101
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Larsson AJM, Coucoravas C, Sandberg R, Reinius B. X-chromosome upregulation is driven by increased burst frequency. Nat Struct Mol Biol 2019; 26:963-969. [PMID: 31582851 DOI: 10.1038/s41594-019-0306-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022]
Abstract
Ohno's hypothesis postulates that upregulation of X-linked genes rectifies their dosage imbalance relative to autosomal genes, which are present in two active copies per cell. Here we have dissected X-chromosome upregulation into the kinetics of transcription, inferred from allele-specific single-cell RNA sequencing data from somatic and embryonic mouse cells. We confirmed increased X-chromosome expression levels in female and male cells and found that the X chromosome achieved upregulation by elevated burst frequencies. By monitoring transcriptional kinetics in differentiating female mouse embryonic stem cells, we found that increased burst frequency was established on the active X chromosome when X inactivation took place on the other allele. Thus, our study provides mechanistic insights into X-chromosome upregulation.
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Affiliation(s)
- Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christos Coucoravas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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102
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Fang H, Disteche CM, Berletch JB. X Inactivation and Escape: Epigenetic and Structural Features. Front Cell Dev Biol 2019; 7:219. [PMID: 31632970 PMCID: PMC6779695 DOI: 10.3389/fcell.2019.00219] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
X inactivation represents a complex multi-layer epigenetic mechanism that profoundly modifies chromatin composition and structure of one X chromosome in females. The heterochromatic inactive X chromosome adopts a unique 3D bipartite structure and a location close to the nuclear periphery or the nucleolus. X-linked lncRNA loci and their transcripts play important roles in the recruitment of proteins that catalyze chromatin and DNA modifications for silencing, as well as in the control of chromatin condensation and location of the inactive X chromosome. A subset of genes escapes X inactivation, raising questions about mechanisms that preserve their expression despite being embedded within heterochromatin. Escape gene expression differs between males and females, which can lead to physiological sex differences. We review recent studies that emphasize challenges in understanding the role of lncRNAs in the control of epigenetic modifications, structural features and nuclear positioning of the inactive X chromosome. Second, we highlight new findings about the distribution of genes that escape X inactivation based on single cell studies, and discuss the roles of escape genes in eliciting sex differences in health and disease.
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Affiliation(s)
- He Fang
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Christine M. Disteche
- Department of Pathology, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Joel B. Berletch
- Department of Pathology, University of Washington, Seattle, WA, United States
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103
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Johansson MM, Pottmeier P, Suciu P, Ahmad T, Zaghlool A, Halvardson J, Darj E, Feuk L, Peuckert C, Jazin E. Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development. Front Genet 2019; 10:891. [PMID: 31608120 PMCID: PMC6769107 DOI: 10.3389/fgene.2019.00891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/23/2019] [Indexed: 01/01/2023] Open
Abstract
Global microarray gene expression analyses previously demonstrated differences in female and male embryos during neurodevelopment. In particular, before sexual maturation of the gonads, the differences seem to concentrate on the expression of genes encoded on the X- and Y-chromosomes. To investigate genome-wide differences in expression during this early developmental window, we combined high-resolution RNA sequencing with qPCR to analyze brain samples from human embryos during the first trimester of development. Our analysis was tailored for maximum sensitivity to discover Y-chromosome gene expression, but at the same time, it was underpowered to detect X-inactivation escapees. Using this approach, we found that 5 out of 13 expressed gametolog pairs showed unbalanced gene dosage, and as a consequence, a male-biased expression. In addition, we found six novel non-annotated long non-coding RNAs on the Y-chromosome with conserved expression patterns in newborn chimpanzee. The tissue specific and time-restricted expression of these long non-coding RNAs strongly suggests important functions during central nervous system development in human males.
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Affiliation(s)
- Martin M Johansson
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Philipp Pottmeier
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Pascalina Suciu
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Tauseef Ahmad
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elisabeth Darj
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden.,Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden.,Department of Molecular Biology, Stockholms University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
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104
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Matarrese P, Tieri P, Anticoli S, Ascione B, Conte M, Franceschi C, Malorni W, Salvioli S, Ruggieri A. X-chromosome-linked miR548am-5p is a key regulator of sex disparity in the susceptibility to mitochondria-mediated apoptosis. Cell Death Dis 2019; 10:673. [PMID: 31511496 PMCID: PMC6739406 DOI: 10.1038/s41419-019-1888-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/24/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022]
Abstract
Sex dimorphism in cell response to stress has previously been investigated by different research groups. This dimorphism could be at least in part accounted for by sex-biased expression of regulatory elements such as microRNAs (miRs). In order to spot previously unknown miR expression differences we took advantage of prior knowledge on specialized databases to identify X chromosome-encoded miRs potentially escaping X chromosome inactivation (XCI). MiR-548am-5p emerged as potentially XCI escaper and was experimentally verified to be significantly up-regulated in human XX primary dermal fibroblasts (DFs) compared to XY ones. Accordingly, miR-548am-5p target mRNAs, e.g. the transcript for Bax, was differently modulated in XX and XY DFs. Functional analyses indicated that XY DFs were more prone to mitochondria-mediated apoptosis than XX ones. Experimentally induced overexpression of miR548am-5p in XY cells by lentivirus vector transduction decreased apoptosis susceptibility, whereas its down-regulation in XX cells enhanced apoptosis susceptibility. These data indicate that this approach could be used to identify previously unreported sex-biased differences in miR expression and that a miR identified with this approach, miR548am-5p, can account for sex-dependent differences observed in the susceptibility to mitochondrial apoptosis of human DFs.
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Affiliation(s)
- Paola Matarrese
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, viale Regina Elena 299, Rome, Italy
| | - Paolo Tieri
- CNR National Research Council, IAC Institute for Applied Computing, Via dei Taurini 19, Rome, Italy.,Data Science Program, La Sapienza University of Rome, Rome, Italy
| | - Simona Anticoli
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, viale Regina Elena 299, Rome, Italy
| | - Barbara Ascione
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, viale Regina Elena 299, Rome, Italy
| | - Maria Conte
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, via San Giacomo 12, 40126, Bologna, Italy
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Via Altura 3, 40139, Bologna, Italy.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Walter Malorni
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, viale Regina Elena 299, Rome, Italy.,School of Mathematical, Physical and Natural Sciences and Faculty of Medicine, University of Tor Vergata, Rome, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy. .,Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, via San Giacomo 12, 40126, Bologna, Italy.
| | - Anna Ruggieri
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, viale Regina Elena 299, Rome, Italy.
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105
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Deng WQ, Mao S, Kalnapenkis A, Esko T, Mägi R, Paré G, Sun L. Analytical strategies to include the X-chromosome in variance heterogeneity analyses: Evidence for trait-specific polygenic variance structure. Genet Epidemiol 2019; 43:815-830. [PMID: 31332826 DOI: 10.1002/gepi.22247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022]
Abstract
Genotype-stratified variance of a quantitative trait could differ in the presence of gene-gene or gene-environment interactions. Genetic markers associated with phenotypic variance are thus considered promising candidates for follow-up interaction or joint location-scale analyses. However, as in studies of main effects, the X-chromosome is routinely excluded from "whole-genome" scans due to analytical challenges. Specifically, as males carry only one copy of the X-chromosome, the inherent sex-genotype dependency could bias the trait-genotype association, through sexual dimorphism in quantitative traits with sex-specific means or variances. Here we investigate phenotypic variance heterogeneity associated with X-chromosome single nucleotide polymorphisms (SNPs) and propose valid and powerful strategies. Among those, a generalized Levene's test has adequate power and remains robust to sexual dimorphism. An alternative approach is a sex-stratified analysis but at the cost of slightly reduced power and modeling flexibility. We applied both methods to an Estonian study of gene expression quantitative trait loci (eQTL; n = 841), and two complex trait studies of height, hip, and waist circumferences, and body mass index from Multi-Ethnic Study of Atherosclerosis (MESA; n = 2,073) and UK Biobank (UKB; n = 327,393). Consistent with previous eQTL findings on mean, we found some but no conclusive evidence for cis regulators being enriched for variance association. SNP rs2681646 is associated with variance of waist circumference (p = 9.5E-07) at X-chromosome-wide significance in UKB, with a suggestive female-specific effect in MESA (p = 0.048). Collectively, an enrichment analysis using permutated UKB (p < 0.1) and MESA (p < 0.01) datasets, suggests a possible polygenic structure for the variance of human height.
