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Radzishevsky I, Odeh M, Bodner O, Zubedat S, Shaulov L, Litvak M, Esaki K, Yoshikawa T, Agranovich B, Li WH, Radzishevsky A, Gottlieb E, Avital A, Wolosker H. Impairment of serine transport across the blood-brain barrier by deletion of Slc38a5 causes developmental delay and motor dysfunction. Proc Natl Acad Sci U S A 2023; 120:e2302780120. [PMID: 37812701 PMCID: PMC10589673 DOI: 10.1073/pnas.2302780120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/08/2023] [Indexed: 10/11/2023] Open
Abstract
Brain L-serine is critical for neurodevelopment and is thought to be synthesized solely from glucose. In contrast, we found that the influx of L-serine across the blood-brain barrier (BBB) is essential for brain development. We identified the endothelial Slc38a5, previously thought to be a glutamine transporter, as an L-serine transporter expressed at the BBB in early postnatal life. Young Slc38a5 knockout (KO) mice exhibit developmental alterations and a decrease in brain L-serine and D-serine, without changes in serum or liver amino acids. Slc38a5-KO brains exhibit accumulation of neurotoxic deoxysphingolipids, synaptic and mitochondrial abnormalities, and decreased neurogenesis at the dentate gyrus. Slc38a5-KO pups exhibit motor impairments that are affected by the administration of L-serine at concentrations that replenish the serine pool in the brain. Our results highlight a critical role of Slc38a5 in supplying L-serine via the BBB for proper brain development.
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Affiliation(s)
- Inna Radzishevsky
- Department of Biochemistry, B. Rappaport Faculty of Medicine, Technion-Israel Institue of Technology, Haifa3109601, Israel
| | - Maali Odeh
- Department of Biochemistry, B. Rappaport Faculty of Medicine, Technion-Israel Institue of Technology, Haifa3109601, Israel
| | - Oded Bodner
- Department of Biochemistry, B. Rappaport Faculty of Medicine, Technion-Israel Institue of Technology, Haifa3109601, Israel
| | - Salman Zubedat
- Department of Occupational Therapy, Faculty of Social Welfare and Health Sciences, University of Haifa, Haifa3498838, Israel
| | - Lihi Shaulov
- Electron Microscopy Unit, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa3109601, Israel
| | - Maxim Litvak
- Department of Biochemistry, B. Rappaport Faculty of Medicine, Technion-Israel Institue of Technology, Haifa3109601, Israel
| | - Kayoko Esaki
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto860-0082, Japan
| | - Takeo Yoshikawa
- Laboratory of Molecular Psychiatry, RIKEN Center for Brain Science, Saitama351-0198, Japan
| | - Bella Agranovich
- Laura and Isaac Perlmutter Metabolomics Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa3109601, Israel
| | - Wen-Hong Li
- Department of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75390-9039
| | | | - Eyal Gottlieb
- Technion-Integrated Cancer Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa3109601, Israel
| | - Avi Avital
- Department of Occupational Therapy, Faculty of Social Welfare and Health Sciences, University of Haifa, Haifa3498838, Israel
| | - Herman Wolosker
- Department of Biochemistry, B. Rappaport Faculty of Medicine, Technion-Israel Institue of Technology, Haifa3109601, Israel
- Laura and Isaac Perlmutter Metabolomics Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa3109601, Israel
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2
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Ayache L, Bushell A, Lee J, Salminen I, Crespi B. Mother's warmth from maternal genes: genomic imprinting of brown adipose tissue. Evol Med Public Health 2023; 11:379-385. [PMID: 37928960 PMCID: PMC10621903 DOI: 10.1093/emph/eoad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/04/2023] [Indexed: 11/07/2023] Open
Abstract
Background and objectives Brown adipose tissue (BAT) plays key roles in mammalian physiology, most notably with regard to thermoregulation in infants and juveniles. Previous studies have suggested that intragenomic conflict, in the form of genomic imprinting, mediates BAT thermogenesis, because it represents a public good for groups of siblings, or a mother with her offspring, who huddle together to conserve warmth. By this hypothesis, maternally expressed imprinted genes should promote BAT, while paternally expressed genes should repress it. Methodology We systematically searched the literature using two curated lists of genes imprinted in humans and/or mice, in association with evidence regarding effects of perturbation to imprinted gene expression on BAT development or activity. Results Overall, enhanced BAT was associated with relatively higher expression of maternally expressed imprinted genes, and relatively lower expression of paternally expressed imprinted genes; this pattern was found for 16 of the 19 genes with sufficient information for robust ascertainment (Binomial test, P < 0.005, 2-tailed). Conclusions and implications These results support the kinship theory of imprinting and indicate that future studies of BAT, and its roles in human health and disease, may usefully focus on effects of imprinted genes and associated genomic conflicts.
