1
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Zhang S, Wang R, Zhang L, Birchler JA, Sun L. Inverse and Proportional Trans Modulation of Gene Expression in Human Aneuploidies. Genes (Basel) 2024; 15:637. [PMID: 38790266 PMCID: PMC11121296 DOI: 10.3390/genes15050637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data from several autosomal and sex chromosome aneuploidies. The results showed that in human aneuploid cells, genes located on unvaried chromosomes are inversely or proportionally trans-modulated, while a subset of genes on the varied chromosomes are compensated. Less genome-wide modulation is found for sex chromosome aneuploidy compared with autosomal aneuploidy due to X inactivation and the retention of dosage sensitive regulators on both sex chromosomes to limit the effective dosage change. We also found that lncRNA and mRNA can have different responses to aneuploidy. Furthermore, we analyzed the relationship between dosage-sensitive transcription factors and their targets, which illustrated the modulations and indicates genomic imbalance is related to stoichiometric changes in components of gene regulatory complexes.In summary, this study demonstrates the existence of trans-acting effects and compensation mechanisms in human aneuploidies and contributes to our understanding of gene expression regulation in unbalanced genomes and disease states.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (S.Z.); (R.W.); (L.Z.)
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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2
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Bravo‐Estupiñan DM, Aguilar‐Guerrero K, Quirós S, Acón M, Marín‐Müller C, Ibáñez‐Hernández M, Mora‐Rodríguez RA. Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer. Cancer Med 2023; 12:22130-22155. [PMID: 37987212 PMCID: PMC10757140 DOI: 10.1002/cam4.6719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage-sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post-translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post-translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems-level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed "gene dosage sensor loops." These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.
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Affiliation(s)
- Diana M. Bravo‐Estupiñan
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Programa de Doctorado en Ciencias, Sistema de Estudios de Posgrado (SEP)Universidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Karol Aguilar‐Guerrero
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Maestría académica en Microbiología, Programa de Posgrado en Microbiología, Parasitología, Química Clínica e InmunologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Steve Quirós
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Man‐Sai Acón
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
| | - Christian Marín‐Müller
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Miguel Ibáñez‐Hernández
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
| | - Rodrigo A. Mora‐Rodríguez
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
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3
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Jachowicz JW. A fine balancing act: how epitranscriptome regulates dosage compensation in mammals. Nat Struct Mol Biol 2023; 30:1057-1059. [PMID: 37524970 DOI: 10.1038/s41594-023-01055-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Affiliation(s)
- Joanna W Jachowicz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
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4
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Rücklé C, Körtel N, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI, König J. RNA stability controlled by m 6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol 2023; 30:1207-1215. [PMID: 37202476 PMCID: PMC10442230 DOI: 10.1038/s41594-023-00997-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/06/2023] [Indexed: 05/20/2023]
Abstract
In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared with two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanisms of X-to-autosome dosage compensation are still under debate. Here we show that X-chromosomal transcripts have fewer m6A modifications and are more stable than their autosomal counterparts. Acute depletion of m6A selectively stabilizes autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.
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Affiliation(s)
| | - Nadine Körtel
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - M Felicia Basilicata
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | | | | | - Marco Bertin
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | - Susann Schweiger
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany.
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5
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Xing Z, Zhang Y, Tian Z, Wang M, Xiao W, Zhu C, Zhao S, Zhu Y, Hu L, Kong X. Escaping but not the inactive X-linked protein complex coding genes may achieve X-chromosome dosage compensation and underlie X chromosome inactivation-related diseases. Heliyon 2023; 9:e17721. [PMID: 37449161 PMCID: PMC10336589 DOI: 10.1016/j.heliyon.2023.e17721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
X chromosome dosage compensation (XDC) refers to the process by which X-linked genes acquire expression equivalence between two sexes. Ohno proposed that XDC is achieved by two-fold upregulations of X-linked genes in both sexes and by silencing one X chromosome (X chromosome inactivation, XCI) in females. However, genes subject to two-fold upregulations as well as the underlying mechanism remain unclear. It's reported that gene dosage changes may only affect X-linked dosage-sensitive genes, such as protein complex coding genes (PCGs). Our results showed that in human PCGs are more likely to escape XCI and escaping PCGs (EsP) show two-fold higher expression than inactivated PCGs (InP) or other X-linked genes at RNA and protein levels in both sexes, which suggest that EsP may achieve upregulations and XDC. The higher expressions of EsP possibly result from the upregulations of the single active X chromosome (Xa), rather than escaping expressions from the inactive X chromosome (Xi). EsP genes have relatively high expression levels in humans and lower dN/dS ratios, suggesting that they are likely under stronger selection pressure over evolutionary time. Our study also suggests that SP1 transcription factor is significantly enriched in EsP and may be involved in the up-regulations of EsP on the active X. Finally, human EsP genes in this study are enriched in the toll-like receptor pathway, NF-kB pathway, apoptotic pathway, and abnormal mental, developmental and reproductive phenotypes. These findings suggest misregulations of EsP may be involved in autoimmune, reproductive, and neurological diseases, providing insight for the diagnosis and treatment of these diseases.
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Affiliation(s)
- Zhihao Xing
- Clinical Laboratory, Institute of Pediatrics, Shenzhen Children’s' Hospital, Shenzhen, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Yuchao Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Zhongyuan Tian
- Zhoukou Traditional Chinese Medicine Hospital, Zhoukou, Henan, China
| | - Meng Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Weiwei Xiao
- Clinical Laboratory, Institute of Pediatrics, Shenzhen Children’s' Hospital, Shenzhen, China
| | - Chunqing Zhu
- Clinical Laboratory, Institute of Pediatrics, Shenzhen Children’s' Hospital, Shenzhen, China
| | - Songhui Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Yufei Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Landian Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Xiangyin Kong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
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6
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Mattimoe T, Payer B. The compleX balancing act of controlling X-chromosome dosage and how it impacts mammalian germline development. Biochem J 2023; 480:521-537. [PMID: 37096944 DOI: 10.1042/bcj20220450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 04/26/2023]
Abstract
In female mammals, the two X chromosomes are subject to epigenetic gene regulation in order to balance X-linked gene dosage with autosomes and in relation to males, which have one X and one Y chromosome. This is achieved by an intricate interplay of several processes; X-chromosome inactivation and reactivation elicit global epigenetic regulation of expression from one X chromosome in a stage-specific manner, whilst the process of X-chromosome upregulation responds to this by fine-tuning transcription levels of the second X. The germline is unique in its function of transmitting both the genetic and epigenetic information from one generation to the next, and remodelling of the X chromosome is one of the key steps in setting the stage for successful development. Here, we provide an overview of the complex dynamics of X-chromosome dosage control during embryonic and germ cell development, and aim to decipher its potential role for normal germline competency.