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Affiliation(s)
- Wei Q Deng
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, Canada
| | - Shihong Mao
- Department of Pathology and Molecular Medicine, Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Canada
| | - Anette Kalnapenkis
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Guillaume Paré
- Department of Pathology and Molecular Medicine, Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Lei Sun
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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106
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McKiernan PJ, Molloy KP, Cryan SA, McElvaney NG, Greene CM. X Chromosome-encoded MicroRNAs Are Functionally Increased in Cystic Fibrosis Monocytes. Am J Respir Crit Care Med 2019; 197:668-670. [PMID: 28796536 DOI: 10.1164/rccm.201707-1417le] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | | | - Sally A Cryan
- 1 Royal College of Surgeons in Ireland Dublin, Ireland
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107
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Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome. Genome Biol Evol 2019; 11:1909-1922. [PMID: 31273378 PMCID: PMC6628874 DOI: 10.1093/gbe/evz133] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3, and H4K20me1 histone marks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.
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Affiliation(s)
- Marion A L Picard
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - David Roquis
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Ingo Bulla
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Ronaldo C Augusto
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Nathalie Arancibia
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Christoph Grunau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Jérôme Boissier
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Céline Cosseau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
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108
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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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109
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Stoklasova J, Zapletalova J, Frysak Z, Hana V, Cap J, Pavlikova M, Soucek O, Lebl J. An isolated Xp deletion is linked to autoimmune diseases in Turner syndrome. J Pediatr Endocrinol Metab 2019; 32:479-488. [PMID: 31075085 DOI: 10.1515/jpem-2019-0067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/25/2019] [Indexed: 11/15/2022]
Abstract
Background Females with Turner syndrome (TS) are prone to develop autoimmune diseases (AIDs). The X chromosome contains several immune-related genes. Growth hormone (GH) and estrogens modulate the immune system. We aimed to clarify whether the loss of a specific X chromosome gene locus and the administration of GH and estradiol facilitate the development of AIDs in TS females. Methods Retrospective data on clinical course, AIDs, karyotype and treatment were analyzed from a cohort of 286 Czech females with TS (current age 2.8-43.3 years; median age 18.7 years). The karyotypes were sorted using two different classification systems: a mosaicism-focused and an isochromosome (isoXq)-focused approach. Karyotype subgroups with a significantly higher prevalence of AIDs were further evaluated. Data of common therapies were correlated with the prevalence of AIDs. Results The most frequent AIDs were autoimmune thyroid disease (AITD; 37.4%; n = 107) and celiac disease (CD; 8.7%; n = 25). All karyotype subgroups were prone to develop AIDs. Females with an isolated Xp deletion had a significantly higher prevalence of AITD and CD compared to all other individuals with TS (AITD: 66.0% vs. 31.5%, p < 0.0001; CD: 17.4% vs. 7.2%; p = 0.04, respectively). We observed no link between the mean age at initiation as well as the duration of GH and/or estrogen administration and the occurrence of AIDs. Conclusions Isolated Xp deletion contributes to the development of AIDs in TS patients. The haploinsufficiency of genes located in Xpter-p11.2 may explain this observation. Common therapies used in TS do not modify the risk of AIDs.
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Affiliation(s)
- Judith Stoklasova
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jirina Zapletalova
- Department of Pediatrics, Faculty of Medicine and Dentistry, Palacky University and Olomouc University Hospital, Olomouc, Czech Republic
| | - Zdenek Frysak
- Department of Internal Medicine, Faculty of Medicine and Dentistry, Palacky University and Olomouc University Hospital, Olomouc, Czech Republic
| | - Vaclav Hana
- 3rd Department of Internal Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jan Cap
- Department of Internal Medicine, Faculty of Medicine in Hradec Kralove, Charles University and Hradec Kralove University Hospital, Hradec Kralove, Czech Republic
| | - Marketa Pavlikova
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Ondrej Soucek
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jan Lebl
- Department of Pediatrics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
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110
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DNA Methylation Contributes to the Differential Expression Levels of Mecp2 in Male Mice Neurons and Astrocytes. Int J Mol Sci 2019; 20:ijms20081845. [PMID: 31013990 PMCID: PMC6514911 DOI: 10.3390/ijms20081845] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 02/01/2023] Open
Abstract
Methyl CpG binding protein-2 (MeCP2) isoforms (E1 and E2) are important epigenetic regulators in brain cells. Accordingly, MeCP2 loss- or gain-of-function mutation causes neurodevelopmental disorders, including Rett syndrome (RTT), MECP2 duplication syndrome (MDS), and autism spectrum disorders (ASD). Within different types of brain cells, highest MeCP2 levels are detected in neurons and the lowest in astrocytes. However, our current knowledge of Mecp2/MeCP2 regulatory mechanisms remains largely elusive. It appears that there is a sex-dependent effect in X-linked MeCP2-associated disorders, as RTT primarily affects females, whereas MDS is found almost exclusively in males. This suggests that Mecp2 expression levels in brain cells might be sex-dependent. Here, we investigated the sex- and cell type-specific expression of Mecp2 isoforms in male and female primary neurons and astrocytes isolated from the murine forebrain. Previously, we reported that DNA methylation of six Mecp2 regulatory elements correlated with Mecp2 levels in the brain. We now show that in male brain cells, DNA methylation is significantly correlated with the transcript expression of these two isoforms. We show that both Mecp2 isoforms are highly expressed in male neurons compared to male astrocytes, with Mecp2e1 expressed at higher levels than Mecp2e2. Our data indicate that higher DNA methylation at the Mecp2 regulatory element(s) is associated with lower levels of Mecp2 isoforms in male astrocytes compared to male neurons.
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111
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A high-resolution X chromosome copy-number variation map in fertile females and women with primary ovarian insufficiency. Genet Med 2019; 21:2275-2284. [PMID: 30948856 DOI: 10.1038/s41436-019-0505-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/20/2019] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Sex-biased expression of genes on the X chromosome is accomplished by a complex mechanism of dosage regulation that leads to anatomical and physiological differences between males and females. Copy-number variations (CNVs) may impact the human genome by either affecting gene dosage or disturbing a chromosome structural and/or functional integrity. METHODS We performed a high-resolution CNV profiling to investigate the X chromosome integrity in cohorts of 269 fertile females and 111 women affected with primary ovarian insufficiency (POI) and assessed CNVs impact into functional and nonfunctional genomic elements. RESULTS In POI patients, we observed a 2.5-fold enrichment for rare CNVs comprising ovary-expressed genes, and genes implicated in autoimmune response and apoptotic signaling. Moreover, there was a higher prevalence of deletions encompassing genes that escape X inactivation, noncoding RNAs, and intergenic DNA sequences among POI females, highlighting structural differences between X chromosomes of fertile and POI females. Furthermore, we discovered a ~4% carrier incidence for X-linked disorders among fertile women. CONCLUSION We constructed a high-resolution map of female-specific CNVs that provides critical insights into the spectrum of human genetic variation, sex-specific disease risk factors, and reproductive potential. We discovered novel CNVs associated with ovarian dysfunction and support polygenic models for POI.
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112
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Lenberg JL, Pretorius DH, Rupe ES, Jones MC, Ramos GA, Andreasen TS. Whole-exome sequencing reveals novel USP9X variant in female fetus with isolated agenesis of the corpus callosum. Clin Case Rep 2019; 7:656-660. [PMID: 30997057 PMCID: PMC6452501 DOI: 10.1002/ccr3.2051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 09/05/2018] [Accepted: 01/22/2019] [Indexed: 01/06/2023] Open
Abstract
Whole-exome sequencing in a female fetus detected a USP9X variant. This X-linked gene was recently associated with intellectual disability and distinct pattern of malformation in females. Isolated agenesis of the corpus callosum has not been reported in association with USP9X. Identifying this variant impacted management of the subsequent pregnancy.
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Affiliation(s)
- Jerica L. Lenberg
- Department of Genetic CounselingAugustana UniversitySioux FallsSouth Dakota
| | | | - Eric S. Rupe
- Department of RadiologyUniversity of CaliforniaSan DiegoCalifornia
| | - Marilyn C. Jones
- Division of Genetics, Department of PediatricsUniversity of CaliforniaSan DiegoCalifornia
| | - Gladys A. Ramos
- Division of Maternal‐Fetal Medicine, Department of Reproductive MedicineUniversity of CaliforniaSan DiegoCalifornia
| | - Tara S. Andreasen
- Division of Genetics, Department of PediatricsUniversity of CaliforniaSan DiegoCalifornia
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113
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Viuff M, Skakkebaek A, Nielsen MM, Chang S, Gravholt CH. Epigenetics and genomics in Turner syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:68-75. [PMID: 30811826 DOI: 10.1002/ajmg.c.31683] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022]
Abstract
The pathogenesis of Turner syndrome (TS) and the genotype-phenotype relationship has been thoroughly investigated during the last decade. It has become evident that the phenotype seen in TS does not only depend on simple gene dosage as a result of X chromosome monosomy. The origin of TS specific comorbidities such as infertility, cardiac malformations, bone dysgenesis, and autoimmune diseases may depend on a complex relationship between genes as well as transcriptional and epigenetic factors affecting gene expression across the genome. Furthermore, two individuals with TS with the exact same karyotype may exhibit completely different traits, suggesting that no conventional genotype-phenotype relationship exists. Here, we review the different genetic mechanisms behind differential gene expression, and highlight potential key-genes essential to the comorbidities seen in TS and other X chromosome aneuploidy syndromes. KDM6A, important for germ cell development, has shown to be differentially expressed and methylated in Turner and Klinefelter syndrome across studies. Furthermore, TIMP1/TIMP3 genes seem to affect the prevalence of bicuspid aortic valve. KDM5C could play a role in the neurocognitive development of Turner and Klinefelter syndrome. However, further research is needed to elucidate the genetic mechanism behind the phenotypic variability and the different phenotypic traits seen in TS.