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Affiliation(s)
- Lynn Ayache
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Aiden Bushell
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jessica Lee
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Iiro Salminen
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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3
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Rodriguez-Caro F, Moore EC, Good JM. Evolution of parent-of-origin effects on placental gene expression in house mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554674. [PMID: 37662315 PMCID: PMC10473692 DOI: 10.1101/2023.08.24.554674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The mammalian placenta is a hotspot for the evolution of genomic imprinting, a form of gene regulation that involves the parent-specific epigenetic silencing of one allele. Imprinted genes are central to placental development and are thought to contribute to the evolution of reproductive barriers between species. However, it is unclear how rapidly imprinting evolves or how functional specialization among placental tissues influences the evolution of imprinted expression. We compared parent-of-origin expression bias across functionally distinct placental layers sampled from reciprocal crosses within three closely related lineages of mice ( Mus ). Using genome-wide gene expression and DNA methylation data from fetal and maternal tissues, we developed an analytical strategy to minimize pervasive bias introduced by maternal contamination of placenta samples. We corroborated imprinted expression at 42 known imprinted genes and identified five candidate imprinted genes showing parent-of-origin specific expression and DNA methylation. Paternally-biased expression was enriched in the labyrinth zone, a layer specialized in nutrient transfer, and maternally-biased genes were enriched in the junctional zone, which specializes in modulation of maternal physiology. Differentially methylated regions were predominantly determined through epigenetic modification of the maternal genome and were associated with both maternally- and paternally-biased gene expression. Lastly, comparisons between lineages revealed a small set of co-regulated genes showing rapid divergence in expression levels and imprinted status in the M. m. domesticus lineage. Together, our results reveal important links between core functional elements of placental biology and the evolution of imprinted gene expression among closely related rodent species.
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Taurino G, Chiu M, Bianchi MG, Griffini E, Bussolati O. The SLC38A5/SNAT5 amino acid transporter: from pathophysiology to pro-cancer roles in the tumor microenvironment. Am J Physiol Cell Physiol 2023; 325:C550-C562. [PMID: 37458433 DOI: 10.1152/ajpcell.00169.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
SLC38A5/SNAT5 is a system N transporter that can mediate net inward or outward transmembrane fluxes of neutral amino acids coupled with Na+ (symport) and H+ (antiport). Its preferential substrates are not only amino acids with side chains containing amide (glutamine and asparagine) or imidazole (histidine) groups, but also serine, glycine, and alanine are transported by the carrier. Expressed in the pancreas, intestinal tract, brain, liver, bone marrow, and placenta, it is regulated at mRNA and protein levels by mTORC1 and WNT/β-catenin pathways, and it is sensitive to pH, nutritional stress, inflammation, and hypoxia. SNAT5 expression has been found to be altered in pathological conditions such as chronic inflammatory diseases, gestational complications, chronic metabolic acidosis, and malnutrition. Growing experimental evidence shows that SNAT5 is overexpressed in several types of cancer cells. Moreover, recently published results indicate that SNAT5 expression in stromal cells can support the metabolic exchanges occurring in the tumor microenvironment of asparagine-auxotroph tumors. We review the functional role of the SNAT5 transporter in pathophysiology and propose that, due to its peculiar operational and regulatory features, SNAT5 may play important pro-cancer roles when expressed either in neoplastic or in stromal cells of glutamine-auxotroph tumors.NEW & NOTEWORTHY The transporter SLC38A5/SNAT5 provides net influx or efflux of glutamine, asparagine, and serine. These amino acids are of particular metabolic relevance in several conditions. Changes in transporter expression or activity have been described in selected types of human cancers, where SNAT5 can mediate amino acid exchanges between tumor and stromal cells, thus providing a potential therapeutic target. This is the first review that recapitulates the characteristics and roles of the transporter in physiology and pathology.