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Affiliation(s)
- Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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7
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Miao N, Zeng Z, Lee T, Guo Q, Zheng W, Cai W, Chen W, Wang J, Sun T. Integrative epigenome profiling of 47XXY provides insights into whole genomic DNA hypermethylation and active chromatin accessibility. Front Mol Biosci 2023; 10:1128739. [PMID: 37051325 PMCID: PMC10083376 DOI: 10.3389/fmolb.2023.1128739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Klinefelter syndrome (KS, 47XXY) is a disorder characterized by sex chromosomal aneuploidy, which may lead to changes in epigenetic regulations of gene expression. To define epigenetic architectures in 47XXY, we annotated DNA methylation in euploid males (46XY) and females (46XX), and 47XXY individuals using whole genome bisulfite sequencing (WGBS) and integrated chromatin accessbilty, and detected abnormal hypermethylation in 47XXY. Furthermore, we detected altered chromatin accessibility in 47XXY, in particular in chromosome X, using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) in cultured amniotic cells. Our results construct the whole genome-wide DNA methylation map in 47XXY, and provide new insights into the early epigenomic dysregulation resulting from an extra chromosome X in 47XXY.
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Affiliation(s)
- Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Zhiwei Zeng
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, New York, NY, United States
| | - Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Wenwei Zheng
- Quanzhou Women and Children’s Hospital, Quanzhou, Fujian, China
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Wanhua Chen
- Department of Clinical Laboratory, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
- *Correspondence: Tao Sun,
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8
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Sakka R, Abdelhedi F, Sellami H, Pichon B, Lajmi Y, Mnif M, Kebaili S, Derbel R, Kamoun H, Gdoura R, Delbaere A, Desir J, Abramowicz M, Vialard F, Dupont JM, Ammar-Keskes L. An unusual familial Xp22.12 microduplication including EIF1AX: A novel candidate dosage-sensitive gene for premature ovarian insufficiency. Eur J Med Genet 2022; 65:104613. [PMID: 36113757 DOI: 10.1016/j.ejmg.2022.104613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 07/22/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022]
Abstract
We report on the results of array-CGH and Whole exome sequencing (WES) studies carried out in a Tunisian family with 46,XX premature ovarian insufficiency (POI). This study has led to the identification of a familial Xp22.12 tandem duplication with a size of 559.4 kb, encompassing only three OMIM genes (RPS6KA3, SH3KBP1and EIF1AX), and a new heterozygous variant in SPIDR gene: NM_001080394.3:c.1845_1853delTATAATTGA (p.Ile616_Asp618del) segregating with POI. Increased mRNA expression levels were detected for SH3KBP1 and EIF1AX, while a normal transcript level for RPS6KA3 was detected in the three affected family members, explaining the absence of intellectual disability (ID). To the best of our knowledge, this is the first duplication involving the Xp22.12 region, reported in a family without ID, but rather with secondary amenorrhea (SA) and female infertility. As EIF1AX is a regulatory gene escaping X-inactivation, which has an extreme dosage sensitivity and highly expressed in the ovary, we suggest that this gene might be a candidate gene for ovarian function. Homozygous nonsense pathogenic variants of SPIDR gene have been reported in familial cases in POI. It has been suggested that chromosomal instability associated with SPIDR molecular defects supports the role of SPIDR protein in double-stranded DNA damage repair in vivo in humans and its causal role in POI. In this family, the variant (p.Ile616_Asp618del), present in a heterozygous state, is located in the domain that interacts with BLM and might disrupt the BLM binding ability of SPIDR protein. These findings strengthen the hypothesis that the additional effect of this variant could lead to POI in this family. Although the work represents the first evidence that EIF1AX duplication might be responsible for POI through its over-expression, further functional studies are needed to clarify and prove EIF1AX involvement in POI phenotype.
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Affiliation(s)
- Rim Sakka
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia; Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Fatma Abdelhedi
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia; Medical Genetics Department, Hedi Chaker Hospital, Sfax, Tunisia.
| | - Hanen Sellami
- Water Researches and Technologies Center (CERTE), University of Carthage, Tourist Road Soliman, Nabeul, Tunisia; Toxicology, Environmental Microbiology and Health Research Laboratory (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Bruno Pichon
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Yosra Lajmi
- Cytogenetics Department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris, Sorbonne Paris Cité, Paris Descartes University, Medical School, Paris, France
| | - Mouna Mnif
- Department of Endocrinology, Hedi Chaker Hospital, Sfax, Tunisia
| | - Sahbi Kebaili
- Department of Gynecology, HediChaker Hospital, Sfax, Tunisia
| | - Rihab Derbel
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetics Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Radhouane Gdoura
- Toxicology, Environmental Microbiology and Health Research Laboratory (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Anne Delbaere
- Fertility Clinic, Department of Gynecology and Obstetrics, Erasme Hospital, UniversitéLibre de Bruxelles, Brussels, Belgium
| | - Julie Desir
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marc Abramowicz
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - François Vialard
- Genetics Department, CHI Poissy St Germain-en-Laye, F-78300, Poissy, France; RHuMA Team, UMR-BREED, INRAE-UVSQ-ENVA, UFR-SVS, F-78180, Montigny le Bretonneux, France
| | - Jean-Michel Dupont
- Cytogenetics Department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris, Sorbonne Paris Cité, Paris Descartes University, Medical School, Paris, France
| | - Leila Ammar-Keskes
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia
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9
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Abstract
Understanding sex differences in physiology and disease requires the identification of the molecular agents that cause phenotypic sex differences. Two groups of such agents are genes located on the sex chromosomes, and gonadal hormones. The former have coherent linkage to chromosomes that form differently in the two sexes under the influence of genomic forces that are not related to reproductive function, whereas the latter have a direct or indirect relationship to reproduction. Evidence published in the past 5 years supports the identification of several agents of sexual differentiation encoded by the X chromosome in mice, including Kdm5c, Kdm6a, Ogt and Xist. These X chromosome agents have wide pleiotropic effects, potentially influencing sex differences in many different tissues, a characteristic shared with the gonadal hormones. The identification of X chromosome agents of sexual differentiation will facilitate understanding of complex intersecting gene pathways underlying sex differences in disease.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
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10
