNAs) are transcripts without protein-coding capacity divided by size (short and long ncRNAs), function (housekeeping RNA and regulatory RNA) and direction of transcription (sense/antisense, bidirectional, intronic and intergenic), containing a broad range of molecules with diverse properties and functions, such as messenger RNA, transfer RNA, microRNA and long non-coding RNAs. (2) Long non-coding RNAs are implicated in many molecular mechanisms, such as transcriptional regulation, post-transcriptional regulation and processing of other short ncRNAs. (3) Long non-coding RNAs play an important role in many physiological processes such as X-chromosome inactivation, cell differentiation, immune response and apoptosis. (4) Long non-coding RNAs have been linked to hallmarks of cancer: (a) sustaining proliferative signaling; (b) evading growth suppressors; (c) enabling replicative immortality; (d) activating invasion and metastasis; (e) inducing angiogenesis; (f) resisting cell death; and (g) reprogramming energy metabolism. (5) Regarding their impact on cancer cells, lncRNAs are divided into two groups: oncogenic and tumor-suppressor lncRNAs. (6) Studies of lncRNA involvement in cancer usually analyze deregulated expression patterns at the RNA level as well as the effects of single nucleotide polymorphisms and copy number variations at the DNA level. (7) Long non-coding RNAs have potential as novel biomarkers due to tissue-specific expression patterns, efficient detection in body fluids and high stability. (8) LncRNAs serve as novel biomarkers for diagnostic, prognostic and monitoring purposes. (9) Tissue specificity of lncRNAs enables the development of selective therapeutic options. (10) Long non-coding RNAs are emerging as commercial biomarkers and therapeutic agents.
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Affiliation(s)
- Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale , Slovenia
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Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP. Considerations when investigating lncRNA function in vivo. eLife 2014; 3:e03058. [PMID: 25124674 PMCID: PMC4132285 DOI: 10.7554/elife.03058] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although a small number of the vast array of animal long non-coding RNAs (lncRNAs) have known effects on cellular processes examined in vitro, the extent of their contributions to normal cell processes throughout development, differentiation and disease for the most part remains less clear. Phenotypes arising from deletion of an entire genomic locus cannot be unequivocally attributed either to the loss of the lncRNA per se or to the associated loss of other overlapping DNA regulatory elements. The distinction between cis- or trans-effects is also often problematic. We discuss the advantages and challenges associated with the current techniques for studying the in vivo function of lncRNAs in the light of different models of lncRNA molecular mechanism, and reflect on the design of experiments to mutate lncRNA loci. These considerations should assist in the further investigation of these transcriptional products of the genome. DOI:http://dx.doi.org/10.7554/eLife.03058.001
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Affiliation(s)
- Andrew R Bassett
- Andrew R Bassett is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
| | - Asifa Akhtar
- Asifa Akhtar is in the Department of Chromatin Regulation, Max-Planck-Institut für Immunbiologie und Epigenetik, Freiburg im Breisgau, Germany
| | - Denise P Barlow
- Denise P Barlow is in the CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrian P Bird
- Adrian P Bird is in the Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil Brockdorff
- Neil Brockdorff is in the Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Denis Duboule
- Denis Duboule is in the School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland; Department of Genetics and Evolution, Université de Genève, Geneva, Switzerland
| | - Anne Ephrussi
- Anne Ephrussi is in the Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne C Ferguson-Smith
- Anne C Ferguson-Smith is in the Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Thomas R Gingeras
- Thomas R Gingeras is in the Functional Genomics Group, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Wilfried Haerty
- Wilfried Haerty is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- Douglas R Higgs is in the MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Eric A Miska
- Eric A Miska is in the Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris P Ponting
- Chris P Ponting is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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Wolf JB, Brandvain Y. Gene interactions in the evolution of genomic imprinting. Heredity (Edinb) 2014; 113:129-37. [PMID: 24619179 PMCID: PMC4105456 DOI: 10.1038/hdy.2014.7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 12/02/2013] [Accepted: 12/05/2013] [Indexed: 12/24/2022] Open
