1
|
Kubasova N, Alves-Pereira CF, Gupta S, Vinogradova S, Gimelbrant A, Barreto VM. In Vivo Clonal Analysis Reveals Random Monoallelic Expression in Lymphocytes That Traces Back to Hematopoietic Stem Cells. Front Cell Dev Biol 2022; 10:827774. [PMID: 36003148 PMCID: PMC9393635 DOI: 10.3389/fcell.2022.827774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Evaluating the epigenetic landscape in the stem cell compartment at the single-cell level is essential to assess the cells’ heterogeneity and predict their fate. Here, using a genome-wide transcriptomics approach in vivo, we evaluated the allelic expression imbalance in the progeny of single hematopoietic cells (HSCs) as a read-out of epigenetic marking. After 4 months of extensive proliferation and differentiation, we found that X-chromosome inactivation (XCI) is tightly maintained in all single-HSC derived hematopoietic cells. In contrast, the vast majority of the autosomal genes did not show clonal patterns of random monoallelic expression (RME). However, a persistent allele-specific autosomal transcription in HSCs and their progeny was found in a rare number of cases, none of which has been previously reported. These data show that: 1) XCI and RME in the autosomal chromosomes are driven by different mechanisms; 2) the previously reported high frequency of genes under RME in clones expanded in vitro (up to 15%) is not found in clones undergoing multiple differentiation steps in vivo; 3) prior to differentiation, HSCs have stable patterns of autosomal RME. We propose that most RME patterns in autosomal chromosomes are erased and established de novo during cell lineage differentiation.
Collapse
Affiliation(s)
- Nadiya Kubasova
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- Genetagus, Egas Moniz – Cooperativa de Ensino Superior, CRL, Monte de Caparica, Portugal
| | - Clara F. Alves-Pereira
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Saumya Gupta
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Svetlana Vinogradova
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Alexander Gimelbrant
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
| | - Vasco M. Barreto
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Costa da Caparica, Portugal
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
| |
Collapse
|
2
|
Sun KY, Oreper D, Schoenrock SA, McMullan R, Giusti-Rodríguez P, Zhabotynsky V, Miller DR, Tarantino LM, Pardo-Manuel de Villena F, Valdar W. Bayesian modeling of skewed X inactivation in genetically diverse mice identifies a novel Xce allele associated with copy number changes. Genetics 2021; 218:6162162. [PMID: 33693696 DOI: 10.1093/genetics/iyab034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Female mammals are functional mosaics of their parental X-linked gene expression due to X chromosome inactivation (XCI). This process inactivates one copy of the X chromosome in each cell during embryogenesis and that state is maintained clonally through mitosis. In mice, the choice of which parental X chromosome remains active is determined by the X chromosome controlling element (Xce), which has been mapped to a 176-kb candidate interval. A series of functional Xce alleles has been characterized or inferred for classical inbred strains based on biased, or skewed, inactivation of the parental X chromosomes in crosses between strains. To further explore the function structure basis and location of the Xce, we measured allele-specific expression of X-linked genes in a large population of F1 females generated from Collaborative Cross (CC) strains. Using published sequence data and applying a Bayesian "Pólya urn" model of XCI skew, we report two major findings. First, inter-individual variability in XCI suggests mouse epiblasts contain on average 20-30 cells contributing to brain. Second, CC founder strain NOD/ShiLtJ has a novel and unique functional allele, Xceg, that is the weakest in the Xce allelic series. Despite phylogenetic analysis confirming that NOD/ShiLtJ carries a haplotype almost identical to the well-characterized C57BL/6J (Xceb), we observed unexpected patterns of XCI skewing in females carrying the NOD/ShiLtJ haplotype within the Xce. Copy number variation is common at the Xce locus and we conclude that the observed allelic series is a product of independent and recurring duplications shared between weak Xce alleles.