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Meisel RP, Asgari D, Schlamp F, Unckless RL. Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex. G3 (BETHESDA, MD.) 2022; 12:6632659. [PMID: 35792851 PMCID: PMC9434221 DOI: 10.1093/g3journal/jkac165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments that have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (upregulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (downregulated) following treatment. We further show that whether a gene is bound by the dosage compensation complex in males can largely explain the paucity of both up- and downregulated genes on the X chromosome. Specifically, genes that are bound by the dosage compensation complex, or close to a dosage compensation complex high-affinity site, are unlikely to be up- or downregulated after treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that dosage compensation complex binding, or the associated chromatin modifications, inhibit both up- and downregulation of X chromosome gene expression within specific contexts, including tissue-specific expression. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first, a component of the dosage compensation complex, as a dampener of gene expression variance in both males and females. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific or induced expression, while the mammalian X has an excess of genes with tissue-specific expression.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5001, USA
| | - Danial Asgari
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5001, USA
| | - Florencia Schlamp
- Department of Medicine, NYU Grossman School of Medicine, 435 E 30th St, New York, NY 10016, USA
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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11
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Moore EC, Thomas GWC, Mortimer S, Kopania EEK, Hunnicutt KE, Clare-Salzler ZJ, Larson EL, Good JM. The evolution of widespread recombination suppression on the dwarf hamster (Phodopus) X chromosome. Genome Biol Evol 2022; 14:6596369. [PMID: 35642315 PMCID: PMC9185382 DOI: 10.1093/gbe/evac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/24/2022] Open
Abstract
The X chromosome of therian mammals shows strong conservation among distantly related species, limiting insights into the distinct selective processes that have shaped sex chromosome evolution. We constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster (Phodopus sungorus), a species reported to show extensive recombination suppression across an entire arm of the X chromosome. Combining a physical genome assembly based on shotgun and long-range proximity ligation sequencing with a dense genetic map, we detected widespread suppression of female recombination across ∼65% of the Phodopus X chromosome. This region of suppressed recombination likely corresponds to the Xp arm, which has previously been shown to be highly heterochromatic. Using additional sequencing data from two closely related species (P. campbelli and P. roborovskii), we show that recombination suppression on Xp appears to be independent of major structural rearrangements. The suppressed Xp arm was enriched for several transposable element families and de-enriched for genes primarily expressed in placenta, but otherwise showed similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm. Phodopus Xp gene content and order was also broadly conserved relative to the more distantly related rat X chromosome. These data suggest that widespread suppression of recombination has likely evolved through the transient induction of facultative heterochromatin on the Phodopus Xp arm without major changes in chromosome structure or genetic content. Thus, substantial changes in the recombination landscape have so far had relatively subtle influences on patterns of X-linked molecular evolution in these species.
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Affiliation(s)
- Emily C Moore
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Gregg W C Thomas
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Sebastian Mortimer
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Emily E K Kopania
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Kelsie E Hunnicutt
- Department of Biological Sciences, The University of Denver, Denver, Colorado, 80208, USA
| | | | - Erica L Larson
- Department of Biological Sciences, The University of Denver, Denver, Colorado, 80208, USA
| | - Jeffrey M Good
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
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12
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Single-cell analysis reveals X upregulation is not global in pre-gastrulation embryos. iScience 2022; 25:104465. [PMID: 35707719 PMCID: PMC9189126 DOI: 10.1016/j.isci.2022.104465] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
In mammals, transcriptional inactivation of one X chromosome in female compensates for the dosage of X-linked gene expression between the sexes. Additionally, it is believed that the upregulation of active X chromosome in male and female balances the dosage of X-linked gene expression relative to autosomal genes, as proposed by Ohno. However, the existence of X chromosome upregulation (XCU) remains controversial. Here, we have profiled gene-wise dynamics of XCU in pre-gastrulation mouse embryos at single-cell level and found that XCU is dynamically linked with X chromosome inactivation (XCI); however, XCU is not global like XCI. Moreover, we show that upregulated genes are enriched with activating marks and have enhanced burst frequency. Finally, our In-silico model predicts that recruitment probabilities of activating factors and a surge of these factors upon X-inactivation trigger XCU. Altogether, our study provides significant insight into the gene-wise dynamics and mechanistic basis of XCU during early development and extends support for Ohno’s hypothesis. X-upregulation coincides with X chromosome inactivation in pre-gastrulation embryos X-upregulation is not chromosome-wide like X-inactivation Upregulated genes have enhanced burst frequency and are enriched with activating marks A surge of activating factors on X-inactivation triggers X-upregulation
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13
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Mank JE. Are plant and animal sex chromosomes really all that different? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210218. [PMID: 35306885 PMCID: PMC8935310 DOI: 10.1098/rstb.2021.0218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sex chromosomes in plants have often been contrasted with those in animals with the goal of identifying key differences that can be used to elucidate fundamental evolutionary properties. For example, the often homomorphic sex chromosomes in plants have been compared to the highly divergent systems in some animal model systems, such as birds, Drosophila and therian mammals, with many hypotheses offered to explain the apparent dissimilarities, including the younger age of plant sex chromosomes, the lesser prevalence of sexual dimorphism, or the greater extent of haploid selection. Furthermore, many plant sex chromosomes lack complete sex chromosome dosage compensation observed in some animals, including therian mammals, Drosophila, some poeciliids, and Anolis, and plant dosage compensation, where it exists, appears to be incomplete. Even the canonical theoretical models of sex chromosome formation differ somewhat between plants and animals. However, the highly divergent sex chromosomes observed in some animal groups are actually the exception, not the norm, and many animal clades are far more similar to plants in their sex chromosome patterns. This begs the question of how different are plant and animal sex chromosomes, and which of the many unique properties of plants would be expected to affect sex chromosome evolution differently than animals? In fact, plant and animal sex chromosomes exhibit more similarities than differences, and it is not at all clear that they differ in terms of sexual conflict, dosage compensation, or even degree of divergence. Overall, the largest difference between these two groups is the greater potential for haploid selection in plants compared to animals. This may act to accelerate the expansion of the non-recombining region at the same time that it maintains gene function within it. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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14