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Affiliation(s)
- Giuseppe Taurino
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Massimiliano G Bianchi
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
| | - Erika Griffini
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
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5
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Lyu Q, Yang Q, Hao J, Yue Y, Wang X, Tian J, An L. A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation. Curr Biol 2022; 32:4397-4410.e5. [PMID: 36108637 DOI: 10.1016/j.cub.2022.08.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
Females have two X chromosomes and males have only one in most mammals. X chromosome inactivation (XCI) occurs in females to equalize X-dosage between sexes. Besides, mammals also balance the dosage between X chromosomes and autosomes via X chromosome upregulation (XCU) to fine-tune X-linked expression and thus maintain genomic homeostasis. Despite some studies highlighting the importance of XCU in somatic cells, little is known about how XCU is achieved and its developmental role during early embryogenesis. Herein, using mouse preimplantation embryos as the model, we reported that XCU initially occurs upon major zygotic genome activation and co-regulates X-linked expression in cooperation with imprinted XCI during preimplantation development. An in-depth analysis further indicated, unexpectedly, only a small proportion of, but not X chromosome-wide, X-linked genes contribute greatly to XCU. Furthermore, we identified that bromodomain containing 4 (BRD4) plays a key role in the transcription activation of XCU during preimplantation development. BRD4 deficiency or inhibition caused an impaired XCU, thus leading to reduced developmental potential and mitochondrial dysfunctions of blastocysts. Our finding was also supported by the tight association of BRD4 dysregulation and XCU disruption in the pathology of cholangiocarcinoma. Thus, our results not only advanced the current knowledge of X-dosage compensation and provided a mechanism for understanding XCU initiation but also presented an important clue for understanding the developmental and pathological role of XCU.
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Affiliation(s)
- Qingji Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jia Hao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Yuan Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Xiaodong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China.
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6
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Aykroyd BRL, Tunster SJ, Sferruzzi-Perri AN. Loss of imprinting of the Igf2-H19 ICR1 enhances placental endocrine capacity via sex-specific alterations in signalling pathways in the mouse. Development 2022; 149:dev199811. [PMID: 34982814 PMCID: PMC8783045 DOI: 10.1242/dev.199811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022]
Abstract
Imprinting control region (ICR1) controls the expression of the Igf2 and H19 genes in a parent-of-origin specific manner. Appropriate expression of the Igf2-H19 locus is fundamental for normal fetal development, yet the importance of ICR1 in the placental production of hormones that promote maternal nutrient allocation to the fetus is unknown. To address this, we used a novel mouse model to selectively delete ICR1 in the endocrine junctional zone (Jz) of the mouse placenta (Jz-ΔICR1). The Jz-ΔICR1 mice exhibit increased Igf2 and decreased H19 expression specifically in the Jz. This was accompanied by an expansion of Jz endocrine cell types due to enhanced rates of proliferation and increased expression of pregnancy-specific glycoprotein 23 in the placenta of both fetal sexes. However, changes in the endocrine phenotype of the placenta were related to sexually-dimorphic alterations to the abundance of Igf2 receptors and downstream signalling pathways (Pi3k-Akt and Mapk). There was no effect of Jz-ΔICR1 on the expression of targets of the H19-embedded miR-675 or on fetal weight. Our results demonstrate that ICR1 controls placental endocrine capacity via sex-dependent changes in signalling.