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Affiliation(s)
- Mette Viuff
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Skakkebaek
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Morten M Nielsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Chang
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Biochemistry, Esbjerg Sygehus, Denmark
| | - Claus H Gravholt
- Department of Endocrinology and Internal Medicine (MEA), Aarhus University Hospital, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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114
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Getz GI, Parag-Sharma K, Reside J, Padilla RJ, Amelio AL. Identification of NSDHL mutations associated with CHILD syndrome in oral verruciform xanthoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2019; 128:60-69. [PMID: 31078502 DOI: 10.1016/j.oooo.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/04/2019] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVE The aim of this study was to perform a systematic analysis of the nicotinamide adenine dinucleotide phosphate (NAD[P])-dependent steroid dehydrogenase-like (NSDHL) gene in cases of oral verruciform xanthoma (VX) and to test for the presence of mutations associated with congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD) syndrome. STUDY DESIGN DNA was extracted from archived paraffin-embedded tissue of oral VX and control cases. Polymerase chain reaction (PCR) was then used to screen exons 4 and 6 of the NSDHL gene for the presence of 4 known germline mutations associated with CHILD syndrome and 1 somatic mutation previously identified in VX lesions with no known association with CHILD syndrome. RESULTS Of the 16 oral VX tissue samples, 8 (50%) had known missense mutations associated with CHILD syndrome. Furthermore, 2 of these 8 tissue samples also had an additional missense mutation previously identified in cutaneous VX lesions. No mutations of exons 4 and 6 were found in the 5 negative control tissue samples. CONCLUSIONS NSDHL gene mutations associated with CHILD syndrome are common in sporadic oral VX cases, suggesting that these mutations confer a greater risk for the development of epithelial barrier defects that promote recurrent oral VX lesions and the potential for direct germline transmission of oral VX susceptibility.
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Affiliation(s)
- George I Getz
- Department of Periodontology, UNC School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology & Physiology, Biological & Biomedical Sciences Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan Reside
- Department of Periodontology, UNC School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ricardo J Padilla
- Department of Diagnostic Sciences, UNC School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antonio L Amelio
- Departments of Oral and Craniofacial Health Sciences and Dental Ecology, UNC School of Dentistry, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC, USA.
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115
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Jordan W, Rieder LE, Larschan E. Diverse Genome Topologies Characterize Dosage Compensation across Species. Trends Genet 2019; 35:308-315. [PMID: 30808531 DOI: 10.1016/j.tig.2019.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 01/19/2023]
Abstract
Dosage compensation is the process by which transcript levels of the X chromosome are equalized with those of autosomes. Although diverse mechanisms of dosage compensation have evolved across species, these mechanisms all involve distinguishing the X chromosome from autosomes. Because one chromosome is singled out from other chromosomes for precise regulation, dosage compensation serves as an important model for understanding how specific cis-elements are identified within the highly compacted 3D genome to co-regulate thousands of genes. Recently, multiple genomic approaches have provided key insights into the mechanisms of dosage compensation, extending what we have learned from classical genetic studies. In the future, newer genomic approaches that require little starting material show great promise to provide an understanding of the heterogeneity of dosage compensation between cells and how it functions in nonmodel organisms.
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Affiliation(s)
- William Jordan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Leila E Rieder
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA; Department of Biology, Emory University, Atlanta, GA, USA
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA.
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116
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Abstract
Evolution of genetic mechanisms of sex determination led to two processes causing sex differences in somatic phenotypes: gonadal differentiation and sex chromosome dosage inequality. In species with heteromorphic sex chromosomes, the sex of the individual is established at the time of formation of the zygote, leading to inherent sex differences in expression of sex chromosome genes beginning as soon as the embryonic transcriptome is activated. The inequality of sex chromosome gene expression causes sexual differentiation of the gonads and of non-gonadal tissues. The difference in gonad type in turn causes lifelong differences in gonadal hormones, which interact with unequal effects of X and Y genes acting within cells. Separating the effects of gonadal hormones and sex chromosomes has been possible using mouse models in which gonadal determination is separated from the sex chromosomes, allowing comparison of XX and XY mice with the same type of gonad. Sex differences caused by gonadal hormones and sex chromosomes affect basic physiology and disease mechanisms in most or all tissues.
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117
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Mishra S, Nyomba BLG. Prohibitin: A hypothetical target for sex-based new therapeutics for metabolic and immune diseases. Exp Biol Med (Maywood) 2019; 244:157-170. [PMID: 30717609 PMCID: PMC6405819 DOI: 10.1177/1535370219828362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
IMPACT STATEMENT Traditional sex-related biases in research are now obsolete, and it is important to identify the sex of humans, animals, and even cells in research protocols, due to the role of sex as a fundamental facet of biology, predisposition to disease, and response to therapy. Genetic sex, epigenetics and hormonal regulations, generate sex-dimorphisms. Recent investigations acknowledge sex differences in metabolic and immune health as well as chronic diseases. Prohibitin, an evolutionarily conserved molecule, has pleotropic functions in mitochondrial housekeeping, plasma membrane signaling, and nuclear genetic transcription. Studies in adipocytes, macrophages, and transgenic mice indicate that prohibitin interacts with sex steroids and plays a role in mediating sex differences in adipose tissues and immune cell types. Prohibitin may, depending on context, modulate predisposition to chronic metabolic diseases and malignancy and, because of these attributes, could be a target for sex-based therapies of metabolic and immune-related diseases as well as cancer.
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Affiliation(s)
- Suresh Mishra
- Department of Internal Medicine, University of Manitoba,
Manitoba R3A1R9, Canada
- Department of Physiology & Pathophysiology, University of
Manitoba, Manitoba R3E0J9, Canada
| | - BL Grégoire Nyomba
- Department of Internal Medicine, University of Manitoba,
Manitoba R3A1R9, Canada
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118
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Ramos-Ibeas P, Sang F, Zhu Q, Tang WWC, Withey S, Klisch D, Wood L, Loose M, Surani MA, Alberio R. Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis. Nat Commun 2019; 10:500. [PMID: 30700715 PMCID: PMC6353908 DOI: 10.1038/s41467-019-08387-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/04/2019] [Indexed: 01/08/2023] Open
Abstract
High-resolution molecular programmes delineating the cellular foundations of mammalian embryogenesis have emerged recently. Similar analysis of human embryos is limited to pre-implantation stages, since early post-implantation embryos are largely inaccessible. Notwithstanding, we previously suggested conserved principles of pig and human early development. For further insight on pluripotent states and lineage delineation, we analysed pig embryos at single cell resolution. Here we show progressive segregation of inner cell mass and trophectoderm in early blastocysts, and of epiblast and hypoblast in late blastocysts. We show that following an emergent short naive pluripotent signature in early embryos, there is a protracted appearance of a primed signature in advanced embryonic stages. Dosage compensation with respect to the X-chromosome in females is attained via X-inactivation in late epiblasts. Detailed human-pig comparison is a basis towards comprehending early human development and a foundation for further studies of human pluripotent stem cell differentiation in pig interspecies chimeras. Lineage segregation from conception to gastrulation has been mapped at the single cell level in mouse, human and monkey. Here, the authors provide a comprehensive analysis of porcine preimplantation development using single cell RNA-seq; mapping metabolic changes, X chromosome inactivation and signalling pathways.
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Affiliation(s)
- Priscila Ramos-Ibeas
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK.,Animal Reproduction Department, National Institute for Agricultural and Food Research and Technology, 28040, Madrid, Spain
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Qifan Zhu
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Walfred W C Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
| | - Sarah Withey
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK.,Stem Cell Engineering Group, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Building 75, St Lucia, QLD, 4072, Australia
| | - Doris Klisch
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Liam Wood
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Matt Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. .,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK. .,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK.