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Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210222. [PMID: 35306896 PMCID: PMC8935305 DOI: 10.1098/rstb.2021.0222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or brings XY male expression back to its ancestral level. Here, we review work on DC in plants, which started as early as the late 1960s with cytological approaches. The use of transcriptomics fired a controversy as to whether DC existed in plants. Further work revealed that various plants exhibit partial DC, including a few species with young and homomorphic sex chromosomes. We are starting to understand the mechanisms responsible for DC in some plants, but in most species, we lack the data to differentiate between global and gene-by-gene DC. Also, it is unknown why some species evolve many dosage compensated genes while others do not. Finally, the forces that drive DC evolution remain mysterious, both in plants and animals. We review the multiple evolutionary theories that have been proposed to explain DC patterns in eukaryotes with XY or ZW sex chromosomes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Aline Muyle
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France
| | - Gabriel A B Marais
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Thomas Lenormand
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
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15
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The mysterious sex chromosomes of haploid plants. Heredity (Edinb) 2022; 129:17-21. [PMID: 35393551 PMCID: PMC9273592 DOI: 10.1038/s41437-022-00524-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 11/09/2022] Open
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16
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Mammalian X-chromosome inactivation: proposed role in suppression of the male programme in genetic females. J Genet 2022. [DOI: 10.1007/s12041-022-01363-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Astro V, Alowaysi M, Fiacco E, Saera-Vila A, Cardona-Londoño KJ, Aiese Cigliano R, Adamo A. Pseudoautosomal Region 1 Overdosage Affects the Global Transcriptome in iPSCs From Patients With Klinefelter Syndrome and High-Grade X Chromosome Aneuploidies. Front Cell Dev Biol 2022; 9:801597. [PMID: 35186953 PMCID: PMC8850648 DOI: 10.3389/fcell.2021.801597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/28/2021] [Indexed: 01/19/2023] Open
Abstract
Klinefelter syndrome (KS) is the most prevalent aneuploidy in males and is characterized by a 47,XXY karyotype. Less frequently, higher grade sex chromosome aneuploidies (HGAs) can also occur. Here, using a paradigmatic cohort of KS and HGA induced pluripotent stem cells (iPSCs) carrying 49,XXXXY, 48,XXXY, and 47,XXY karyotypes, we identified the genes within the pseudoautosomal region 1 (PAR1) as the most susceptible to dosage-dependent transcriptional dysregulation and therefore potentially responsible for the progressively worsening phenotype in higher grade X aneuploidies. By contrast, the biallelically expressed non-PAR escape genes displayed high interclonal and interpatient variability in iPSCs and differentiated derivatives, suggesting that these genes could be associated with variable KS traits. By interrogating KS and HGA iPSCs at the single-cell resolution we showed that PAR1 and non-PAR escape genes are not only resilient to the X-inactive specific transcript (XIST)-mediated inactivation but also that their transcriptional regulation is disjointed from the absolute XIST expression level. Finally, we explored the transcriptional effects of X chromosome overdosage on autosomes and identified the nuclear respiratory factor 1 (NRF1) as a key regulator of the zinc finger protein X-linked (ZFX). Our study provides the first evidence of an X-dosage-sensitive autosomal transcription factor regulating an X-linked gene in low- and high-grade X aneuploidies.
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Affiliation(s)
- Veronica Astro
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maryam Alowaysi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elisabetta Fiacco
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Kelly J. Cardona-Londoño
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Antonio Adamo
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- *Correspondence: Antonio Adamo,
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18
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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19
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Birchler JA, Veitia RA. One Hundred Years of Gene Balance: How Stoichiometric Issues Affect Gene Expression, Genome Evolution, and Quantitative Traits. Cytogenet Genome Res 2021; 161:529-550. [PMID: 34814143 DOI: 10.1159/000519592] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
A century ago experiments with the flowering plant Datura stramonium and the fruit fly Drosophila melanogaster revealed that adding an extra chromosome to a karyotype was much more detrimental than adding a whole set of chromosomes. This phenomenon was referred to as gene balance and has been recapitulated across eukaryotic species. Here, we retrace some developments in this field. Molecular studies suggest that the basis of balance involves stoichiometric relationships of multi-component interactions. This concept has implication for the mechanisms controlling gene expression, genome evolution, sex chromosome evolution/dosage compensation, speciation mechanisms, and the underlying genetics of quantitative traits.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Reiner A Veitia
- Université de Paris, Paris, France.,Institut Jacques Monod, Université de Paris/CNRS, Paris, France.,Institut de Biologie F. Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, Fontenay aux Roses, France
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21
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Talon I, Janiszewski A, Theeuwes B, Lefevre T, Song J, Bervoets G, Vanheer L, De Geest N, Poovathingal S, Allsop R, Marine JC, Rambow F, Voet T, Pasque V. Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals. Genome Biol 2021; 22:302. [PMID: 34724962 PMCID: PMC8558763 DOI: 10.1186/s13059-021-02518-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated during development in the inner cell mass and in germ cells through X chromosome reactivation, which can be studied in vitro by reprogramming of somatic cells to pluripotency. How chromatin processes and gene regulatory networks evolved to regulate X chromosome dosage in the somatic state and during X chromosome reactivation remains unclear. RESULTS Using genome-wide approaches, allele-specific ATAC-seq and single-cell RNA-seq, in female embryonic fibroblasts and during reprogramming to pluripotency, we show that chromatin accessibility on the upregulated mammalian active X chromosome is increased compared to autosomes. We further show that increased accessibility on the active X chromosome is erased by reprogramming, accompanied by erasure of transcriptional X chromosome upregulation and the loss of increased transcriptional burst frequency. In addition, we characterize gene regulatory networks during reprogramming and X chromosome reactivation, revealing changes in regulatory states. Our data show that ZFP42/REX1, a pluripotency-associated gene that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency. CONCLUSIONS Our data reveal the existence of intrinsic compensatory mechanisms that involve modulation of chromatin accessibility to counteract X-to-Autosome gene dosage imbalances caused by evolutionary or in vitro X chromosome loss and X chromosome inactivation in mammalian cells.