Collapse
Affiliation(s)
- Kathie Y Sun
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Computational Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel Oreper
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Computational Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Neuroscience Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel McMullan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Genetics and Molecular Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paola Giusti-Rodríguez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vasyl Zhabotynsky
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa M Tarantino
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
3
|
Lyu C, Shen J, Zhang J, Xue F, Liu X, Liu W, Fu R, Zhang L, Li H, Zhang D, Zhang X, Cheng T, Yang R, Zhang L. The State of Skewed X Chromosome Inactivation is Retained in the Induced Pluripotent Stem Cells from a Female with Hemophilia B. Stem Cells Dev 2017; 26:1003-1011. [PMID: 28401797 DOI: 10.1089/scd.2016.0323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Skewed X chromosome inactivation (XCI) is a rare reason for hemophilia B in females. It is indefinite whether X chromosome reactivation (XCR) would occur when cells of hemophilia B patients with skewed XCI were reprogrammed into induced pluripotent stem cells (iPSCs). In this study, we investigated a female hemophilia B patient with a known F9 gene mutation: c.676C>T, p.Arg226Trp. We demonstrated that skewed XCI was the pathogenesis of the patient, and we successfully generated numerous iPSC colonies of the patient from peripheral blood mononuclear cells (PBMNCs), which was the first time for generating hemophilia-specific iPSCs from PBMNCs. Then we detected the XCI state of these iPSCs. Ninety-two iPSC lines were picked for XCI analysis. All of them retained an inactive X chromosome, which could be proved by amplification of the androgen receptor gene and XIST (X inactivation-specific transcript), expression of H3K27me3, and existence of XIST clouds in XIST RNA fluorescence in situ hybridization (FISH) analysis. We attempted to obtain iPSC lines with the wild-type F9 gene on the active X chromosome for further disease treatment. But it turned out that the patient's iPSCs were still skewed such as the somatic cells with 92 iPSC lines having mutant F9 on the active X chromosome. In conclusion, skewed XCI is one reason for hemophilia in females. PBMNCs are excellent somatic cell resources for hemophilia patients to do reprogramming. More attentions should be paid to generate naive iPSCs with two active X chromosomes for further clinical disease treatment. The state of skewed XCI is retained in the iPSCs from a female with hemophilia B.
Collapse
Affiliation(s)
- Cuicui Lyu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China .,2 Department of Hematology, The First Central Hospital of Tianjin , Tianjin, China
| | - Jun Shen
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jianping Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Feng Xue
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaofan Liu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Wei Liu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Rongfeng Fu
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Liyan Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huiyuan Li
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Donglei Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaobing Zhang
- 3 Division of Regenerative Medicine MC1528B, Department of Medicine, Loma Linda University , Loma Linda, California
| | - Tao Cheng
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Renchi Yang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lei Zhang
- 1 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital , Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| |
Collapse
|
4
|
Have humans lost control: The elusive X-controlling element. Semin Cell Dev Biol 2016; 56:71-77. [DOI: 10.1016/j.semcdb.2016.01.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 02/01/2023]
|
5
|
Dandulakis MG, Meganathan K, Kroll KL, Bonni A, Constantino JN. Complexities of X chromosome inactivation status in female human induced pluripotent stem cells-a brief review and scientific update for autism research. J Neurodev Disord 2016; 8:22. [PMID: 27303449 PMCID: PMC4907282 DOI: 10.1186/s11689-016-9155-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/20/2016] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) allow researchers to make customized patient-derived cell lines by reprogramming noninvasively retrieved somatic cells. These cell lines have the potential to faithfully represent an individual’s genetic background; therefore, in the absence of available human brain tissue from a living patient, these models have a significant advantage relative to other models of neurodevelopmental disease. When using human induced pluripotent stem cells (hiPSCs) to model X-linked developmental disorders or inherited conditions that undergo sex-specific modulation of penetrance (e.g., autism spectrum disorders), there are significant complexities in the course and status of X chromosome inactivation (XCI) that are crucial to consider in establishing the validity of cellular models. There are major gaps and inconsistencies in the existing literature regarding XCI status during the derivation and maintenance of hiPSCs and their differentiation into neurons. Here, we briefly describe the importance of the problem, review the findings and inconsistencies of the existing literature, delineate options for specifying XCI status in clonal populations, and develop recommendations for future studies.
Collapse
Affiliation(s)
- Mary G Dandulakis
- School of Medicine, Washington University in St. Louis, St. Louis, USA
| | - Kesavan Meganathan
- Department of Developmental Biology, Washington University in St. Louis, Campus Box 8103, 660 S. Euclid Ave., St. Louis, MO 63110-1093 USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University in St. Louis, Campus Box 8103, 660 S. Euclid Ave., St. Louis, MO 63110-1093 USA
| | - Azad Bonni
- Department of Neuroscience, Washington University in St. Louis, Campus Box 8108, 660 S. Euclid Ave., St. Louis, MO 63110-1093 USA
| | - John N Constantino
- Department of Psychiatry, Washington University in St. Louis, Campus Box 8134, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| |
Collapse
|
6
|
Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
Collapse
Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
| |
Collapse
|
7
|
Vacca M, Della Ragione F, Scalabrì F, D'Esposito M. X inactivation and reactivation in X-linked diseases. Semin Cell Dev Biol 2016; 56:78-87. [PMID: 26994527 DOI: 10.1016/j.semcdb.2016.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/22/2022]
Abstract
X chromosome inactivation (XCI) is the phenomenon by which mammals compensate for dosage of X-linked genes in females (XX) versus males (XY). XCI patterns can be random or show extreme skewing, and can modify the mode of inheritance of X-driven phenotypes, which contributes to the variability of human pathologies. Recent findings have shown reversibility of the XCI process, which has opened new avenues in the approaches used for the treatment of X-linked diseases.