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119
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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. PLoS Genet 2019; 15:e1007874. [PMID: 30625149 PMCID: PMC6342324 DOI: 10.1371/journal.pgen.1007874] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/22/2019] [Accepted: 12/04/2018] [Indexed: 12/03/2022] Open
Abstract
Extensive cell-to-cell variation exists even among putatively identical cells, and there is great interest in understanding how the properties of transcription relate to this heterogeneity. Differential expression from the two gene copies in diploid cells could potentially contribute, yet our ability to measure from which gene copy individual RNAs originated remains limited, particularly in the context of tissues. Here, we demonstrate quantitative, single molecule allele-specific RNA FISH adapted for use on tissue sections, allowing us to determine the chromosome of origin of individual RNA molecules in formaldehyde-fixed tissues. We used this method to visualize the allele-specific expression of Xist and multiple autosomal genes in mouse kidney. By combining these data with mathematical modeling, we evaluated models for allele-specific heterogeneity, in particular demonstrating that apparent expression from only one of the alleles in single cells can arise as a consequence of low-level mRNA abundance and transcriptional bursting. In mammals, most cells of the body contain two genetic datasets: one from the mother and one from the father, and—in theory—these two sets of information could contribute equally to produce the molecules in a given cell. In practice, however, this is not always the case, which can have dramatic implications for many traits, including visible features (such as fur color) and even disease outcomes. However, it remains difficult to measure the parental origin of individual molecules in a given cell and thus to assess what processes lead to an imbalance of the maternal and paternal contribution. We adapted a microscopy technique—called allele-specific single molecule RNA FISH—that uses a combination of fluorescent tags to specifically label one type of molecule, RNA, depending on its origin, for use in mouse kidney sections. Focusing on RNAs that were previously reported to show imbalance, we performed measurements and combined these with mathematical modeling to quantify imbalance in tissues and explain how these can arise. We found that we could recapitulate the observed imbalances using models that only take into account the random processes that produce RNA, without the need to invoke special regulatory mechanisms to create unequal contributions.
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120
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Jiang B, Liu J, He W, Wei S, Hu Y, Zhang X. The effects of preconception examinations on birth defects: a population-based cohort study in Dongguan City, China. J Matern Fetal Neonatal Med 2019; 33:2691-2696. [PMID: 30522364 DOI: 10.1080/14767058.2018.1557141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Objective: To evaluate the effect of preconception examinations programs on the prevention of birth defects in Dongguan City during 2013-2017.Methods: The data were from preconception examinations system and the birth defects surveillance system during 2013-2017. The study population included 63,175 infants born to mothers accepted preconception examinations during pregnancy (the screening group) and 649,862 infants whose mother did not check (the control group). The infants included for stillbirth, dead fetus, live birth between 28 weeks of gestation and 7 days after birth and legal pregnancy termination. The risk ratios (RRs) and 95% confidence intervals (CIs) were calculated to examine for the association between birth defects and preconception examinations. We also conducted a stratified analysis based on infant gender and disease classification, and maternal age and region.Results: The incidence of birth defects in the screening group was 134.55/10,000, while that in the control group was 241.53/10,000. Preconception examinations can effectively reduce the incidence of birth defects (BDs) (RR: 0.557, 95%CI: 0.520-0.597). Bifid spine (RR: 0.076, 95%CI: 0.011-0.545), anencephalia (RR: 0.134, 95%CI: 0.033-0.543) and anorectal atresia or stenosis (RR: 0.151, 95%CI: 0.048-0.471) were controlled best, and Down syndrome (RR: 0.684, 95%CI: 0.435-1.075) was no effect. Young maternal age (14-19 years) and old maternal age will increase the risk of birth defects. Preconception examinations had the best effect for pregnant women under 25 years of age (RR: 0.465, 95%CI: 0.387-0.559), and were relatively poor for women aged 30-34 years (RR: 0.678, 95%CI: 0.593-0.776). The incidence of the urban was significantly higher than that of the rural. The effect of preconception examinations to prevent birth defects was more effective in urban areas (RR: 0.453, 95%CI: 0.391-0.525) than in rural areas (RR: 0.577, 95%CI: 0.533-0.625). The incidence of BDs in males was higher than that in females.Conclusions: By implementing preconception examinations project, birth defects in Dongguan have been well controlled. This can provide reference for other developing countries to prevent birth defects.
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Affiliation(s)
- Bi Jiang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, China
| | - Jianxin Liu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, China
| | - Weichao He
- Dongguan Maternal and Child Health Care Hospital, Dongguan, China
| | - Sisi Wei
- Dongguan Maternal and Child Health Care Hospital, Dongguan, China
| | - Yanmei Hu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, China
| | - Xinjian Zhang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, China
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121
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Wang P, Zhang Y, Wang BQ, Li JL, Wang YX, Pan D, Wu XB, Fung WK, Zhou JY. A statistical measure for the skewness of X chromosome inactivation based on case-control design. BMC Bioinformatics 2019; 20:11. [PMID: 30616589 PMCID: PMC6323862 DOI: 10.1186/s12859-018-2587-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/18/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked diseases. However, no statistical method is available in the literature to measure the degree of the skewness of XCI for case-control design. Therefore, it is necessary to develop methods for such a task. RESULTS In this article, we first proposed a statistical measure for the degree of XCI skewing by using a case-control design, which is a ratio of two logistic regression coefficients after a simple reparameterization. Based on the point estimate of the ratio, we further developed three types of confidence intervals (the likelihood ratio, Fieller's and delta methods) to evaluate its variation. Simulation results demonstrated that the likelihood ratio method and the Fieller's method have more accurate coverage probability and more balanced tail errors than the delta method. We also applied these proposed methods to analyze the Graves' disease data for their practical use and found that rs3827440 probably undergoes a skewed XCI pattern with 68.7% of cells in heterozygous females having the risk allele T active, while the other 31.3% of cells keeping the normal allele C active. CONCLUSIONS For practical application, we suggest using the Fieller's method in large samples due to the non-iterative computation procedure and using the LR method otherwise for its robustness despite its slightly heavy computational burden.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, No. 1023, South Shatai Road, Baiyun District, Guangzhou, 510515 China
| | - Yu Zhang
- State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, No. 1023, South Shatai Road, Baiyun District, Guangzhou, 510515 China
| | - Bei-Qi Wang
- State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, No. 1023, South Shatai Road, Baiyun District, Guangzhou, 510515 China
| | - Jian-Long Li
- State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, No. 1023, South Shatai Road, Baiyun District, Guangzhou, 510515 China
| | - Yi-Xin Wang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongdong Pan
- Yunnan Key Laboratory of Statistical Modeling and Data Analysis, Yunnan University, Kunming, China
| | - Xian-Bo Wu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong, China
| | - Ji-Yuan Zhou
- State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, No. 1023, South Shatai Road, Baiyun District, Guangzhou, 510515 China
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122
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Sex differences and the neurobiology of affective disorders. Neuropsychopharmacology 2019; 44:111-128. [PMID: 30061743 PMCID: PMC6235863 DOI: 10.1038/s41386-018-0148-z] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/14/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Observations of the disproportionate incidence of depression in women compared with men have long preceded the recent explosion of interest in sex differences. Nonetheless, the source and implications of this epidemiologic sex difference remain unclear, as does the practical significance of the multitude of sex differences that have been reported in brain structure and function. In this article, we attempt to provide a framework for thinking about how sex and reproductive hormones (particularly estradiol as an example) might contribute to affective illness. After briefly reviewing some observed sex differences in depression, we discuss how sex might alter brain function through hormonal effects (both organizational (programmed) and activational (acute)), sex chromosome effects, and the interaction of sex with the environment. We next review sex differences in the brain at the structural, cellular, and network levels. We then focus on how sex and reproductive hormones regulate systems implicated in the pathophysiology of depression, including neuroplasticity, genetic and neural networks, the stress axis, and immune function. Finally, we suggest several models that might explain a sex-dependent differential regulation of affect and susceptibility to affective illness. As a disclaimer, the studies cited in this review are not intended to be comprehensive but rather serve as examples of the multitude of levels at which sex and reproductive hormones regulate brain structure and function. As such and despite our current ignorance regarding both the ontogeny of affective illness and the impact of sex on that ontogeny, sex differences may provide a lens through which we may better view the mechanisms underlying affective regulation and dysfunction.
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123
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Skewed X-inactivation is common in the general female population. Eur J Hum Genet 2018; 27:455-465. [PMID: 30552425 PMCID: PMC6460563 DOI: 10.1038/s41431-018-0291-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/30/2018] [Accepted: 09/28/2018] [Indexed: 12/19/2022] Open
Abstract
X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants.