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Affiliation(s)
- Irene Talon
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Bart Theeuwes
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Thomas Lefevre
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Juan Song
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Vanheer
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Suresh Poovathingal
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Ryan Allsop
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Jean-Christophe Marine
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
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22
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Bista B, Wu Z, Literman R, Valenzuela N. Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200101. [PMID: 34304598 DOI: 10.1098/rstb.2020.0101] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sex chromosome dosage compensation (SCDC) overcomes gene-dose imbalances that disturb transcriptional networks, as when ZW females or XY males are hemizygous for Z/X genes. Mounting data from non-model organisms reveal diverse SCDC mechanisms, yet their evolution remains obscure, because most informative lineages with variable sex chromosomes are unstudied. Here, we discovered SCDC in turtles and an unprecedented thermosensitive SCDC in eukaryotes. We contrasted RNA-seq expression of Z-genes, their autosomal orthologues, and control autosomal genes in Apalone spinifera (ZZ/ZW) and Chrysemys picta turtles with temperature-dependent sex determination (TSD) (proxy for ancestral expression). This approach disentangled chromosomal context effects on Z-linked and autosomal expression, from lineage effects owing to selection or drift. Embryonic Apalone SCDC is tissue- and age-dependent, regulated gene-by-gene, complete in females via Z-upregulation in both sexes (Type IV) but partial and environmentally plastic via Z-downregulation in males (accentuated at colder temperature), present in female hatchlings and a weakly suggestive in adult liver (Type I). Results indicate that embryonic SCDC evolved with/after sex chromosomes in Apalone's family Tryonichidae, while co-opting Z-gene upregulation present in the TSD ancestor. Notably, Apalone's SCDC resembles pygmy snake's, and differs from the full-SCDC of Anolis lizards who share homologous sex chromosomes (XY), advancing our understanding of how XX/XY and ZZ/ZW systems compensate gene-dose imbalance. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.,Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People's Republic of China
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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23
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Charlesworth D. The timing of genetic degeneration of sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200093. [PMID: 34247501 DOI: 10.1098/rstb.2020.0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic degeneration is an extraordinary feature of sex chromosomes, with the loss of functions of Y-linked genes in species with XY systems, and W-linked genes in ZW systems, eventually affecting almost all genes. Although degeneration is familiar to most biologists, important aspects are not yet well understood, including how quickly a Y or W chromosome can become completely degenerated. I review the current understanding of the time-course of degeneration. Degeneration starts after crossing over between the sex chromosome pair stops, and theoretical models predict an initially fast degeneration rate and a later much slower one. It has become possible to estimate the two quantities that the models suggest are the most important in determining degeneration rates-the size of the sex-linked region, and the time when recombination became suppressed (which can be estimated using Y-X or W-Z sequence divergence). However, quantifying degeneration is still difficult. I review evidence on gene losses (based on coverage analysis) or loss of function (by classifying coding sequences into functional alleles and pseudogenes). I also review evidence about whether small genome regions degenerate, or only large ones, whether selective constraints on the genes in a sex-linked region also strongly affect degeneration rates, and about how long it takes before all (or almost all) genes are lost. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
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24
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Metzger DCH, Sandkam BA, Darolti I, Mank JE. Rapid Evolution of Complete Dosage Compensation in Poecilia. Genome Biol Evol 2021; 13:6317675. [PMID: 34240180 PMCID: PMC8325565 DOI: 10.1093/gbe/evab155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Dosage compensation balances gene expression between the sexes in systems with diverged heterogametic sex chromosomes. Theory predicts that dosage compensation should rapidly evolve in tandem with the divergence of sex chromosomes to prevent the deleterious effects of dosage imbalances that occur as a result of sex chromosome divergence. Examples of complete dosage compensation, where gene expression of the entire sex chromosome is compensated, are rare, and have only been found in relatively ancient sex chromosome systems. Consequently, very little is known about the evolutionary dynamics of complete dosage compensation systems. Within the family Poeciliidae the subgenus Lebistes share the same sex chromosome system which originated 18.48–26.08 Ma. In Poecilia reticulata and P. wingei, the Y chromosome has been largely maintained, whereas the Y in the closely related species P. picta and P. parae has rapidly degraded. We recently found P. picta to be the first example of complete dosage compensation in a fish. Here, we show that P. parae also has complete dosage compensation, thus complete dosage compensation likely evolved in the short (∼3.7 Myr) interval after the split of the ancestor of these two species from P. reticulata, but before they diverged from each other. These data suggest that novel dosage compensation mechanisms can evolve rapidly, thus supporting the longstanding theoretical prediction that such mechanisms arise in tandem with rapidly diverging sex chromosomes.
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Affiliation(s)
- David C H Metzger
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Canada
| | - Benjamin A Sandkam
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Canada
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Canada
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Canada.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, United Kingdom
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25
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Couger MB, Roy SW, Anderson N, Gozashti L, Pirro S, Millward LS, Kim M, Kilburn D, Liu KJ, Wilson TM, Epps CW, Dizney L, Ruedas LA, Campbell P. Sex chromosome transformation and the origin of a male-specific X chromosome in the creeping vole. Science 2021; 372:592-600. [PMID: 33958470 DOI: 10.1126/science.abg7019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022]
Abstract
The mammalian sex chromosome system (XX female/XY male) is ancient and highly conserved. The sex chromosome karyotype of the creeping vole (Microtus oregoni) represents a long-standing anomaly, with an X chromosome that is unpaired in females (X0) and exclusively maternally transmitted. We produced a highly contiguous male genome assembly, together with short-read genomes and transcriptomes for both sexes. We show that M. oregoni has lost an independently segregating Y chromosome and that the male-specific sex chromosome is a second X chromosome that is largely homologous to the maternally transmitted X. Both maternally inherited and male-specific sex chromosomes carry fragments of the ancestral Y chromosome. Consequences of this recently transformed sex chromosome system include Y-like degeneration and gene amplification on the male-specific X, expression of ancestral Y-linked genes in females, and X inactivation of the male-specific chromosome in male somatic cells. The genome of M. oregoni elucidates the processes that shape the gene content and dosage of mammalian sex chromosomes and exemplifies a rare case of plasticity in an ancient sex chromosome system.
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Affiliation(s)
- Matthew B Couger
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston MA, 02115, USA
| | - Scott W Roy
- Department of Biology, San Francisco State University, San Francisco, CA 94117, USA.,Department of Molecular and Cell Biology, University of California, Merced, Merced, CA 95343, USA
| | - Noelle Anderson
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA 95343, USA
| | - Landen Gozashti
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD 20817, USA
| | - Lindsay S Millward
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97330, USA
| | | | | | | | - Todd M Wilson
- US Forest Service, PNW Research Station, Corvallis, OR 97331, USA
| | - Clinton W Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97330, USA
| | - Laurie Dizney
- Department of Biology, University of Portland, Portland, OR 97203, USA
| | - Luis A Ruedas
- Department of Biology and Museum of Natural History, Portland State University, Portland, OR 97207, USA
| | - Polly Campbell
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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26
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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27
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Rovatsos M, Kratochvíl L. Evolution of dosage compensation does not depend on genomic background. Mol Ecol 2021; 30:1836-1845. [PMID: 33606326 DOI: 10.1111/mec.15853] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022]
Abstract
Organisms have evolved various mechanisms to cope with the differences in the gene copy numbers between sexes caused by degeneration of Y and W sex chromosomes. Complete dosage compensation or at least expression balance between sexes has been reported predominantly in XX/XY systems, but rarely in ZZ/ZW systems. However, this often-reported pattern is based on comparisons of lineages where sex chromosomes evolved from nonhomologous genomic regions, potentially differing in sensitivity to differences in gene copy numbers. Here we document that two reptilian lineages (XX/XY iguanas and ZZ/ZW softshell turtles), which independently co-opted the same ancestral genomic region for the function of sex chromosomes, evolved different gene dose regulatory mechanisms. The independent co-option of the same genomic region for the role of sex chromosomes as in the iguanas and the softshell turtles offers great opportunity for testing evolutionary scenarios on sex chromosome evolution under the explicit control of the genomic background and gene identity. We show that the parallel loss of functional genes from the Y chromosome of the green anole and the W chromosome of the Florida softshell turtle led to different dosage compensation mechanisms. Our approach controlling for genetic background thus does not support that the variability in the regulation of gene dose differences is a consequence of ancestral autosomal gene content.