Collapse
Affiliation(s)
- Marcella Vacca
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy.
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| |
Collapse
|
8
|
Fahim AT, Daiger SP. The Role of X-Chromosome Inactivation in Retinal Development and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 854:325-31. [PMID: 26427428 DOI: 10.1007/978-3-319-17121-0_43] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The expression of X-linked genes is equalized between males and females in mammalian species through X-Chromosome inactivation (XCI). Every cell in a female mammalian embryo randomly chooses one X Chromosome for epigenetic silencing at the 8-16 cell stage, resulting in a Gaussian distribution of XCI ratios with a peak at 50:50. At the tail extremes of this distribution, X-linked recessive mutations can manifest in disease in female carriers if the mutant allele is disproportionately active. The role of XCI skewing, if any, in X-linked retinal disease is still unknown, although many have speculated that such skewing accounts for phenotypic variation in female carriers of X-linked retinitis pigmentosa (XlRP). Some investigators have used clinical findings such as tapetal-like reflex, pigmentary changes, and multifocal ERG parameters to approximate XCI patches in the retina. These studies are limited by small cohorts and the relative inaccessibility of retinal tissue for genetic and epigenetic analysis. Although blood has been used as a proxy for other tissues in determining XCI ratios, blood XCI skews with age out of proportion to other tissues and may not accurately reflect retinal XCI ratios. Future investigations in determining retinal XCI ratios and the contribution of XCI to phenotype could potentially impact prognosis for female carriers of X-linked retinal disease.
Collapse
Affiliation(s)
- Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, University of Michigan, Kellogg Eye Center, 1000 Wall Street, 48105, Ann Arbor, MI, USA.
| | - Stephen P Daiger
- School of Public Health, University of Texas Health Science Center, 1200 Herman Pressler Drive, RAS W-522, 77030, Houston, TX, USA.
| |
Collapse
|
9
|
Bonthuis PJ, Huang WC, Stacher Hörndli CN, Ferris E, Cheng T, Gregg C. Noncanonical Genomic Imprinting Effects in Offspring. Cell Rep 2015; 12:979-91. [PMID: 26235621 DOI: 10.1016/j.celrep.2015.07.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 06/19/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022] Open
Abstract
Here, we describe an RNA-sequencing (RNA-seq)-based approach that accurately detects even modest maternal or paternal allele expression biases at the tissue level, which we call noncanonical genomic imprinting effects. We profile imprinting in the arcuate nucleus (ARN) and dorsal raphe nucleus of the female mouse brain as well as skeletal muscle (mesodermal) and liver (endodermal). Our study uncovers hundreds of noncanonical autosomal and X-linked imprinting effects. Noncanonical imprinting is highly tissue-specific and enriched in the ARN, but rare in the liver. These effects are reproducible across different genetic backgrounds and associated with allele-specific chromatin. Using in situ hybridization for nascent RNAs, we discover that autosomal noncanonical imprinted genes with a tissue-level allele bias exhibit allele-specific expression effects in subpopulations of neurons in the brain in vivo. We define noncanonical imprinted genes that regulate monoamine signaling and determine that these effects influence the impact of inherited mutations on offspring behavior.
Collapse
Affiliation(s)
- Paul J Bonthuis
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| | - Wei-Chao Huang
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| | - Cornelia N Stacher Hörndli
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| | - Elliott Ferris
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| | - Tong Cheng
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA
| | - Christopher Gregg
- Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132-3401, USA.
| |
Collapse
|
10
|
Predazzi IM, Sobota RS, Sanna S, Bush WS, Bartlett J, Lilley JS, Linton MF, Schlessinger D, Cucca F, Fazio S, Williams SM. Sex-Specific Parental Effects on Offspring Lipid Levels. J Am Heart Assoc 2015; 4:JAHA.115.001951. [PMID: 26126546 PMCID: PMC4608079 DOI: 10.1161/jaha.115.001951] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Plasma lipid levels are highly heritable traits, but known genetic loci can only explain a small portion of their heritability. Methods and Results In this study, we analyzed the role of parental levels of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TGs) in explaining the values of the corresponding traits in adult offspring. We also evaluated the contribution of nongenetic factors that influence lipid traits (age, body mass index, smoking, medications, and menopause) alone and in combination with variability at the genetic loci known to associate with TC, LDL-C, HDL-C, and TG levels. We performed comparisons among different sex-specific regression models in 416 families from the Framingham Heart Study and 304 from the SardiNIA cohort. Models including parental lipid levels explain significantly more of the trait variation than models without these measures, explaining up to ≈39% of the total trait variation. Of this variation, the parent-of-origin effect explains as much as ≈15% and it does so in a sex-specific way. This observation is not owing to shared environment, given that spouse-pair correlations were negligible (<1.5% explained variation in all cases) and is distinct from previous genetic and acquired factors that are known to influence serum lipid levels. Conclusions These findings support the concept that unknown genetic and epigenetic contributors are responsible for most of the heritable component of the plasma lipid phenotype, and that, at present, the clinical utility of knowing age-matched parental lipid levels in assessing risk of dyslipidemia supersedes individual locus effects. Our results support the clinical utility of knowing parental lipid levels in assessing future risk of dyslipidemia.