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Affiliation(s)
| | | | - Amanda N. Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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7
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Kleinbrink EL, Gomez-Lopez N, Ju D, Done B, Goustin AS, Tarca AL, Romero R, Lipovich L. Gestational Age Dependence of the Maternal Circulating Long Non-Coding RNA Transcriptome During Normal Pregnancy Highlights Antisense and Pseudogene Transcripts. Front Genet 2021; 12:760849. [PMID: 34880903 PMCID: PMC8645989 DOI: 10.3389/fgene.2021.760849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/29/2021] [Indexed: 01/22/2023] Open
Abstract
In the post-genomic era, our understanding of the molecular regulators of physiologic and pathologic processes in pregnancy is expanding at the whole-genome level. Longitudinal changes in the known protein-coding transcriptome during normal pregnancy, which we recently reported (Gomez-Lopez et al., 2019), have improved our definition of the major operant networks, yet pregnancy-related functions of the non-coding RNA transcriptome remain poorly understood. A key finding of the ENCODE (Encyclopedia of DNA Elements) Consortium, the successor of the Human Genome Project, was that the human genome contains approximately 60,000 genes, the majority of which do not encode proteins. The total transcriptional output of non-protein-coding RNA genes, collectively referred to as the non-coding transcriptome, is comprised mainly of long non-coding RNA (lncRNA) transcripts (Derrien et al., 2012). Although the ncRNA transcriptome eclipses its protein-coding counterpart in abundance, it has until recently lacked a comprehensive, unbiased, genome-scale characterization over the timecourse of normal human pregnancy. Here, we annotated, characterized, and selectively validated the longitudinal changes in the non-coding transcriptome of maternal whole blood during normal pregnancy to term. We identified nine long non-coding RNAs (lncRNAs), including long intergenic non-coding RNAs (lincRNAs) as well as lncRNAs antisense to or otherwise in the immediate vicinity of protein-coding genes, that were differentially expressed with advancing gestation in normal pregnancy: AL355711, BC039551 (expressed mainly in the placenta), JHDM1D-AS1, A2M-AS1, MANEA-AS1, NR_034004, LINC00649, LINC00861, and LINC01094. By cross-referencing our dataset against major public pseudogene catalogs, we also identified six transcribed pseudogenes that were differentially expressed over time during normal pregnancy in maternal blood: UBBP4, FOXO3B, two Makorin (MKRN) pseudogenes (MKRN9P and LOC441455), PSME2P2, and YBX3P1. We also identified three non-coding RNAs belonging to other classes that were modulated during gestation: the microRNA MIR4439, the small nucleolar RNA (snoRNA) SNORD41, and the small Cajal-body specific ncRNA SCARNA2. The expression profiles of most hits were broadly suggestive of functions in pregnancy. These time-dependent changes of the non-coding transcriptome during normal pregnancy, which may confer specific regulatory impacts on their protein-coding gene targets, will facilitate a deeper molecular understanding of pregnancy and lncRNA-mediated molecular pathways at the maternal-fetal interface and of how these pathways impact maternal and fetal health.
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Affiliation(s)
- Erica L Kleinbrink
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI, United States.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Donghong Ju
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Bogdan Done
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI, United States
| | - Anton-Scott Goustin
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI, United States.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, United States
| | - Roberto Romero
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States.,Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI, United States.,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, United States.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States.,Detroit Medical Center, Detroit, MI, United States
| | - Leonard Lipovich
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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8
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Brekke TD, Moore EC, Campbell-Staton SC, Callahan CM, Cheviron ZA, Good JM. X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. Genetics 2021; 218:6168998. [PMID: 33710276 DOI: 10.1093/genetics/iyab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/16/2021] [Indexed: 11/14/2022] Open
Abstract
Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.
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Affiliation(s)
- Thomas D Brekke
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Emily C Moore
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Shane C Campbell-Staton
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,Department of Ecology and Evolutionary Biology; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Colin M Callahan
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
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9
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Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME. Using long-read sequencing to detect imprinted DNA methylation. Nucleic Acids Res 2019; 47:e46. [PMID: 30793194 PMCID: PMC6486641 DOI: 10.1093/nar/gkz107] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 02/01/2023] Open
Abstract
Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of ∼10, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterize, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions (ICRs) as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new ICRs.
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Affiliation(s)
- Scott Gigante
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Genetics, Yale University, 333 Cedar Street, New Haven CT 06510, USA
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility, 305 Grattan Street, Melbourne VIC 3000, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia
| | - Matthew Tinning
- Australian Genome Research Facility, 305 Grattan Street, Melbourne VIC 3000, Australia
| | - Lavinia Gordon
- Australian Genome Research Facility, 305 Grattan Street, Melbourne VIC 3000, Australia
| | - Chris Woodruff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia
| | - Terence P Speed
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,School of Mathematics and Statistics, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia.,School of Mathematics and Statistics, The University of Melbourne, Melbourne VIC 3010, Australia
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10
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Abstract
X chromosome inactivation silences one X chromosome in female mammals. However, this silencing is incomplete, and some genes escape X inactivation. We describe methods to determine the chromosome-wide X inactivation status of genes in tissues or cell lines derived from mice using a combination of skewing of X inactivation and allele-specific analyses of gene expression based on RNA-seq.