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Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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28
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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29
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The evolution of sex chromosome dosage compensation in animals. J Genet Genomics 2020; 47:681-693. [PMID: 33579636 DOI: 10.1016/j.jgg.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 02/02/2023]
Abstract
The evolution of heteromorphic sex chromosomes shall lead to gene expression dosage problems, as in at least one of the sexes, the sex-linked gene dose has been reduced by half. It has been proposed that the transcriptional output of the whole X or Z chromosome should be doubled for complete dosage compensation in heterogametic sex. However, owing to the variability of the existing methods to determine the transcriptional differences between sex chromosomes and autosomes (S:A ratios) in different studies, we collected more than 500 public RNA-Seq data set from multiple tissues and species in major clades and proposed a unified computational framework for unbiased and comparable measurement of the S:A ratios of multiple species. We also tested the evolution of dosage compensation more directly by assessing changes in the expression levels of the current sex-linked genes relative to those of the ancestral sex-linked genes. We found that in mammals and birds, the S:A ratio is approximately 0.5, whereas in insects, fishes, and flatworms, the S:A ratio is approximately 1.0. Further analysis showed that the fraction of dosage-sensitive housekeeping genes on the X/Z chromosome is significantly correlated with the S:A ratio. In addition, the degree of degeneration of the Y chromosome may be responsible for the change in the S:A ratio in mammals without a dosage compensation mechanism. Our observations offer unequivocal support for the sex chromosome insensitivity hypothesis in animals and suggest that dosage sensitivity states of sex chromosomes are a major factor underlying different evolutionary strategies of dosage compensation.
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30
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X-chromosome regulation and sex differences in brain anatomy. Neurosci Biobehav Rev 2020; 120:28-47. [PMID: 33171144 DOI: 10.1016/j.neubiorev.2020.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023]
Abstract
Humans show reproducible sex-differences in cognition and psychopathology that may be contributed to by influences of gonadal sex-steroids and/or sex-chromosomes on regional brain development. Gonadal sex-steroids are well known to play a major role in sexual differentiation of the vertebrate brain, but far less is known regarding the role of sex-chromosomes. Our review focuses on this latter issue by bridging together two literatures that have to date been largely disconnected. We first consider "bottom-up" genetic and molecular studies focused on sex-chromosome gene content and regulation. This literature nominates specific sex-chromosome genes that could drive developmental sex-differences by virtue of their sex-biased expression and their functions within the brain. We then consider the complementary "top down" view, from magnetic resonance imaging studies that map sex- and sex chromosome effects on regional brain anatomy, and link these maps to regional gene-expression within the brain. By connecting these top-down and bottom-up approaches, we emphasize the potential role of X-linked genes in driving sex-biased brain development and outline key goals for future work in this field.
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31
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Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes (Basel) 2020; 11:E787. [PMID: 32668777 PMCID: PMC7397054 DOI: 10.3390/genes11070787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023] Open
Abstract
About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the >1300 sex-linked genes studied, maximum X-Y divergence was 0.13-0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.
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Affiliation(s)
- Cécile Fruchard
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - Hélène Badouin
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Ravi S. Devani
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA;
| | - Bénédicte Rhoné
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
- Institut de Recherche pour le Développement (IRD), Université Montpellier, DIADE, F-34394 Montpellier, France
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany;
| | - Anjan K. Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Gabriel A. B. Marais
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
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32
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Nielsen MM, Trolle C, Vang S, Hornshøj H, Skakkebaek A, Hedegaard J, Nordentoft I, Pedersen JS, Gravholt CH. Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:279-293. [PMID: 32489015 DOI: 10.1002/ajmg.c.31799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/21/2023]
Abstract
47,XXX (triple X) and Turner syndrome (45,X) are sex chromosomal abnormalities with detrimental effects on health with increased mortality and morbidity. In karyotypical normal females, X-chromosome inactivation balances gene expression between sexes and upregulation of the X chromosome in both sexes maintain stoichiometry with the autosomes. In 47,XXX and Turner syndrome a gene dosage imbalance may ensue from increased or decreased expression from the genes that escape X inactivation, as well as from incomplete X chromosome inactivation in 47,XXX. We aim to study genome-wide DNA-methylation and RNA-expression changes can explain phenotypic traits in 47,XXX syndrome. We compare DNA-methylation and RNA-expression data derived from white blood cells of seven women with 47,XXX syndrome, with data from seven female controls, as well as with seven women with Turner syndrome (45,X). To address these questions, we explored genome-wide DNA-methylation and transcriptome data in blood from seven females with 47,XXX syndrome, seven females with Turner syndrome, and seven karyotypically normal females (46,XX). Based on promoter methylation, we describe a demethylation of six X-chromosomal genes (AMOT, HTR2C, IL1RAPL2, STAG2, TCEANC, ZNF673), increased methylation for GEMIN8, and four differentially methylated autosomal regions related to four genes (SPEG, MUC4, SP6, and ZNF492). We illustrate how these changes seem compensated at the transcriptome level although several genes show differential exon usage. In conclusion, our results suggest an impact of the supernumerary X chromosome in 47,XXX syndrome on the methylation status of selected genes despite an overall comparable expression profile.
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Affiliation(s)
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Skakkebaek
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Claus Højbjerg Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark
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33
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Brooks W. An Epigenetics-Based Hypothesis of Autoantigen Development in Systemic Lupus Erythematosus. EPIGENOMES 2020; 4:epigenomes4020006. [PMID: 34968240 PMCID: PMC8594704 DOI: 10.3390/epigenomes4020006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/20/2020] [Indexed: 11/16/2022] Open
Abstract
Currently, we have a limited understanding of mechanisms leading to systemic lupus erythematosus, but we know that genetics, environmental factors, and epigenetics contribute to the disease. One common aspect of the various environmental triggers is that they can cause cellular stress. When extraordinary stress occurs, such as viral activation, a cell's response can include increased nucleolar volume and activity to produce more machinery (e.g., ribosomes) to help the cell recover. However, nucleolar expansion can disrupt the epigenetic control in neighboring heterochromatin that comprises the nucleolar shell. This disruption can open underlying vulnerabilities that provoke an autoimmune reaction. Here, we review the "X chromosome-nucleolus nexus" hypothesis, which explains how nucleolar stress can disrupt epigenetically silenced chromatin, especially the neighboring inactive X chromosome (aka the nucleolar satellite). Chromatin disruption can lead to the expression of sequestered DNA, such as Alu elements and fully functional LINE-1 reverse transcriptase genes. In addition, Alu transcripts can disrupt the nucleolar structural integrity, leading to nucleolar disintegration. Such disintegration can leave nucleolar components and products in autoantigenic forms, such as abnormal conformations or incomplete macromolecular assemblies. Recent research on DNA sensing pathways can now be incorporated into the hypothesis to provide further details explaining how autoantibodies to endogenous nucleic acids arise.