Collapse
Affiliation(s)
- Irene M Predazzi
- Atherosclerosis Research Unit, Departments of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN (I.M.P., J.S.L., M.R.F.L., S.F.) Knight Cardiovascular Institute, Center for Preventive Cardiology, Oregon Health and Science University, Portland, OR (I.M.P., S.F.)
| | - Rafal S Sobota
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN (R.S.S., W.S.B.) Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH (R.S.S., J.B., S.M.W.)
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy (S.S., F.C.)
| | - William S Bush
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN (R.S.S., W.S.B.) Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH (W.S.B.)
| | - Jacquelaine Bartlett
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH (R.S.S., J.B., S.M.W.)
| | - Jessica S Lilley
- Atherosclerosis Research Unit, Departments of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN (I.M.P., J.S.L., M.R.F.L., S.F.) Division of Endocrinology, Department of Pediatrics, University of Mississippi School of Medicine, Jackson, MS (J.S.L.)
| | - MacRae F Linton
- Atherosclerosis Research Unit, Departments of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN (I.M.P., J.S.L., M.R.F.L., S.F.)
| | | | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy (S.S., F.C.)
| | - Sergio Fazio
- Atherosclerosis Research Unit, Departments of Medicine and Pharmacology, Vanderbilt University Medical Center, Nashville, TN (I.M.P., J.S.L., M.R.F.L., S.F.) Knight Cardiovascular Institute, Center for Preventive Cardiology, Oregon Health and Science University, Portland, OR (I.M.P., S.F.)
| | - Scott M Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH (R.S.S., J.B., S.M.W.)
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Genetic architecture of skewed X inactivation in the laboratory mouse. PLoS Genet 2013; 9:e1003853. [PMID: 24098153 PMCID: PMC3789830 DOI: 10.1371/journal.pgen.1003853] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 08/19/2013] [Indexed: 11/19/2022] Open
Abstract
X chromosome inactivation (XCI) is the mammalian mechanism of dosage compensation that balances X-linked gene expression between the sexes. Early during female development, each cell of the embryo proper independently inactivates one of its two parental X-chromosomes. In mice, the choice of which X chromosome is inactivated is affected by the genotype of a cis-acting locus, the X-chromosome controlling element (Xce). Xce has been localized to a 1.9 Mb interval within the X-inactivation center (Xic), yet its molecular identity and mechanism of action remain unknown. We combined genotype and sequence data for mouse stocks with detailed phenotyping of ten inbred strains and with the development of a statistical model that incorporates phenotyping data from multiple sources to disentangle sources of XCI phenotypic variance in natural female populations on X inactivation. We have reduced the Xce candidate 10-fold to a 176 kb region located approximately 500 kb proximal to Xist. We propose that structural variation in this interval explains the presence of multiple functional Xce alleles in the genus Mus. We have identified a new allele, Xcee present in Mus musculus and a possible sixth functional allele in Mus spicilegus. We have also confirmed a parent-of-origin effect on X inactivation choice and provide evidence that maternal inheritance magnifies the skewing associated with strong Xce alleles. Based on the phylogenetic analysis of 155 laboratory strains and wild mice we conclude that Xcea is either a derived allele that arose concurrently with the domestication of fancy mice but prior the derivation of most classical inbred strains or a rare allele in the wild. Furthermore, we have found that despite the presence of multiple haplotypes in the wild Mus musculus domesticus has only one functional Xce allele, Xceb. Lastly, we conclude that each mouse taxa examined has a different functional Xce allele. Although mammalian females have two X chromosomes in each cell, only one is functional, while gene expression from the other is silenced through a process called X chromosome inactivation. Little is known about the early stages of this process including how one parental X chromosome is inactivated over the other on a cell-by-cell basis. It has been shown, however, that certain inbred mouse strains are functionally different at a locus that controls this choice that provides an opportunity to identify the locus and determine its molecular mechanism. This has been the goal of many researchers over the past 40 years with incremental success. Here we took advantage of new mouse genotype and whole genome sequencing data to pinpoint the locus controlling choice. Our results identified a smaller region on the X chromosome that contains large duplicated sequences. We propose an explanation for multiple functional alleles in mouse and provide insight into the possible molecular mechanism of X chromosome inactivation choice. Our evolutionary analysis reveals why functional diversity at this locus appears to be common in laboratory mice and offers an explanation as to why we do not see this level of diversity in humans.