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11
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Jégu T, Blum R, Cochrane JC, Yang L, Wang CY, Gilles ME, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT. Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. Nat Struct Mol Biol 2019; 26:96-109. [PMID: 30664740 PMCID: PMC6421574 DOI: 10.1038/s41594-018-0176-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023]
Abstract
The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion triggers a gain of accessibility of selective chromatin regions that is regulated by BRG1, an ATPase subunit of the SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits nucleosome remodeling and ATPase activities of BRG1, while in cell culture Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, starting from pre-existing BRG1 sites that are free of Xist. BRG1 re-association correlates with cohesin binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi “superloops.” Thus, Xist binding inhibits BRG1’s nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.
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Affiliation(s)
- Teddy Jégu
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roy Blum
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jesse C Cochrane
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Yang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chen-Yu Wang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maud-Emmanuelle Gilles
- Institute for RNA Medicine, Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David Colognori
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Attila Szanto
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Boston, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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12
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Guernsey MW, Chuong EB, Cornelis G, Renfree MB, Baker JC. Molecular conservation of marsupial and eutherian placentation and lactation. eLife 2017; 6. [PMID: 28895534 PMCID: PMC5595433 DOI: 10.7554/elife.27450] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/24/2017] [Indexed: 12/18/2022] Open
Abstract
Eutherians are often mistakenly termed 'placental mammals', but marsupials also have a placenta to mediate early embryonic development. Lactation is necessary for both infant and fetal development in eutherians and marsupials, although marsupials have a far more complex milk repertoire that facilitates morphogenesis of developmentally immature young. In this study, we demonstrate that the anatomically simple tammar placenta expresses a dynamic molecular program that is reminiscent of eutherian placentation, including both fetal and maternal signals. Further, we provide evidence that genes facilitating fetal development and nutrient transport display convergent co-option by placental and mammary gland cell types to optimize offspring success.
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Affiliation(s)
- Michael W Guernsey
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Edward B Chuong
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Guillaume Cornelis
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Marilyn B Renfree
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
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13
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Andergassen D, Dotter CP, Wenzel D, Sigl V, Bammer PC, Muckenhuber M, Mayer D, Kulinski TM, Theussl HC, Penninger JM, Bock C, Barlow DP, Pauler FM, Hudson QJ. Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression. eLife 2017; 6. [PMID: 28806168 PMCID: PMC5555720 DOI: 10.7554/elife.25125] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/14/2017] [Indexed: 01/02/2023] Open
Abstract
To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta. DOI:http://dx.doi.org/10.7554/eLife.25125.001
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Affiliation(s)
- Daniel Andergassen
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph P Dotter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniel Wenzel
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Verena Sigl
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp C Bammer
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Markus Muckenhuber
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniela Mayer
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tomasz M Kulinski
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Bock
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Denise P Barlow
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian M Pauler
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Quanah J Hudson
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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14
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Buckberry S, Bianco-Miotto T, Bent SJ, Clifton V, Shoubridge C, Shankar K, Roberts CT. Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics 2017; 18:10. [PMID: 28049421 PMCID: PMC5209944 DOI: 10.1186/s12864-016-3384-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 12/07/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation. We identified modules of co-expressed genes that are preserved across human gestation, and also identifed modules conserved in the mouse indicating conserved molecular networks involved in placental development and gene expression patterns more specific to late gestation. Analysis of co-expressed gene flanking sequences indicated that conserved co-expression modules in the placenta are regulated by a core set of transcription factors, including ZNF423 and EBF1. Additionally, we identified a gene co-expression module enriched for genes implicated in the pregnancy pathology preeclampsia. By using an independnet transcriptome dataset, we show that these co-expressed genes are differentially expressed in preeclampsia. CONCLUSIONS This study represents a comprehensive characterisation of placental co-expression and provides insight into potential transcriptional regulators that govern conserved molecular programs fundamental to placental development.