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Affiliation(s)
- Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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34
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A robust test for X-chromosome genetic association accounting for X-chromosome inactivation and imprinting. Genet Res (Camb) 2020; 102:e2. [PMID: 32234109 PMCID: PMC7132553 DOI: 10.1017/s0016672320000026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The X chromosome is known to play an important role in many sex-specific diseases. However, only a few single-nucleotide polymorphisms on the X chromosome have been found to be associated with diseases. Compared to the autosomes, conducting association tests on the X chromosome is more intractable due to the difference in the number of X chromosomes between females and males. On the other hand, X-chromosome inactivation takes place in female mammals, which is a phenomenon in which the expression of one copy of two X chromosomes in females is silenced in order to achieve the same gene expression level as that in males. In addition, imprinting effects may be related to certain diseases. Currently, there are some existing approaches taking X-chromosome inactivation into account when testing for associations on the X chromosome. However, none of them allows for imprinting effects. Therefore, in this paper, we propose a robust test, ZXCII, which accounts for both X-chromosome inactivation and imprinting effects without requiring specifying the genetic models in advance. Simulation studies are conducted in order to investigate the validity and performance of ZXCII under various scenarios of different parameter values. The simulation results show that ZXCII controls the type I error rate well when there is no association. Furthermore, with regards to power, ZXCII is robust in all of the situations considered and generally outperforms most of the existing methods in the presence of imprinting effects, especially under complete imprinting effects.
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35
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Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage. Proc Natl Acad Sci U S A 2020; 117:4864-4873. [PMID: 32071206 PMCID: PMC7060706 DOI: 10.1073/pnas.1910003117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Turner syndrome (TS) is caused by having only one X chromosome (X0), and Klinefelter syndrome (KS) by having two X chromosomes and one Y chromosome (XXY). In this study we carried out a direct comparison analysis of the effect these chromosome copy number aberrations have on gene expression networks, analyzing genes located on the X chromosome or anywhere else in the genome, in primary samples from KS and TS patients. In both KS and TS, we found gene expression level changes not only in genes on the X chromosome, but also in many genes on all the other chromosomes, revealing a genomewide ripple effect of the chromosome X copy number aberrations. In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. We report a comparative analysis of TS vs. KS regarding differences at the genomic network level measured in primary samples by analyzing gene expression, DNA methylation, and chromatin conformation. X-chromosome inactivation (XCI) silences transcription from one X chromosome in female mammals, on which most genes are inactive, and some genes escape from XCI. In TS, almost all differentially expressed escape genes are down-regulated but most differentially expressed inactive genes are up-regulated. In KS, differentially expressed escape genes are up-regulated while the majority of inactive genes appear unchanged. Interestingly, 94 differentially expressed genes (DEGs) overlapped between TS and female and KS and male comparisons; and these almost uniformly display expression changes into opposite directions. DEGs on the X chromosome and the autosomes are coexpressed in both syndromes, indicating that there are molecular ripple effects of the changes in X chromosome dosage. Six potential candidate genes (RPS4X, SEPT6, NKRF, CX0rf57, NAA10, and FLNA) for KS are identified on Xq, as well as candidate central genes on Xp for TS. Only promoters of inactive genes are differentially methylated in both syndromes while escape gene promoters remain unchanged. The intrachromosomal contact map of the X chromosome in TS exhibits the structure of an active X chromosome. The discovery of shared DEGs indicates the existence of common molecular mechanisms for gene regulation in TS and KS that transmit the gene dosage changes to the transcriptome.
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36
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Bajic VP, Essack M, Zivkovic L, Stewart A, Zafirovic S, Bajic VB, Gojobori T, Isenovic E, Spremo-Potparevic B. The X Files: "The Mystery of X Chromosome Instability in Alzheimer's Disease". Front Genet 2020; 10:1368. [PMID: 32047510 PMCID: PMC6997486 DOI: 10.3389/fgene.2019.01368] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics.
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Affiliation(s)
- Vladan P Bajic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lada Zivkovic
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Alan Stewart
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Sonja Zafirovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Esma Isenovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
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37
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Abstract
Diverse dosage compensation mechanisms have evolved across species to equalize gene expression between sexes and between the sex chromosomes and autosomes. New results show that two opposite modes of dosage compensation can occur within one species, the monarch butterfly.
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Affiliation(s)
- Jingyue Duan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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38
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Posynick BJ, Brown CJ. Escape From X-Chromosome Inactivation: An Evolutionary Perspective. Front Cell Dev Biol 2019; 7:241. [PMID: 31696116 PMCID: PMC6817483 DOI: 10.3389/fcell.2019.00241] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes originate as a pair of homologus autosomes that then follow a general pattern of divergence. This is evident in mammalian sex chromosomes, which have undergone stepwise recombination suppression events that left footprints of evolutionary strata on the X chromosome. The loss of genes on the Y chromosome led to Ohno’s hypothesis of dosage equivalence between XY males and XX females, which is achieved through X-chromosome inactivation (XCI). This process transcriptionally silences all but one X chromosome in each female cell, although 15–30% of human X-linked genes still escape inactivation. There are multiple evolutionary pathways that may lead to a gene escaping XCI, including remaining Y chromosome homology, or female advantage to escape. The conservation of some escape genes across multiple species and the ability of the mouse inactive X to recapitulate human escape status both suggest that escape from XCI is controlled by conserved processes. Evolutionary pressures to minimize dosage imbalances have led to the accumulation of genetic elements that favor either silencing or escape; lack of dosage sensitivity might also allow for the escape of flanking genes near another escapee, if a boundary element is not present between them. Delineation of the elements involved in escape is progressing, but mechanistic understanding of how they interact to allow escape from XCI is still lacking. Although increasingly well-studied in humans and mice, non-trivial challenges to studying escape have impeded progress in other species. Mouse models that can dissect the role of the sex chromosomes distinct from sex of the organism reveal an important contribution for escape genes to multiple diseases. In humans, with their elevated number of escape genes, the phenotypic consequences of sex chromosome aneuplodies and sexual dimorphism in disease both highlight the importance of escape genes.
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Affiliation(s)
- Bronwyn J Posynick
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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39
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Gravholt CH, Viuff MH, Brun S, Stochholm K, Andersen NH. Turner syndrome: mechanisms and management. Nat Rev Endocrinol 2019; 15:601-614. [PMID: 31213699 DOI: 10.1038/s41574-019-0224-4] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Turner syndrome is a rare condition in women that is associated with either complete or partial loss of one X chromosome, often in mosaic karyotypes. Turner syndrome is associated with short stature, delayed puberty, ovarian dysgenesis, hypergonadotropic hypogonadism, infertility, congenital malformations of the heart, endocrine disorders such as type 1 and type 2 diabetes mellitus, osteoporosis and autoimmune disorders. Morbidity and mortality are increased in women with Turner syndrome compared with the general population and the involvement of multiple organs through all stages of life necessitates a multidisciplinary approach to care. Despite an often conspicuous phenotype, the diagnostic delay can be substantial and the average age at diagnosis is around 15 years of age. However, numerous important clinical advances have been achieved, covering all specialty fields involved in the care of girls and women with Turner syndrome. Here, we present an updated Review of Turner syndrome, covering advances in genetic and genomic mechanisms of disease, associated disorders and multidisciplinary approaches to patient management, including growth hormone therapy and hormone replacement therapy.