Collapse
|
13
|
Savova V, Vigneau S, Gimelbrant AA. Autosomal monoallelic expression: genetics of epigenetic diversity? Curr Opin Genet Dev 2013; 23:642-8. [PMID: 24075575 DOI: 10.1016/j.gde.2013.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 11/17/2022]
Abstract
In mammals, relative expression of the two parental alleles of many genes is controlled by one of three major epigenetic phenomena: X chromosome inactivation, imprinting, and mitotically stable autosomal monoallelic expression (MAE). MAE affects a large fraction of human autosomal genes and introduces enormous epigenetic heterogeneity in otherwise similar cell populations. Despite its prevalence, many functional and mechanistic aspects of MAE biology remain unknown. Several lines of evidence imply that MAE establishment and maintenance are controlled by a variety of genetic elements. Based on known genomic features regulating X-inactivation and imprinting, we outline likely features of MAE-controlling elements. We also assess implications of MAE for genotype-phenotype relationship, with a focus on haploinsufficiency.
Collapse
Affiliation(s)
- Virginia Savova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Genetics, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, United States
| | | | | |
Collapse
|
14
|
An ex vivo model for imprinting: mutually exclusive binding of Cdx2 and Oct4 as a switch for imprinted and random X-inactivation. Genetics 2012; 192:857-68. [PMID: 22942124 DOI: 10.1534/genetics.112.144121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the early mammalian embryo, X chromosome inactivation (XCI) achieves dosage parity between males and females for X-linked genes. During mouse development, imprinted paternal XCI is observed first and switches to random XCI in the epiblast but not placental lineages. The mechanism by which this epigenetic switch occurs is currently unknown. Here, we establish an ex vivo model for imprinting and identify a novel trans-acting regulatory factor for imprinted XCI. Using an induced trophoblast stem cell (iTS) model, we show that embryonic stem (ES) cells transdifferentiated into trophoblasts retain partial memory of the XCI imprint. Cdx2, a stem cell factor that determines commitment to the extraembryonic lineage, directly binds Xist and activates expression of Xist RNA in extrembryonic cells. Cdx2 competes with Oct4, a stem cell factor that determines commitment to the embryonic lineage, for overlapping binding sites within Xist. We propose that mutually exclusive binding between Cdx2 and Oct4 in Xist underlies the switch between imprinted and random XCI in the early mouse embryo.
Collapse
|
15
|
Nonrandom X chromosome inactivation is influenced by multiple regions on the murine X chromosome. Genetics 2012; 192:1095-107. [PMID: 22887817 DOI: 10.1534/genetics.112.144477] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
During the development of female mammals, one of the two X chromosomes is inactivated, serving as a dosage-compensation mechanism to equalize the expression of X-linked genes in females and males. While the choice of which X chromosome to inactivate is normally random, X chromosome inactivation can be skewed in F1 hybrid mice, as determined by alleles at the X chromosome controlling element (Xce), a locus defined genetically by Cattanach over 40 years ago. Four Xce alleles have been defined in inbred mice in order of the tendency of the X chromosome to remain active: Xce(a) < Xce(b) < Xce(c) < Xce(d). While the identity of the Xce locus remains unknown, previous efforts to map sequences responsible for the Xce effect in hybrid mice have localized the Xce to candidate regions that overlap the X chromosome inactivation center (Xic), which includes the Xist and Tsix genes. Here, we have intercrossed 129S1/SvImJ, which carries the Xce(a) allele, and Mus musculus castaneus EiJ, which carries the Xce(c) allele, to generate recombinant lines with single or double recombinant breakpoints near or within the Xce candidate region. In female progeny of 129S1/SvImJ females mated to recombinant males, we have measured the X chromosome inactivation ratio using allele-specific expression assays of genes on the X chromosome. We have identified regions, both proximal and distal to Xist/Tsix, that contribute to the choice of which X chromosome to inactivate, indicating that multiple elements on the X chromosome contribute to the Xce.
Collapse
|
16
|
Abstract
Chromosomes acquire different epigenetic marks during oogenesis and spermatogenesis. After fertilization, if retained and selected, these differences may result in imprinting effects. Rather than being an oddity, imprinting effects have been found in many sexually reproducing organisms. Interestingly, imprinting can result in disparate effects under different selective forces. At the same time, epigenetic mechanisms and selective pressures shared by sexually reproducing organisms could underlie common imprinting effects. Large-scale studies are revealing that parent-of-origin effects are more common than previously thought and supporting the important contribution of imprinting to many traits and diseases.