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124
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Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts. Proc Natl Acad Sci U S A 2018; 115:13015-13020. [PMID: 30510006 DOI: 10.1073/pnas.1806811115] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single-cell RNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. In this framework we integrated an original method to identify and exclude doublets of cells. In fibroblast cells, we have identified 55 genes as escapees including five undescribed escapee genes. Moreover, we observed that all genes exhibit a variable propensity to escape XCI in each cell and cell type and that each cell displays a distinct expression profile of the escapee genes. A metric, the Inactivation Score-defined as the mean of the allelic expression profiles of the escapees per cell-enables us to discover a heterogeneous and continuous degree of cellular XCI with extremes represented by "inactive" cells, i.e., cells exclusively expressing the escaping genes from the active X chromosome and "escaping" cells expressing the escapees from both alleles. We found that this effect is associated with cell-cycle phases and, independently, with the XIST expression level, which is higher in the quiescent phase (G0). Single-cell allele-specific expression is a powerful tool to identify novel escapees in different tissues and provide evidence of an unexpected cellular heterogeneity of XCI.
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125
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Ng KK, Yui MA, Mehta A, Siu S, Irwin B, Pease S, Hirose S, Elowitz MB, Rothenberg EV, Kueh HY. A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment. eLife 2018; 7:37851. [PMID: 30457103 PMCID: PMC6245732 DOI: 10.7554/elife.37851] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
Cell fate decisions occur through the switch-like, irreversible activation of fate-specifying genes. These activation events are often assumed to be tightly coupled to changes in upstream transcription factors, but could also be constrained by cis-epigenetic mechanisms at individual gene loci. Here, we studied the activation of Bcl11b, which controls T-cell fate commitment. To disentangle cis and trans effects, we generated mice where two Bcl11b copies are tagged with distinguishable fluorescent proteins. Quantitative live microscopy of progenitors from these mice revealed that Bcl11b turned on after a stochastic delay averaging multiple days, which varied not only between cells but also between Bcl11b alleles within the same cell. Genetic perturbations, together with mathematical modeling, showed that a distal enhancer controls the rate of epigenetic activation, while a parallel Notch-dependent trans-acting step stimulates expression from activated loci. These results show that developmental fate transitions can be controlled by stochastic cis-acting events on individual loci.
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Affiliation(s)
- Kenneth Kh Ng
- Department of Bioengineering, University of Washington, Seattle, United States.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Mary A Yui
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Arnav Mehta
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | | | - Blythe Irwin
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Shirley Pease
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Satoshi Hirose
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Department of Applied Physics, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, United States.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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126
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Epigenetic and Cellular Diversity in the Brain through Allele-Specific Effects. Trends Neurosci 2018; 41:925-937. [PMID: 30098802 DOI: 10.1016/j.tins.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 01/18/2023]
Abstract
The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence for diverse allele-specific expression and epigenetic states in mammalian brain cells, which suggest that diploidy expands the landscape of gene regulatory and expression programs in cells. Allele-specific expression has been thought to be restricted to a few specific classes of genes. However, new studies show novel genomic imprinting effects that are brain-region-, cell-type- and age-dependent. In addition, novel forms of random monoallelic expression that impact many autosomal genes have been described in vitro and in vivo. We discuss the implications for understanding the benefits of diploidy, and the mechanisms shaping brain development, function, and disease.
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127
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Gong S, Sovio U, Aye IL, Gaccioli F, Dopierala J, Johnson MD, Wood AM, Cook E, Jenkins BJ, Koulman A, Casero RA, Constância M, Charnock-Jones DS, Smith GC. Placental polyamine metabolism differs by fetal sex, fetal growth restriction, and preeclampsia. JCI Insight 2018; 3:120723. [PMID: 29997303 PMCID: PMC6124516 DOI: 10.1172/jci.insight.120723] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/31/2018] [Indexed: 02/02/2023] Open
Abstract
Preeclampsia and fetal growth restriction (FGR) are major causes of the more than 5 million perinatal and infant deaths occurring globally each year, and both are associated with placental dysfunction. The risk of perinatal and infant death is greater in males, but the mechanisms are unclear. We studied data and biological samples from the Pregnancy Outcome Prediction (POP) study, a prospective cohort study that followed 4,212 women having first pregnancies from their dating ultrasound scan through delivery. We tested the hypothesis that fetal sex would be associated with altered placental function using multiomic and targeted analyses. We found that spermine synthase (SMS) escapes X-chromosome inactivation (XCI) in the placenta and is expressed at lower levels in male primary trophoblast cells, and male cells were more sensitive to polyamine depletion. The spermine metabolite N1,N12-diacetylspermine (DiAcSpm) was higher in the female placenta and in the serum of women pregnant with a female fetus. Higher maternal serum levels of DiAcSpm increased the risk of preeclampsia but decreased the risk of FGR. To our knowledge, DiAcSpm is the first maternal biomarker to demonstrate opposite associations with preeclampsia and FGR, and this is the first evidence to implicate polyamine metabolism in sex-related differences in placentally related complications of human pregnancy.
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Affiliation(s)
- Sungsam Gong
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre
| | - Ulla Sovio
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
| | - Irving L.M.H. Aye
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
| | - Francesca Gaccioli
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
| | - Justyna Dopierala
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
| | - Michelle D. Johnson
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
| | | | - Emma Cook
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre
| | - Benjamin J. Jenkins
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Albert Koulman
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Robert A. Casero
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miguel Constância
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience,,University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, United Kingdom
| | - D. Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
| | - Gordon C.S. Smith
- Department of Obstetrics and Gynaecology, NIHR Cambridge Comprehensive Biomedical Research Centre,,Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience
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128
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Abstract
A fundamental question in the biology of sex differences has eluded direct study in humans: How does sex-chromosome dosage (SCD) shape genome function? To address this, we developed a systematic map of SCD effects on gene function by analyzing genome-wide expression data in humans with diverse sex-chromosome aneuploidies (XO, XXX, XXY, XYY, and XXYY). For sex chromosomes, we demonstrate a pattern of obligate dosage sensitivity among evolutionarily preserved X-Y homologs and update prevailing theoretical models for SCD compensation by detecting X-linked genes that increase expression with decreasing X- and/or Y-chromosome dosage. We further show that SCD-sensitive sex-chromosome genes regulate specific coexpression networks of SCD-sensitive autosomal genes with critical cellular functions and a demonstrable potential to mediate previously documented SCD effects on disease. These gene coexpression results converge with analysis of transcription factor binding site enrichment and measures of gene expression in murine knockout models to spotlight the dosage-sensitive X-linked transcription factor ZFX as a key mediator of SCD effects on wider genome expression. Our findings characterize the effects of SCD broadly across the genome, with potential implications for human phenotypic variation.
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129
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Sahakyan A, Yang Y, Plath K. The Role of Xist in X-Chromosome Dosage Compensation. Trends Cell Biol 2018; 28:999-1013. [PMID: 29910081 DOI: 10.1016/j.tcb.2018.05.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 01/15/2023]
Abstract
In each somatic cell of a female mammal one X chromosome is transcriptionally silenced via X-chromosome inactivation (XCI), initiating early in development. Although XCI events are conserved in mouse and human postimplantation development, regulation of X-chromosome dosage in preimplantation development occurs differently. In preimplantation development, mouse embryos undergo imprinted form of XCI, yet humans lack imprinted XCI and instead regulate gene expression of both X chromosomes by dampening transcription. The long non-coding RNA Xist/XIST is expressed in mouse and human preimplantation and postimplantation development to orchestrate XCI, but its role in dampening is unclear. In this review, we discuss recent advances in our understanding of the role of Xist in X chromosome dosage compensation in mouse and human.
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Affiliation(s)
- Anna Sahakyan
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yihao Yang
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.
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130
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O'Driscoll DN, Greene CM, Molloy EJ. Immune function? A missing link in the gender disparity in preterm neonatal outcomes. Expert Rev Clin Immunol 2018; 13:1061-1071. [PMID: 28972799 DOI: 10.1080/1744666x.2017.1386555] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION In neonatology, males exhibit a more severe disease course and poorer prognosis in many pathological states when compared to females. Perinatal brain injury, respiratory morbidity, and sepsis, among other complications, preferentially affect males. Preterm neonates (born <37 weeks gestation) display a particularly marked sexual disparity in pathology, especially at the borders of viability. The sex biases in preterm neonatal outcomes and underlying multifactorial mechanisms have been incompletely explored. Sex-specific clinical phenomena may be partially explained by intrinsic differences in immune function. The distinct immune system of preterm neonates renders this patient population vulnerable, and it is increasingly important to consider biological sex in disease processes and to strive for improved outcomes for both sexes. Areas covered: We discuss the cellular responses and molecular intermediates in immune function which are strongly dependent on sex-specific factors such as the genetic and hormonal milieu of premature birth and consider novel findings in a clinical context. Expert commentary: The role of immune function in the manifestation of sex-specific disease manifestations and outcomes in preterm neonates is a critical prognostic variable. Further mechanistic elucidation will yield valuable translational and clinical information of disease processes in preterm neonates which may be harnessed for modulation.