Abstract
Numerous evolutionary theories have been developed to explain the epigenetic phenomenon of genomic imprinting. Here, we explore a subset of theories wherein non-additive genetic interactions can favour imprinting. In the simplest genic interaction--the case of underdominance--imprinting can be favoured to hide effectively low-fitness heterozygous genotypes; however, as there is no asymmetry between maternally and paternally inherited alleles in this model, other means of enforcing monoallelic expression may be more plausible evolutionary outcomes than genomic imprinting. By contrast, more successful interaction models of imprinting rely on an asymmetry between the maternally and paternally inherited alleles at a locus that favours the silencing of one allele as a means of coordinating the expression of high-fitness allelic combinations. For example, with interactions between autosomal loci, imprinting functionally preserves high-fitness genotypes that were favoured by selection in the previous generation. In this scenario, once a focal locus becomes imprinted, selection at interacting loci favours a matching imprint. Uniparental transmission generates similar asymmetries for sex chromosomes and cytoplasmic factors interacting with autosomal loci, with selection favouring the expression of either maternal or paternally derived autosomal alleles depending on the pattern of transmission of the uniparentally inherited factor. In a final class of models, asymmetries arise when genes expressed in offspring interact with genes expressed in one of its parents. Under such a scenario, a locus evolves to have imprinted expression in offspring to coordinate the interaction with its parent's genome. We illustrate these models and explore key links and differences using a unified framework.
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Affiliation(s)
- J B Wolf
- Department of Biology and Biochemistry, University of Bath, Bath, Claverton Down, UK
| | - Y Brandvain
- Department of Plant Biology, University of Minnesota, St Paul, MN, USA
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46
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Chen XP, Chen YG, Lan JY, Shen ZJ. MicroRNA-370 suppresses proliferation and promotes endometrioid ovarian cancer chemosensitivity to cDDP by negatively regulating ENG. Cancer Lett 2014; 353:201-10. [PMID: 25063739 DOI: 10.1016/j.canlet.2014.07.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 07/14/2014] [Accepted: 07/14/2014] [Indexed: 01/29/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs that post-transcriptionally inhibit gene expression. In this study, we discovered that microRNA-370 (miR-370) was down-regulated in endometrioid ovarian cancer cells. In IGROV1 and TOV112D endometrioid ovarian cancer cells, miR-370 suppressed cellular viability and colony formation. miR-370 also enhanced endometrioid ovarian cancer cell chemosensitivity to cDDP. Endoglin (ENG) was directly and negatively regulated by miR-370. In addition, hypermethylation was a potential mechanism of miR-370 epigenetic silencing. We conclude that miR-370 acts as a tumor suppressor in endometrioid ovarian cancer via ENG regulation.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antineoplastic Agents/pharmacology
- Base Sequence
- Carcinoma, Endometrioid/drug therapy
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/pathology
- Cell Line, Tumor
- Cell Proliferation
- Cisplatin/pharmacology
- Down-Regulation
- Drug Resistance, Neoplasm
- Endoglin
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mice
- Mice, Nude
- MicroRNAs/physiology
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- RNA Interference
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Tumor Burden
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Xiao-Ping Chen
- Department of Obstetrics and Gynaecology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China; Department of Obstetrics and Gynaecology, Yancheng 1th People Hospital, Yancheng, Jiangsu Province, China
| | - You-Guo Chen
- Department of Obstetrics and Gynaecology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Jian-Yun Lan
- Department of Obstetrics and Gynaecology, Yancheng 1th People Hospital, Yancheng, Jiangsu Province, China
| | - Zong-Ji Shen
- Department of Obstetrics and Gynaecology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China.
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Abstract
Along the lines of established players like chromatin modifiers and transcription factors, noncoding RNA (ncRNA) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription. With increasing evidence of ncRNAs in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature. In addition, we attempt to understand and speculate how these RNA dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.