Collapse
|
17
|
Orischenko KE, Elisaphenko EA, Zakian SM. Role of G(-43)A polymorphism in the promoter region of the Xist gene in non-random x-chromosome inactivation in intraspecific hybrid voles. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410100224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Gregg C, Zhang J, Butler JE, Haig D, Dulac C. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 2010; 329:682-5. [PMID: 20616234 PMCID: PMC2997643 DOI: 10.1126/science.1190831] [Citation(s) in RCA: 282] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genomic imprinting results in preferential gene expression from paternally versus maternally inherited chromosomes. We used a genome-wide approach to uncover sex-specific parent-of-origin allelic effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Moreover, analysis of the cortex and hypothalamus identified 347 autosomal genes with sex-specific imprinting features. In the hypothalamus, sex-specific imprinted genes were mostly found in females, which suggests parental influence over the hypothalamic function of daughters. We show that interleukin-18, a gene linked to diseases with sex-specific prevalence, is subject to complex, regional, and sex-specific parental effects in the brain. Parent-of-origin effects thus provide new avenues for investigation of sexual dimorphism in brain function and disease.
Collapse
Affiliation(s)
- Christopher Gregg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jiangwen Zhang
- FAS Research Computing, Harvard University, Cambridge, MA 02138, USA
| | - James E. Butler
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
19
|
Wang X, Soloway PD, Clark AG. Paternally biased X inactivation in mouse neonatal brain. Genome Biol 2010; 11:R79. [PMID: 20663224 PMCID: PMC2926790 DOI: 10.1186/gb-2010-11-7-r79] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 05/10/2010] [Accepted: 07/27/2010] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND X inactivation in female eutherian mammals has long been considered to occur at random in embryonic and postnatal tissues. Methods for scoring allele-specific differential expression with a high degree of accuracy have recently motivated a quantitative reassessment of the randomness of X inactivation. RESULTS After RNA-seq data revealed what appeared to be a chromosome-wide bias toward under-expression of paternal alleles in mouse tissue, we applied pyrosequencing to mouse brain cDNA samples from reciprocal cross F1 progeny of divergent strains and found a small but consistent and highly statistically significant excess tendency to under-express the paternal X chromosome. CONCLUSIONS The bias toward paternal X inactivation is reminiscent of marsupials (and extraembryonic tissues in eutherians), suggesting that there may be retained an evolutionarily conserved epigenetic mark driving the bias. Allelic bias in expression is also influenced by the sampling effect of X inactivation and by cis-acting regulatory variation (eQTL), and for each gene we quantify the contributions of these effects in two different mouse strain combinations while controlling for variability in Xce alleles. In addition, we propose an efficient method to identify and confirm genes that escape X inactivation in normal mice by directly comparing the allele-specific expression ratio profile of multiple X-linked genes in multiple individuals.
Collapse
Affiliation(s)
- Xu Wang
- Deptartment of Molecular Biology and Genetics, Cornell University, 227 Biotechnology Building, Ithaca, NY 14853, USA
- Cornell Center for Comparative and Population Genomics, 130 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Paul D Soloway
- Division of Nutritional Sciences, College of Agriculture and Life Sciences, 211 Weill Hall, Cornell University, Ithaca, NY 14853, USA
| | - Andrew G Clark
- Deptartment of Molecular Biology and Genetics, Cornell University, 227 Biotechnology Building, Ithaca, NY 14853, USA
- Cornell Center for Comparative and Population Genomics, 130 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
20
|
X-inactivation analysis of embryonic lethality in Ocrl wt/-; Inpp5b-/- mice. Mamm Genome 2010; 21:186-94. [PMID: 20195868 PMCID: PMC2844970 DOI: 10.1007/s00335-010-9255-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 02/04/2010] [Indexed: 10/25/2022]
Abstract
Mutations in the human OCRL gene, which encodes a phosphatidylinositol(4,5)bisphosphate 5-phosphatase, result in the X-linked oculocerebrorenal syndrome of Lowe. Mice with a targeted disruption of Ocrl have no phenotypic abnormalities. Targeted disruption of its closest paralog, Inpp5b, causes male infertility in the 129S6 background. Mice with disruptions of both genes are lost in utero prior to 9.5-10.5 dpc, indicating that there is a functional overlap between the two paralogs early in development. We analyzed the pattern of X-inactivation in four tissues of distinct embryonic origin from Ocrl (wt/-);Inpp5b (-/-) females to explore the timing and tissue distribution of the functional overlap. X-inactivation was strongly skewed against the disrupted Ocrl (-) allele being on the active X chromosome in all four tissues tested, indicating that there is early selection against cell lineages lacking both Ocrl and Inpp5b. Extraembryonic tissue was also involved in the lethality because there were never any live-born Ocrl (wt/-);Inpp5b (-/-) females when the functional Ocrl (wt ) allele was on the paternal X chromosome, which is preferentially inactivated in trophoblast-derived extraembryonic tissues. Live-born Ocrl (wt/-);Inpp5b (-/-) females were found when the functional Ocrl (wt) allele was maternal, although in fewer numbers than expected. The importance of the extraembryonic tissues in the early embryonic lethality of embryos lacking both Ocrl and Inpp5b is reinforced by the successful isolation of a viable 40,XX Ocrl (-/-);Inpp5b (-/-) embryonic stem cell from the inner cell mass of a 3.5-dpc blastocyst prior to implantation. These results indicate a functional overlap of Ocrl and Inpp5b in most cell lineages, especially in extraembryonic tissues.