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Affiliation(s)
- David N O'Driscoll
- a Neonatology , National Maternity Hospital , Dublin , Ireland.,b Pediatrics, Trinity College, Trinity Centre for Health Sciences , The University of Dublin, National Children's Hospital, AMNCH , Dublin , Ireland
| | - Catherine M Greene
- c Clinical Microbiology , Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital , Dublin , Ireland
| | - Eleanor J Molloy
- a Neonatology , National Maternity Hospital , Dublin , Ireland.,b Pediatrics, Trinity College, Trinity Centre for Health Sciences , The University of Dublin, National Children's Hospital, AMNCH , Dublin , Ireland.,d Neonatology , Coombe Women and Infants' University Hospital , Dublin , Ireland.,e Neonatology , Our Lady's Children's Hospital Crumlin , Dublin , Ireland
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131
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Leung YK, Ouyang B, Niu L, Xie C, Ying J, Medvedovic M, Chen A, Weihe P, Valvi D, Grandjean P, Ho SM. Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. Epigenetics 2018; 13:290-300. [PMID: 29560787 DOI: 10.1080/15592294.2018.1445901] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures. We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood. The cord blood DNA methylome was profiled using Infinium HumanMethylation450 BeadChips. We determined the associations of CpG site changes with concentrations of MeHg, major PCBs, other organochlorine compounds [hexachlorobenzene (HCB), p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) and p,p'-dichlorodiphenyltrichloroethane], and perfluoroalkyl substances. In a combined sex analysis, among the 16 chemicals studied, PCB congener 105 (CB-105) exposure was associated with the majority of differentially methylated CpG sites (214 out of a total of 250). In female-only analysis, only 73 CB-105 associated CpG sites were detected, 44 of which were mapped to genes in the ELAV1-associated cancer network. In males-only, methylation changes were seen for perfluorooctane sulfonate, HCB, and p,p'-DDE in 10,598, 1,238, and 1,473 CpG sites, respectively, 15% of which were enriched in cytobands of the X-chromosome associated with neurological disorders. In this multiple-pollutant and genome-wide study, we identified key epigenetic toxicants. The significant enrichment of specific X-chromosome sites in males implies potential sex-specific epigenome responses to prenatal chemical exposures.
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Affiliation(s)
- Yuet-Kin Leung
- a Division of Environmental Genetics and Molecular Toxicology.,e Center of Environmental Genetics.,f Cincinnati Cancer Center , University of Cincinnati Medical Center , Cincinnati , USA
| | - Bin Ouyang
- a Division of Environmental Genetics and Molecular Toxicology.,e Center of Environmental Genetics
| | - Liang Niu
- b Biostatistics & Bioinformatics.,e Center of Environmental Genetics
| | - Changchun Xie
- b Biostatistics & Bioinformatics.,e Center of Environmental Genetics
| | - Jun Ying
- b Biostatistics & Bioinformatics.,c Public Health Science and
| | - Mario Medvedovic
- b Biostatistics & Bioinformatics.,e Center of Environmental Genetics.,f Cincinnati Cancer Center , University of Cincinnati Medical Center , Cincinnati , USA
| | - Aimin Chen
- d Epidemiology Department of Environmental Health.,e Center of Environmental Genetics
| | - Pal Weihe
- h Department of Occupational Medicine and Public Health , Faroese Hospital System , Torshavn , Faroe Islands
| | - Damaskini Valvi
- i Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , USA
| | - Philippe Grandjean
- i Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , USA.,j Department of Environmental Medicine , University of Southern Denmark , Odense , Denmark
| | - Shuk-Mei Ho
- a Division of Environmental Genetics and Molecular Toxicology.,e Center of Environmental Genetics.,f Cincinnati Cancer Center , University of Cincinnati Medical Center , Cincinnati , USA.,g Cincinnati Veteran Affairs Medical Center , Cincinnati , USA
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132
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Bonora G, Disteche CM. Structural aspects of the inactive X chromosome. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0357. [PMID: 28947656 PMCID: PMC5627159 DOI: 10.1098/rstb.2016.0357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2017] [Indexed: 12/20/2022] Open
Abstract
A striking difference between male and female nuclei was recognized early on by the presence of a condensed chromatin body only in female cells. Mary Lyon proposed that X inactivation or silencing of one X chromosome at random in females caused this structural difference. Subsequent studies have shown that the inactive X chromosome (Xi) does indeed have a very distinctive structure compared to its active counterpart and all autosomes in female mammals. In this review, we will recap the discovery of this fascinating biological phenomenon and seminal studies in the field. We will summarize imaging studies using traditional microscopy and super-resolution technology, which revealed uneven compaction of the Xi. We will then discuss recent findings based on high-throughput sequencing techniques, which uncovered the distinct three-dimensional bipartite configuration of the Xi and the role of specific long non-coding RNAs in eliciting and maintaining this structure. The relative position of specific genomic elements, including genes that escape X inactivation, repeat elements and chromatin features, will be reviewed. Finally, we will discuss the position of the Xi, either near the nuclear periphery or the nucleolus, and the elements implicated in this positioning. This article is part of the themed issue ‘X-chromosome inactivation: a tribute to Mary Lyon’.
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Affiliation(s)
- Giancarlo Bonora
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA 98195, USA .,Department of Medicine, University of Washington, Seattle, WA 98195, USA
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133
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Sangrithi MN, Turner JMA. Mammalian X Chromosome Dosage Compensation: Perspectives From the Germ Line. Bioessays 2018; 40:e1800024. [PMID: 29756331 DOI: 10.1002/bies.201800024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/15/2018] [Indexed: 01/04/2023]
Abstract
Sex chromosomes are advantageous to mammals, allowing them to adopt a genetic rather than environmental sex determination system. However, sex chromosome evolution also carries a burden, because it results in an imbalance in gene dosage between females (XX) and males (XY). This imbalance is resolved by X dosage compensation, which comprises both X chromosome inactivation and X chromosome upregulation. X dosage compensation has been well characterized in the soma, but not in the germ line. Germ cells face a special challenge, because genome wide reprogramming erases epigenetic marks responsible for maintaining the X dosage compensated state. Here we explain how evolution has influenced the gene content and germ line specialization of the mammalian sex chromosomes. We discuss new research uncovering unusual X dosage compensation states in germ cells, which we postulate influence sexual dimorphisms in germ line development and cause infertility in individuals with sex chromosome aneuploidy.
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Affiliation(s)
- Mahesh N Sangrithi
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore.,Duke-NUS Graduate Medical School, Singapore, 119077, Singapore
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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134
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Akiyama T, User SD, Gibson MC. Somatic clones heterozygous for recessive disease alleles of BMPR1A exhibit unexpected phenotypes in Drosophila. eLife 2018; 7:35258. [PMID: 29745898 PMCID: PMC5963922 DOI: 10.7554/elife.35258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/02/2018] [Indexed: 01/02/2023] Open
Abstract
The majority of mutations studied in animal models are designated as recessive based on the absence of visible phenotypes in germline heterozygotes. Accordingly, genetic studies primarily rely on homozygous loss-of-function to determine gene requirements, and a conceptually-related ‘two-hit model’ remains the central paradigm in cancer genetics. Here we investigate pathogenesis due to somatic mutation in epithelial tissues, a process that predominantly generates heterozygous cell clones. To study somatic mutation in Drosophila, we generated inducible alleles that mimic human Juvenile polyposis-associated BMPR1A mutations. Unexpectedly, four of these mutations had no phenotype in heterozygous carriers but exhibited clear tissue-level effects when present in somatic clones of heterozygous cells. We conclude that these alleles are indeed recessive when present in the germline, but nevertheless deleterious when present in heterozygous clones. This unforeseen effect, deleterious heteromosaicism, suggests a ‘one-hit’ mechanism for disease initiation that may explain some instances of pathogenesis associated with spontaneous mutation.
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Affiliation(s)
- Takuya Akiyama
- Stowers Institute for Medical Research, Kansas City, United States
| | - Sırma D User
- Stowers Institute for Medical Research, Kansas City, United States
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, United States
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135
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Bikchurina TI, Tishakova KV, Kizilova EA, Romanenko SA, Serdyukova NA, Torgasheva AA, Borodin PM. Chromosome Synapsis and Recombination in Male-Sterile and Female-Fertile Interspecies Hybrids of the Dwarf Hamsters ( Phodopus, Cricetidae). Genes (Basel) 2018; 9:genes9050227. [PMID: 29693587 PMCID: PMC5977167 DOI: 10.3390/genes9050227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023] Open
Abstract
Hybrid sterility is an important step in the speciation process. Hybrids between dwarf hamsters Phodopus sungorus and P.campbelli provide a good model for studies in cytological and genetic mechanisms of hybrid sterility. Previous studies in hybrids detected multiple abnormalities of spermatogenesis and a high frequency of dissociation between the X and Y chromosomes at the meiotic prophase. In this study, we found that the autosomes of the hybrid males and females underwent paring and recombination as normally as their parental forms did. The male hybrids showed a significantly higher frequency of asynapsis and recombination failure between the heterochromatic arms of the X and Y chromosomes than the males of the parental species. Female hybrids as well as the females of the parental species demonstrated a high incidence of centromere misalignment at the XX bivalent and partial asynapsis of the ends of its heterochromatic arms. In all three karyotypes, recombination was completely suppressed in the heterochromatic arm of the X chromosome, where the pseudoautosomal region is located. We propose that this recombination pattern speeds up divergence of the X- and Y-linked pseudoautosomal regions between the parental species and results in their incompatibility in the male hybrids.