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Affiliation(s)
- Sam Buckberry
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,University of Western Australia, Harry Perkins Institute of Medical Research, Perth, 6009, Australia.,University of Western Australia, Australian Research Council Centre of Excellence in Plant Energy Biology, Perth, 6009, Australia
| | - Tina Bianco-Miotto
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,The University of Adelaide, School of agriculture, food and wine, Adelaide, 5005, Australia
| | - Stephen J Bent
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Vicki Clifton
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Cheryl Shoubridge
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Kartik Shankar
- University of Arkansas for Medical Sciences, The Department of Pediatrics, Little Rock, 72202, USA
| | - Claire T Roberts
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
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15
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Brekke TD, Henry LA, Good JM. Genomic imprinting, disrupted placental expression, and speciation. Evolution 2016; 70:2690-2703. [PMID: 27714796 PMCID: PMC5123974 DOI: 10.1111/evo.13085] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022]
Abstract
The importance of regulatory incompatibilities to the early stages of speciation remains unclear. Hybrid mammals often show extreme parent-of-origin growth effects that are thought to be a consequence of disrupted genetic imprinting (parent-specific epigenetic gene silencing) during early development. Here, we test the long-standing hypothesis that abnormal hybrid growth reflects disrupted gene expression due to loss of imprinting (LOI) in hybrid placentas, resulting in dosage imbalances between paternal growth factors and maternal growth repressors. We analyzed placental gene expression in reciprocal dwarf hamster hybrids that show extreme parent-of-origin growth effects relative to their parental species. In massively enlarged hybrid placentas, we observed both extensive transgressive expression of growth-related genes and biallelic expression of many genes that were paternally silenced in normal sized hybrids. However, the apparent widespread disruption of paternal silencing was coupled with reduced gene expression levels overall. These patterns are contrary to the predictions of the LOI model and indicate that hybrid misexpression of dosage-sensitive genes is caused by other regulatory mechanisms in this system. Collectively, our results support a central role for disrupted gene expression and imprinting in the evolution of mammalian hybrid inviability, but call into question the generality of the widely invoked LOI model.
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Affiliation(s)
- Thomas D. Brekke
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Lindy A. Henry
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
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16
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Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
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17
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Wang F, Shin J, Shea JM, Yu J, Bošković A, Byron M, Zhu X, Shalek AK, Regev A, Lawrence JB, Torres EM, Zhu LJ, Rando OJ, Bach I. Regulation of X-linked gene expression during early mouse development by Rlim. eLife 2016; 5. [PMID: 27642011 PMCID: PMC5059138 DOI: 10.7554/elife.19127] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/15/2016] [Indexed: 01/22/2023] Open
Abstract
Mammalian X-linked gene expression is highly regulated as female cells contain two and male one X chromosome (X). To adjust the X gene dosage between genders, female mouse preimplantation embryos undergo an imprinted form of X chromosome inactivation (iXCI) that requires both Rlim (also known as Rnf12) and the long non-coding RNA Xist. Moreover, it is thought that gene expression from the single active X is upregulated to correct for bi-allelic autosomal (A) gene expression. We have combined mouse genetics with RNA-seq on single mouse embryos to investigate functions of Rlim on the temporal regulation of iXCI and Xist. Our results reveal crucial roles of Rlim for the maintenance of high Xist RNA levels, Xist clouds and X-silencing in female embryos at blastocyst stages, while initial Xist expression appears Rlim-independent. We find further that X/A upregulation is initiated in early male and female preimplantation embryos. DOI:http://dx.doi.org/10.7554/eLife.19127.001
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - JongDae Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Cell Biology, College of Medicine, Konyang University, Daejeon, Korea
| | - Jeremy M Shea
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Ana Bošković
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Meg Byron
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Xiaochun Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Alex K Shalek
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, United States
| | - Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Lihua J Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
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18
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Perez JD, Rubinstein ND, Dulac C. New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain. Annu Rev Neurosci 2016; 39:347-84. [PMID: 27145912 DOI: 10.1146/annurev-neuro-061010-113708] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian evolution entailed multiple innovations in gene regulation, including the emergence of genomic imprinting, an epigenetic regulation leading to the preferential expression of a gene from its maternal or paternal allele. Genomic imprinting is highly prevalent in the brain, yet, until recently, its central roles in neural processes have not been fully appreciated. Here, we provide a comprehensive survey of adult and developmental brain functions influenced by imprinted genes, from neural development and wiring to synaptic function and plasticity, energy balance, social behaviors, emotions, and cognition. We further review the widespread identification of parental biases alongside monoallelic expression in brain tissues, discuss their potential roles in dosage regulation of key neural pathways, and suggest possible mechanisms underlying the dynamic regulation of imprinting in the brain. This review should help provide a better understanding of the significance of genomic imprinting in the normal and pathological brain of mammals including humans.