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Affiliation(s)
- Tanmoy Mondal
- Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Medicinaregatan 9A, 40530, Gothenburg, Sweden
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48
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Zhang YJ, Yang JH, Shi QS, Zheng LL, Liu J, Zhou H, Zhang H, Qu LH. Rapid birth-and-death evolution of imprinted snoRNAs in the Prader-Willi syndrome locus: implications for neural development in Euarchontoglires. PLoS One 2014; 9:e100329. [PMID: 24945811 PMCID: PMC4063771 DOI: 10.1371/journal.pone.0100329] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/23/2014] [Indexed: 11/24/2022] Open
Abstract
Imprinted small nucleolar RNAs (snoRNAs) are only found in eutherian genomes and closely related to brain functions. A complex human neurological disease, Prader-Willi syndrome (PWS), is primarily attributed to the deletion of imprinted snoRNAs in chromosome 15q11-q13. Here we investigated the snoRNA repertoires in the PWS locus of 12 mammalian genomes and their evolution processes. A total of 613 imprinted snoRNAs were identified in the PWS homologous loci and the gene number was highly variable across lineages, with a peak in Euarchontoglires. Lineage-specific gene gain and loss events account for most extant genes of the HBII-52 (SNORD115) and the HBII-85 (SNORD116) gene family, and remarkable high gene-birth rates were observed in the primates and the rodents. Meanwhile, rapid sequence substitution occurred only in imprinted snoRNA genes, rather than their flanking sequences or the protein-coding genes located in the same imprinted locus. Strong selective constraints on the functional elements of these imprinted snoRNAs further suggest that they are subjected to birth-and-death evolution. Our data suggest that the regulatory role of HBII-52 on 5-HT2CR pre-mRNA might originate in the Euarchontoglires through adaptive process. We propose that the rapid evolution of PWS-related imprinted snoRNAs has contributed to the neural development of Euarchontoglires.
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Affiliation(s)
- Yi-Jun Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Qiao-Su Shi
- Laboratory of Liver Disease Hospital, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- * E-mail:
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49
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Wei Y, Su J, Liu H, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q, Zhang Y. MetaImprint: an information repository of mammalian imprinted genes. Development 2014; 141:2516-23. [DOI: 10.1242/dev.105320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomic imprinting is a complex genetic and epigenetic phenomenon that plays important roles in mammalian development and diseases. Mammalian imprinted genes have been identified widely by experimental strategies or predicted using computational methods. Systematic information for these genes would be necessary for the identification of novel imprinted genes and the analysis of their regulatory mechanisms and functions. Here, a well-designed information repository, MetaImprint (http://bioinfo.hrbmu.edu.cn/MetaImprint), is presented, which focuses on the collection of information concerning mammalian imprinted genes. The current version of MetaImprint incorporates 539 imprinted genes, including 255 experimentally confirmed genes, and their detailed research courses from eight mammalian species. MetaImprint also hosts genome-wide genetic and epigenetic information of imprinted genes, including imprinting control regions, single nucleotide polymorphisms, non-coding RNAs, DNA methylation and histone modifications. Information related to human diseases and functional annotation was also integrated into MetaImprint. To facilitate data extraction, MetaImprint supports multiple search options, such as by gene ID and disease name. Moreover, a configurable Imprinted Gene Browser was developed to visualize the information on imprinted genes in a genomic context. In addition, an Epigenetic Changes Analysis Tool is provided for online analysis of DNA methylation and histone modification differences of imprinted genes among multiple tissues and cell types. MetaImprint provides a comprehensive information repository of imprinted genes, allowing researchers to investigate systematically the genetic and epigenetic regulatory mechanisms of imprinted genes and their functions in development and diseases.
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Affiliation(s)
- Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jianzhong Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongbo Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haidan Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanhua Wen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hui Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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50
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Epigenetically regulated microRNAs in Alzheimer's disease. Neurobiol Aging 2014; 35:731-45. [DOI: 10.1016/j.neurobiolaging.2013.10.082] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 12/12/2022]
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