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Affiliation(s)
- Tatiana I Bikchurina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Katerina V Tishakova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Elena A Kizilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Svetlana A Romanenko
- Novosibirsk State University, Novosibirsk 630090, Russia.
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Natalya A Serdyukova
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Anna A Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
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136
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Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
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Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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137
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Geens M, Chuva De Sousa Lopes SM. X chromosome inactivation in human pluripotent stem cells as a model for human development: back to the drawing board? Hum Reprod Update 2018; 23:520-532. [PMID: 28582519 DOI: 10.1093/humupd/dmx015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 05/17/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells (hPSC), both embryonic and induced (hESC and hiPSC), are regarded as a valuable in vitro model for early human development. In order to fulfil this promise, it is important that these cells mimic as closely as possible the in vivo molecular events, both at the genetic and epigenetic level. One of the most important epigenetic events during early human development is X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female cells. XCI is important for proper development and aberrant XCI has been linked to several pathologies. Recently, novel data obtained using high throughput single-cell technology during human preimplantation development have suggested that the XCI mechanism is substantially different from XCI in mouse. It has also been suggested that hPSC show higher complexity in XCI than the mouse. Here we compare the available recent data to understand whether XCI during human preimplantation can be properly recapitulated using hPSC. OBJECTIVE AND RATIONALE We will summarize what is known on the timing and mechanisms of XCI during human preimplantation development. We will compare this to the XCI patterns that are observed during hPSC derivation, culture and differentiation, and comment on the cause of the aberrant XCI patterns observed in hPSC. Finally, we will discuss the implications of the aberrant XCI patterns on the applicability of hPSC as an in vitro model for human development and as cell source for regenerative medicine. SEARCH METHODS Combinations of the following keywords were applied as search criteria in the PubMed database: X chromosome inactivation, preimplantation development, embryonic stem cells, induced pluripotent stem cells, primordial germ cells, differentiation. OUTCOMES Recent single-cell RNASeq data have shed new light on the XCI process during human preimplantation development. These indicate a gradual inactivation on both XX chromosomes, starting from Day 4 of development and followed by a random choice to inactivate one of them, instead of the mechanism in mice where imprinted XCI is followed by random XCI. We have put these new findings in perspective using previous data obtained in human (and mouse) embryos. In addition, there is an ongoing discussion whether or not hPSC lines show X chromosome reactivation upon derivation, mimicking the earliest embryonic cells, and the XCI states observed during culture of hPSC are highly variable. Recent studies have shown that hPSC rapidly progress to highly aberrant XCI patterns and that this process is probably driven by suboptimal culture conditions. Importantly, these aberrant XCI states seem to be inherited by the differentiated hPSC-progeny. WIDER IMPLICATIONS The aberrant XCI states (and epigenetic instability) observed in hPSC throw a shadow on their applicability as an in vitro model for development and disease modelling. Moreover, as the aberrant XCI states observed in hPSC seem to shift to a more malignant phenotype, this may also have important consequences for the safety aspect of using hPSC in the clinic.
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Affiliation(s)
- Mieke Geens
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - Susana M Chuva De Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands.,Department of Reproductive Medicine, Ghent-Fertility and Stem Cell Team (G-FaST), Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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138
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Turano A, Osborne BF, Schwarz JM. Sexual Differentiation and Sex Differences in Neural Development. Curr Top Behav Neurosci 2018; 43:69-110. [PMID: 29967999 DOI: 10.1007/7854_2018_56] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sex determination occurs at the moment of conception, as a result of XX or XY chromosome pairing. From that point, the body undergoes the process of sexual differentiation, inducing the development of physical characteristics that are easily distinguishable between the sexes and are often reflected in one's physical appearance and gender identity. Although less apparent, the brain also undergoes sexual differentiation. Sex differences in the brain are organized during a critical period of neural development and have an instrumental role in determining the physiology and behavior of an individual throughout the lifespan. Understanding the extent of sex differences in neurodevelopment also influences our understanding of the potential risk for a number of neurodevelopmental, neurological, and mental health disorders that exhibit strong sex biases. Advances made in our understanding of sexually dimorphic brain nuclei, sex differences in neural cell communication, and sex differences in the communication between the brain and peripheral organs are all research fields that have provided valuable information related to the physiological and behavioral outcomes of sex differences in brain development. More recently, investigations into the impact of epigenetic mechanisms on sexual differentiation of the brain have indicated that changes in gene expression, via epigenetic modifications, also contribute to sexual differentiation of the developing brain. Still, there are a number of important questions and ideas that have arisen from our current understanding of sex differences in neurodevelopmental processes that necessitate more time and attention in this field.
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Affiliation(s)
- Alexandra Turano
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Brittany F Osborne
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Jaclyn M Schwarz
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA.
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139
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Abstract
Sex chromosome aneuploidies comprise a relatively common group of chromosome disorders characterized by the loss or gain of one or more sex chromosomes. We discuss five of the better-known sex aneuploidies: Turner syndrome (XO), Klinefelter syndrome (XXY), trisomy X (XXX), XYY, and XXYY. Despite their prevalence in the general population, these disorders are underdiagnosed and the specific genetic mechanisms underlying their phenotypes are poorly understood. Although there is considerable variation between them in terms of associated functional impairment, each disorder has a characteristic physical, cognitive, and neurologic profile. The most common cause of sex chromosome aneuploidies is nondisjunction, which can occur during meiosis or during the early stages of postzygotic development. The loss or gain of genetic material can affect all daughter cells or it may be partial, leading to tissue mosaicism. In both typical and atypical sex chromosome karyotypes, there is random inactivation of all but one X chromosome. The mechanisms by which a phenotype results from sex chromosome aneuploidies are twofold: dosage imbalance arising from a small number of genes that escape inactivation, and their endocrinologic consequences.
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Affiliation(s)
- David Skuse
- Brain and Behaviour Science Unit, UCL Institute of Child Health, London, United Kingdom.
| | - Frida Printzlau
- Brain and Behaviour Science Unit, UCL Institute of Child Health, London, United Kingdom
| | - Jeanne Wolstencroft
- Brain and Behaviour Science Unit, UCL Institute of Child Health, London, United Kingdom
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140
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Abstract
Epigenetic mechanisms that cause maternally and paternally inherited alleles to be expressed differently in offspring have the potential to radically change our understanding of the mechanisms that shape disease susceptibility, phenotypic variation, cell fate, and gene expression. However, the nature and prevalence of these effects
in vivo have been unclear and are debated. Here, I consider major new studies of epigenetic allelic effects in cell lines and primary cells and
in vivo. The emerging picture is that these effects take on diverse forms, and this review attempts to clarify the nature of the different forms that have been uncovered for genomic imprinting and random monoallelic expression (RME). I also discuss apparent discrepancies between
in vitro and
in vivo studies. Importantly, multiple studies suggest that allelic effects are prevalent and can be developmental stage- and cell type-specific. I propose some possible functions and consider roles for allelic effects within the broader context of gene regulatory networks, cellular diversity, and plasticity. Overall, the field is ripe for discovery and is in need of mechanistic and functional studies.
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141
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de Souza Santos R, Frank AP, Clegg DJ. The impact of sex and sex hormones on cell function. Steroids 2017; 128:72-74. [PMID: 29104097 DOI: 10.1016/j.steroids.2017.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/20/2017] [Accepted: 10/30/2017] [Indexed: 11/23/2022]
Abstract
The influence of sex on cellular function and metabolism is often ill defined in many human and animal studies. The National Institute of Health (NIH) recognized this gap in scientific knowledge and mandated that sex be factored into the design and data analysis of all cell culture and animal studies. Therefore, it is critical to understand how to incorporate sex in pre-clinical and clinical research. Here, we discuss how the sexual identify of cells influences experimental responses in cell culture and we highlight the importance of the culture media and its constituents to the function of cells. We further discuss the importance of understanding the influence and interactions between sex hormones and sex chromosomes. A deeper understanding of how sex chromosomes and sex hormones function as variables in complex biological systems may lead to better, more personalized medical therapies.