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Affiliation(s)
- Julio D Perez
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
| | - Nimrod D Rubinstein
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
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19
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Abstract
The placenta is an ephemeral but critical organ for the survival of all eutherian mammals and marsupials. It is the primary messenger system between the mother and fetus, where communicational signals, nutrients, waste, gases, and extrinsic factors are exchanged. Although the placenta may buffer the fetus from various environmental insults, placental dysfunction might also contribute to detrimental developmental origins of adult health and disease effects. The placenta of one sex over the other might possess greater ability to respond and buffer against environmental insults. Given the potential role of the placenta in effecting the lifetime health of the offspring, it is not surprising that there has been a resurging interest in this organ, including the Human Placental Project launched by the National Institutes of Child Health and Human Development. In this review, we will compare embryological development of the laboratory mouse and human chorioallantoic placentae. Next, evidence that various species, including humans, exhibit normal sex-dependent structural and functional placental differences will be examined followed by how in utero environmental changes (nutritional state, stress, and exposure to environmental chemicals) might interact with fetal sex to affect this organ. Recent data also suggest that paternal state impacts placental function in a sex-dependent manner. The research to date linking placental maladaptive responses and later developmental origins of adult health and disease effects will be explored. Finally, we will focus on how sex chromosomes and epimutations may contribute to sex-dependent differences in placental function, the unanswered questions, and future directions that warrant further consideration.
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Affiliation(s)
- Cheryl S Rosenfeld
- Departments of Bond Life Sciences Center, Biomedical Sciences, Genetics Area Program, and Research Faculty Member for the Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, Missouri 65211
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20
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Lowe R, Gemma C, Rakyan VK, Holland ML. Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development. BMC Genomics 2015; 16:295. [PMID: 25888192 PMCID: PMC4410000 DOI: 10.1186/s12864-015-1506-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/30/2015] [Indexed: 11/23/2022] Open
Abstract
Background As sex determines mammalian development, understanding the nature and developmental dynamics of the sexually dimorphic transcriptome is important. To explore this, we generated 76 genome-wide RNA-seq profiles from mouse eight-cell embryos, late gestation and adult livers, together with 4 ground-state pluripotent embryonic (ES) cell lines from which we generated both RNA-seq and multiple ChIP-seq profiles. We complemented this with previously published data to yield 5 snap-shots of pre-implantation development, late-gestation placenta and somatic tissue and multiple adult tissues for integrative analysis. Results We define a high-confidence sex-dimorphic signature of 69 genes in eight-cell embryos. Sex-chromosome-linked components of this signature are largely conserved throughout pre-implantation development and in ES cells, whilst the autosomal component is more dynamic. Sex-biased gene expression is reflected by enrichment for activating and repressive histone modifications. The eight-cell signature is largely non-overlapping with that defined from fetal liver, neither was it correlated with adult liver or other tissues analysed. The number of sex-dimorphic genes increases throughout development. We identified many more dimorphic genes in adult compared to fetal liver. However, approximately two thirds of the dimorphic genes identified in fetal liver were also dimorphic in adult liver. Sex-biased expression differences unique to adult liver were enriched for growth hormone-responsiveness. Sexually dimorphic gene expression in pre-implantation development is driven by sex-chromosome based transcription, whilst later development is characterised by sex dimorphic autosomal transcription. Conclusion This systematic study identifies three distinct phases of sex dimorphism throughout mouse development, and has significant implications for understanding the developmental origins of sex-specific phenotypes and disease in mammals. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1506-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Lowe
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK.
| | - Carolina Gemma
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK.
| | - Vardhman K Rakyan
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK.
| | - Michelle L Holland
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK.