Collapse
|
21
|
Muers MR, Sharpe JA, Garrick D, Sloane-Stanley J, Nolan PM, Hacker T, Wood WG, Higgs DR, Gibbons RJ. Defining the cause of skewed X-chromosome inactivation in X-linked mental retardation by use of a mouse model. Am J Hum Genet 2007; 80:1138-49. [PMID: 17503331 PMCID: PMC1867101 DOI: 10.1086/518369] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/22/2007] [Indexed: 11/03/2022] Open
Abstract
Extreme skewing of X-chromosome inactivation (XCI) is rare in the normal female population but is observed frequently in carriers of some X-linked mutations. Recently, it has been shown that various forms of X-linked mental retardation (XLMR) have a strong association with skewed XCI in female carriers, but the mechanisms underlying this skewing are unknown. ATR-X syndrome, caused by mutations in a ubiquitously expressed, chromatin-associated protein, provides a clear example of XLMR in which phenotypically normal female carriers virtually all have highly skewed XCI biased against the X chromosome that harbors the mutant allele. Here, we have used a mouse model to understand the processes causing skewed XCI. In female mice heterozygous for a null Atrx allele, we found that XCI is balanced early in embryogenesis but becomes skewed over the course of development, because of selection favoring cells expressing the wild-type Atrx allele. Unexpectedly, selection does not appear to be the result of general cellular-viability defects in Atrx-deficient cells, since it is restricted to specific stages of development and is not ongoing throughout the life of the animal. Instead, there is evidence that selection results from independent tissue-specific effects. This illustrates an important mechanism by which skewed XCI may occur in carriers of XLMR and provides insight into the normal role of ATRX in regulating cell fate.
Collapse
Affiliation(s)
- Mary R Muers
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Renault NK, Dyack S, Dobson MJ, Costa T, Lam WL, Greer WL. Heritable skewed X-chromosome inactivation leads to haemophilia A expression in heterozygous females. Eur J Hum Genet 2007; 15:628-37. [PMID: 17342157 DOI: 10.1038/sj.ejhg.5201799] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Factor VIII gene, F8, mutations cause haemophilia A (HA), an X-linked recessive disorder. Expression in heterozygous females has been ascribed to skewed X-chromosome inactivation (XCI). To investigate the cause of HA in three heterozygous females within an Atlantic Canadian kindred, the proband (severely affected girl, FVIII activity: 2%) and 17 relatives across three generations were studied. F8 genotype, FVIII activity, XCI ratio (XCIR) (paternal active X: maternal active X), karyotype, submegabase resolution tiling set array competitive genome hybridization (competitive genomic hybridization (SMRT)), and microsatellite analyses were utilized. A positive linear relationship between FVIII activity and percentage-activated normal X-chromosome was found in HA heterozygous females (R(2)=0.87). All affected, but no unaffected females, had an XCIR skewed toward activation of the mutant X-chromosome (proband 92:8, SD 2). Unexpectedly, high numbers of females have dramatically skewed XCIRs (>80:20 or <20:80) (P<0.05). The distribution of XCIR frequencies within this family was significantly different than predicted by normal population data or models of random XCI (P<0.025), with more females having higher degrees of skewing. Known causes of skewing, such as chromosomal abnormalities, selection against deleterious alleles, and X-inactive-specific transcript mutations, are not consistent with our results. This study shows that FVIII activity in HA heterozygous females can be directly related to XCI skewing, and that low FVIII activity in females in this family is due to unfavourable XCI skewing. Further, the findings suggest that these XCI ratios are genetically influenced, consistent with a novel heritable human X controlling element (XCE) functioning similarly to the mouse Xce.
Collapse
Affiliation(s)
- Nisa K Renault
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | | | | | | |
Collapse
|
23
|
Amos-Landgraf JM, Cottle A, Plenge RM, Friez M, Schwartz CE, Longshore J, Willard HF. X chromosome-inactivation patterns of 1,005 phenotypically unaffected females. Am J Hum Genet 2006; 79:493-9. [PMID: 16909387 PMCID: PMC1559535 DOI: 10.1086/507565] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 07/05/2006] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is widely believed to be random in early female development and to result in a mosaic distribution of cells, approximately half with the paternally derived X chromosome inactive and half with the maternally derived X chromosome inactive. Significant departures from such a random pattern are hallmarks of a variety of clinical states, including being carriers for severe X-linked diseases or X-chromosome cytogenetic abnormalities. To evaluate the significance of skewed patterns of X inactivation, we examined patterns of X inactivation in a population of >1,000 phenotypically unaffected females. The data demonstrate that only a very small proportion of unaffected females show significantly skewed inactivation, especially during the neonatal period. By comparison with this data set, the degree of skewed inactivation in a given individual can now be quantified and evaluated for its potential clinical significance.