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Affiliation(s)
- Roberta de Souza Santos
- Biomedical Research Department, Diabetes and Obesity Research Division, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
| | - Aaron P Frank
- Biomedical Research Department, Diabetes and Obesity Research Division, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
| | - Deborah J Clegg
- Biomedical Research Department, Diabetes and Obesity Research Division, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
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142
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Printzlau F, Wolstencroft J, Skuse DH. Cognitive, behavioral, and neural consequences of sex chromosome aneuploidy. J Neurosci Res 2017; 95:311-319. [PMID: 27870409 DOI: 10.1002/jnr.23951] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 02/04/2023]
Abstract
The X chromosome has played a critical role in the development of sexually selected characteristics for over 300 million years, and during that time it has accumulated a disproportionate number of genes concerned with mental functions. There are relatively specific effects of X-linked genes on social cognition, language, emotional regulation, visuospatial, and numerical skills. Many human X-linked genes outside the X-Y pairing pseudoautosomal regions escape X-inactivation. Dosage differences in the expression of such genes (which constitute at least 15% of the total) are likely to play an important role in male-female neural differentiation, and in cognitive deficits and behavioral characteristics, particularly in the realm of social communication, that are associated with sex chromosome aneuploidies. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Frida Printzlau
- Great Ormond Street Hospital Institute of Child Health, University College London, United Kingdom
| | - Jeanne Wolstencroft
- Great Ormond Street Hospital Institute of Child Health, University College London, United Kingdom
| | - David H Skuse
- Great Ormond Street Hospital Institute of Child Health, University College London, United Kingdom
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143
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Arnold AP. A general theory of sexual differentiation. J Neurosci Res 2017; 95:291-300. [PMID: 27870435 DOI: 10.1002/jnr.23884] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/16/2022]
Abstract
A general theory of mammalian sexual differentiation is proposed. All biological sex differences are the result of the inequality in effects of the sex chromosomes, which are the only factors that differ in XX vs. XY zygotes. This inequality leads to male-specific effects of the Y chromosome, including expression of the testis-determining gene Sry that causes differentiation of testes. Thus, Sry sets up lifelong sex differences in effects of gonadal hormones. Y genes also act outside of the gonads to cause male-specific effects. Differences in the number of X chromosomes between XX and XY cells cause sex differences in expression (1) of Xist, (2) of X genes that escape inactivation, and (3) of parentally imprinted X genes. Sex differences in phenotype are ultimately the result of multiple, independent sex-biasing factors, hormonal and sex chromosomal. These factors act in parallel and in combination to induce sex differences. They also can offset each other to reduce sex differences. Other mechanisms, operating at the level of populations, cause groups of males to differ on average from groups of females. The theory frames questions for further study, and directs attention to inherent sex-biasing factors that operate in many tissues to cause sex differences, and to cause sex-biased protection from disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology & Physiology, and Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, Los Angeles, California
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144
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Sharma D, Koshy G, Gupta S, Sharma B, Grover S. Deciphering the Role of the Barr Body in Malignancy: An insight into head and neck cancer. Sultan Qaboos Univ Med J 2017; 17:e389-e397. [PMID: 29372079 PMCID: PMC5766293 DOI: 10.18295/squmj.2017.17.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 08/03/2017] [Accepted: 08/24/2017] [Indexed: 01/20/2023] Open
Abstract
X chromosome inactivation is the epitome of epigenetic regulation and long non-coding ribonucleic acid function. The differentiation status of cells has been ascribed to X chromosome activity, with two active X chromosomes generally only observed in undifferentiated or poorly differentiated cells. Recently, several studies have indicated that the reactivation of an inactive X chromosome or X chromosome multiplication correlates with the development of malignancy; however, this concept is still controversial. This review sought to shed light on the role of the X chromosome in cancer development. In particular, there is a need for further exploration of the expression patterns of X-linked genes in cancer cells, especially those in head and neck squamous cell carcinoma (HNSCC), in order to identify different prognostic subpopulations with distinct clinical implications. This article proposes a functional relationship between the loss of the Barr body and the disproportional expression of X-linked genes in HNSCC development.
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Affiliation(s)
- Deepti Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - George Koshy
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Shruti Gupta
- Department of Oral Anatomy, Postgraduate Institute of Dental Sciences, Rohtak, Haryana, India
| | - Bhushan Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Sonal Grover
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
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145
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Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res 2017; 27:1961-1973. [PMID: 29079676 PMCID: PMC5741053 DOI: 10.1101/gr.225391.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022]
Abstract
Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set to analyze male and female miRNA expression profiles in mouse, opossum, and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, with the largest proportion found in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z Chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W Chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z Chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalize male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism.
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146
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Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues. Nature 2017; 550:244-248. [PMID: 29022598 PMCID: PMC5685192 DOI: 10.1038/nature24265] [Citation(s) in RCA: 630] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/28/2017] [Indexed: 12/16/2022]
Abstract
X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals. The extent to which XCI is shared between cells and tissues remains poorly characterized, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression and phenotypic traits. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.
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Affiliation(s)
- Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manuel A. Rivas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jamie L. Marshall
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- New York Genome Center, New York, NY 10013, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Matt Aguirre
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura Gauthier
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark Fleharty
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Kirby
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beryl B. Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephane E. Castel
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Konrad J. Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrea Byrnes
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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147
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Mirsafian H, Ripen AM, Leong WM, Manaharan T, Mohamad SB, Merican AF. Transcriptome landscape of human primary monocytes at different sequencing depth. Genomics 2017; 109:463-470. [DOI: 10.1016/j.ygeno.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/15/2017] [Accepted: 07/17/2017] [Indexed: 12/16/2022]
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148
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Abstract
Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there is an innate capacity for an organism to regain haploidy and that haploidy may confer evolutionary benefits. Haploid embryonic stem cells have been experimentally generated from mouse, rat, monkey, and humans. Haploidy results in major differences in cell size and gene expression levels while also affecting parental imprinting, X chromosome inactivation, and mitochondrial metabolism genes. We discuss here haploidy in evolution and the barriers to haploidy, in particular in the human context.
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149
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Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations. Nat Commun 2017; 8:690. [PMID: 28947736 PMCID: PMC5612955 DOI: 10.1038/s41467-017-00528-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 02/02/2023] Open
Abstract
Xist is indispensable for X chromosome inactivation. However, how Xist RNA directs chromosome-wide silencing and why some regions are more efficiently silenced than others remains unknown. Here, we explore the function of Xist by inducing ectopic Xist expression from multiple different X-linked and autosomal loci in mouse aneuploid and female diploid embryonic stem cells in which Xist-mediated silencing does not lead to lethal functional monosomy. We show that ectopic Xist expression faithfully recapitulates endogenous X chromosome inactivation from any location on the X chromosome, whereas long-range silencing of autosomal genes is less efficient. Long interspersed elements facilitate inactivation of genes located far away from the Xist transcription locus, and genes escaping X chromosome inactivation show enrichment of CTCF on X chromosomal but not autosomal loci. Our findings highlight important genomic and epigenetic features acquired during sex chromosome evolution to facilitate an efficient X chromosome inactivation process.Xist RNA is required for X chromosome inactivation but it is not well understood how Xist silences some regions more efficiently than others. Here, the authors induce ectopic Xist expression from multiple different X-linked and autosomal loci in cells to explore Xist function.
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150
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Sierra MI, Rubio L, Bayón GF, Cobo I, Menendez P, Morales P, Mangas C, Urdinguio RG, Lopez V, Valdes A, Vales G, Marcos R, Torrecillas R, Fernández AF, Fraga MF. DNA methylation changes in human lung epithelia cells exposed to multi-walled carbon nanotubes. Nanotoxicology 2017; 11:857-870. [DOI: 10.1080/17435390.2017.1371350] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Marta I. Sierra
- Cancer Epigenetics Lab, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Laura Rubio
- Grup de Mutagenesi, Departament de Genetica i de Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, Barcelona, Spain; CIBER Epidemiologia y Salud Publica, ISCIII, Madrid, Spain
| | - Gustavo F. Bayón
- Cancer Epigenetics Lab, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Isabel Cobo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
| | - Pablo Menendez
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Paula Morales
- Cancer Epigenetics Lab, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Cristina Mangas
- Cancer Epigenetics Lab, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rocio G. Urdinguio
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Asturias, Spain
| | - Virginia Lopez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Asturias, Spain
| | - Adolfo Valdes
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Asturias, Spain
| | - Gerard Vales
- Grup de Mutagenesi, Departament de Genetica i de Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, Barcelona, Spain; CIBER Epidemiologia y Salud Publica, ISCIII, Madrid, Spain
| | - Ricard Marcos
- Grup de Mutagenesi, Departament de Genetica i de Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, Barcelona, Spain; CIBER Epidemiologia y Salud Publica, ISCIII, Madrid, Spain
| | - Ramon Torrecillas
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Asturias, Spain
| | - Agustin F. Fernández
- Cancer Epigenetics Lab, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mario F. Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Asturias, Spain
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