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21
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The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol 2015; 16:52. [PMID: 25887447 PMCID: PMC4391730 DOI: 10.1186/s13059-015-0618-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, X chromosome genes are present in one copy in males and two in females. To balance the dosage of X-linked gene expression between the sexes, one of the X chromosomes in females is silenced. X inactivation is initiated by upregulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. RESULTS Here, we show a novel role for the lncRNA Firre in anchoring the inactive mouse X chromosome and preserving one of its main epigenetic features, H3K27me3. Similar to Dxz4, Firre is X-linked and expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding sites, and is preferentially located adjacent to the nucleolus. CTCF binding present initially in both male and female mouse embryonic stem cells is lost from the active X during development. Knockdown of Firre disrupts perinucleolar targeting and H3K27me3 levels in mouse fibroblasts, demonstrating a role in maintenance of an important epigenetic feature of the inactive X chromosome. No X-linked gene reactivation is seen after Firre knockdown; however, a compensatory increase in the expression of chromatin modifier genes implicated in X silencing is observed. Further experiments in female embryonic stem cells suggest that Firre does not play a role in X inactivation onset. CONCLUSIONS The X-linked lncRNA Firre helps to position the inactive X chromosome near the nucleolus and to preserve one of its main epigenetic features.
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22
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Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X. Escape from X inactivation varies in mouse tissues. PLoS Genet 2015; 11:e1005079. [PMID: 25785854 PMCID: PMC4364777 DOI: 10.1371/journal.pgen.1005079] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/17/2015] [Indexed: 12/22/2022] Open
Abstract
X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape genes in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a binomial model to assess allelic expression, we demonstrate a continuum between complete silencing and expression from the inactive X (Xi). The validity of the RNA-seq approach was verified using RT-PCR with species-specific primers or Sanger sequencing. Both common escape genes and genes with significant differences in XCI status between tissues were identified. Such genes may be candidates for tissue-specific sex differences. Overall, few genes (3-7%) escape XCI in any of the mouse tissues examined, suggesting stringent silencing and escape controls. In contrast, an in vitro system represented by the embryonic-kidney-derived Patski cell line showed a higher density of escape genes (21%), representing both kidney-specific escape genes and cell-line specific escape genes. Allele-specific RNA polymerase II occupancy and DNase I hypersensitivity at the promoter of genes on the Xi correlated well with levels of escape, consistent with an open chromatin structure at escape genes. Allele-specific CTCF binding on the Xi clustered at escape genes and was denser in brain compared to the Patski cell line, possibly contributing to a more compartmentalized structure of the Xi and fewer escape genes in brain compared to the cell line where larger domains of escape were observed.
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Affiliation(s)
- Joel B. Berletch
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Wenxiu Ma
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Fan Yang
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christine M. Disteche
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Xinxian Deng
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
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23
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Gregg C. Known unknowns for allele-specific expression and genomic imprinting effects. F1000PRIME REPORTS 2014; 6:75. [PMID: 25343032 PMCID: PMC4166941 DOI: 10.12703/p6-75] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent studies have provided evidence for non-canonical imprinting effects that are associated with allele-specific expression biases at the tissue level in mice. These imprinting effects have features that are distinct from canonical imprinting effects that involve allele silencing. Here, I discuss some of the evidence for non-canonical imprinting effects in the context of random X-inactivation and epigenetic allele-specific expression effects on the autosomes. I propose several mechanisms that may underlie non-canonical imprinting effects and outline future directions and approaches to study these effects at the cellular level in vivo. The growing evidence for complex allele-specific expression effects that are cell- and developmental stage-specific has opened a new frontier for study. Currently, the function of these effects and the underlying regulatory mechanisms are largely unknown.
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Affiliation(s)
- Christopher Gregg
- Department of Neurobiology & Anatomy and Human Genetics, University of Utah School of Medicine, 323 Wintrobe Bldg 530, University of Utah, School of Medicine20 North 1900 East, Salt Lake City, UT 84132-3401USA
- The New York Stem Cell Foundation178 Columbus Avenue #237064, New York, NY 10023USA
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