Collapse
|
24
|
Chadwick LH, Pertz LM, Broman KW, Bartolomei MS, Willard HF. Genetic control of X chromosome inactivation in mice: definition of the Xce candidate interval. Genetics 2006; 173:2103-10. [PMID: 16582439 PMCID: PMC1569705 DOI: 10.1534/genetics.105.054882] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Accepted: 03/30/2006] [Indexed: 12/29/2022] Open
Abstract
In early mammalian development, one of the two X chromosomes is silenced in each female cell as a result of X chromosome inactivation, the mammalian dosage compensation mechanism. In the mouse epiblast, the choice of which chromosome is inactivated is essentially random, but can be biased by alleles at the X-linked X controlling element (Xce). Although this locus was first described nearly four decades ago, the identity and precise genomic localization of Xce remains elusive. Within the X inactivation center region of the X chromosome, previous linkage disequilibrium studies comparing strains of known Xce genotypes have suggested that Xce is physically distinct from Xist, although this has not yet been established by genetic mapping or progeny testing. In this report, we used quantitative trait locus (QTL) mapping strategies to define the minimal Xce candidate interval. Subsequent analysis of recombinant chromosomes allowed for the establishment of a maximum 1.85-Mb candidate region for the Xce locus. Finally, we use QTL approaches in an effort to identify additional modifiers of the X chromosome choice, as we have previously demonstrated that choice in Xce heterozygous females is significantly influenced by genetic variation present on autosomes (Chadwick and Willard 2005). We did not identify any autosomal loci with significant associations and thus show conclusively that Xce is the only major locus to influence X inactivation patterns in the crosses analyzed. This study provides a foundation for future analyses into the genetic control of X chromosome inactivation and defines a 1.85-Mb interval encompassing all the major elements of the Xce locus.
Collapse
|
25
|
Thorvaldsen JL, Verona RI, Bartolomei MS. X-tra! X-tra! News from the mouse X chromosome. Dev Biol 2006; 298:344-53. [PMID: 16916508 DOI: 10.1016/j.ydbio.2006.07.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/05/2006] [Accepted: 07/11/2006] [Indexed: 11/29/2022]
Abstract
X chromosome inactivation (XCI) is the phenomenon through which one of the two X chromosomes in female mammals is silenced to achieve dosage compensation with males. XCI is a highly complex, tightly controlled and developmentally regulated process. The mouse undergoes two forms of XCI: imprinted, which occurs in all cells of the preimplantation embryo and in the extraembryonic lineage, and random, which occurs in somatic cells after implantation. This review presents results and hypotheses that have recently been proposed concerning important aspects of both imprinted and random XCI in mice. We focus on how imprinted XCI occurs during preimplantation development, including a brief discussion of the debate as to when silencing initiates. We also discuss regulation of random XCI, focusing on the requirement for Tsix antisense transcription through the Xist locus, on the regulation of Xist chromatin structure by Tsix and on the effect of Tsix regulatory elements on choice and counting. Finally, we review exciting new data revealing that X chromosomes co-localize during random XCI. To conclude, we highlight other aspects of X-linked gene regulation that make it a suitable model for epigenetics at work.
Collapse
Affiliation(s)
- Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | | |
Collapse
|
26
|
Clerc P, Avner P. Random X-chromosome inactivation: skewing lessons for mice and men. Curr Opin Genet Dev 2006; 16:246-53. [PMID: 16647851 DOI: 10.1016/j.gde.2006.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
The mammalian X-chromosome exists in two flavors, active and inactive, in each cell of the adult female. This phenomenon originates from the process of random choice occurring early in development in a small number of progenitor cells in which the decision is made to inactivate either one or the other X chromosome on a cell-autonomous basis. Once made, this initial decision is irreversible, although exceptions exist in specific chromosomal territories and cell lineages. Recent findings implicate various factors, including non-coding RNAs and chromatin modification complexes, as effectors in the initiation and maintenance of X-chromosome inactivation. The functional redundancy of such factors almost certainly plays an important role in the stability of the inactive X. Studying skewing or bias opens an important opportunity for understanding facets of the random choice process.
Collapse
Affiliation(s)
- Philippe Clerc
- Génétique Moléculaire Murine, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | | |
Collapse
|