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Affiliation(s)
- Claus H Gravholt
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| | - Mette H Viuff
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sara Brun
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Kirstine Stochholm
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Centre for Rare Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Niels H Andersen
- Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
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40
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Xu H, Liu JJ, Liu Z, Li Y, Jin YS, Zhang J. Synchronization of stochastic expressions drives the clustering of functionally related genes. SCIENCE ADVANCES 2019; 5:eaax6525. [PMID: 31633028 PMCID: PMC6785257 DOI: 10.1126/sciadv.aax6525] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 05/18/2023]
Abstract
Functionally related genes tend to be chromosomally clustered in eukaryotic genomes even after the exclusion of tandem duplicates, but the biological significance of this widespread phenomenon is unclear. We propose that stochastic expression fluctuations of neighboring genes resulting from chromatin dynamics are more or less synchronized such that their expression ratio is more stable than that for unlinked genes. Consequently, chromosomal clustering could be advantageous when the expression ratio of the clustered genes needs to stay constant, for example, because of the accumulation of toxic compounds when this ratio is altered. Evidence from manipulative experiments on the yeast GAL cluster, comprising three chromosomally adjacent genes encoding enzymes catalyzing consecutive reactions in galactose catabolism, unequivocally supports this hypothesis and elucidates how disorder in one biological phenomenon-gene expression noise-could prompt the emergence of order in another-genome organization.
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Affiliation(s)
- Haiqing Xu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhen Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ying Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author.
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41
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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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42
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Peeters SB, Korecki AJ, Baldry SEL, Yang C, Tosefsky K, Balaton BP, Simpson EM, Brown CJ. How do genes that escape from X-chromosome inactivation contribute to Turner syndrome? AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:28-35. [PMID: 30779428 DOI: 10.1002/ajmg.c.31672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022]
Abstract
X-chromosome inactivation generally results in dosage equivalence for expression of X-linked genes between 46,XY males and 46,XX females. The 20-30% of genes that escape silencing are thus candidates for having a role in the phenotype of Turner syndrome. Understanding which genes escape from silencing, and how they avoid this chromosome-wide inactivation is therefore an important step toward understanding Turner Syndrome. We have examined the mechanism of escape using a previously reported knock-in of a BAC containing the human escape gene RPS4X in mouse. We now demonstrate that escape from inactivation for RPS4X is already established by embryonic Day 9.5, and that both silencing and escape are faithfully maintained across the lifespan. No overt abnormalities were observed for transgenic mice up to 1 year of age despite robust transcription of the human RPS4X gene with no detectable downregulation of the mouse homolog. However, there was no significant increase in protein levels, suggesting translational compensation in the mouse. Finally, while many of the protein-coding genes have been assessed for their inactivation status, less is known about the X-linked RNA genes, and we propose that for many microRNA genes their inactivation status can be predicted as they are intronic to genes for which the inactivation status is known.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Sarah E L Baldry
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Christine Yang
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Kira Tosefsky
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Bradley P Balaton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Elizabeth M Simpson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
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43
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Abstract
Sex differences exist in the regulation of energy homeostasis. Better understanding of the underlying mechanisms for sexual dimorphism in energy balance may facilitate development of gender-specific therapies for human diseases, e.g. obesity. Multiple organs, including the brain, liver, fat and muscle, play important roles in the regulations of feeding behavior, energy expenditure and physical activity, which therefore contribute to the maintenance of energy balance. It has been increasingly appreciated that this multi-organ system is under different regulations in male vs. female animals. Much of effort has been focused on roles of sex hormones (including androgens, estrogens and progesterone) and sex chromosomes in this sex-specific regulation of energy balance. Emerging evidence also indicates that other factors (not sex hormones/receptors and not encoded by the sex chromosomes) exist to regulate energy homeostasis differentially in males vs. females. In this review, we summarize factors and signals that have been shown to regulate energy homeostasis in a sexually dimorphic fashion and propose a framework where these factors and signals may be integrated to mediate sex differences in energy homeostasis.
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Affiliation(s)
- Chunmei Wang
- Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030
| | - Yong Xu
- Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030
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44
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Martin H, Carpentier F, Gallina S, Godé C, Schmitt E, Muyle A, Marais GAB, Touzet P. Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems. Genome Biol Evol 2019; 11:350-361. [PMID: 30649306 PMCID: PMC6364797 DOI: 10.1093/gbe/evz001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 12/14/2022] Open
Abstract
In the last decade, progress has been made in methods to identify the sex determination system in plants. This gives the opportunity to study sex chromosomes that arose independently at different phylogenetic scales, and thus allows the discovery and the understanding of early stages of sex chromosome evolution. In the genus Silene, sex chromosomes have evolved independently in at least two clades from a nondioecious ancestor, the Melandrium and Otites sections. In the latter, sex chromosomes could be younger than in the section Melandrium, based on phylogenetic studies and as no heteromorphic sex chromosomes have been detected. This section might also exhibit lability in sex determination, because male heterogamy and female heterogamy have been suggested to occur. In this study, we investigated the sex determination system of two dioecious species in the section Otites (Silene otites and its close relative Silene pseudotites). Applying the new probabilistic method SEX-DETector on RNA-seq data from cross-controlled progenies, we inferred their most likely sex determination system and a list of putative autosomal and sex-linked contigs. We showed that the two phylogenetically close species differed in their sex determination system (XY versus ZW) with sex chromosomes that derived from two different pairs of autosomes. We built a genetic map of the sex chromosomes and showed that both pairs exhibited a large region with lack of recombination. However, the sex-limited chromosomes exhibited no strong degeneration. Finally, using the “ancestral” autosomal expression of sex-linked orthologs of nondioecious S. nutans, we found a slight signature of dosage compensation in the heterogametic females of S. otites.
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Affiliation(s)
- Hélène Martin
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France.,Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Fantin Carpentier
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France.,Ecologie Systématique Evolution, Université Paris Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | | | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France
| | - Eric Schmitt
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France
| | - Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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45
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Duan JE, Flock K, Jue N, Zhang M, Jones A, Seesi SA, Mandoiu I, Pillai S, Hoffman M, O'Neill R, Zinn S, Govoni K, Reed S, Jiang H, Jiang ZC, Tian XC. Dosage Compensation and Gene Expression of the X Chromosome in Sheep. G3 (BETHESDA, MD.) 2019; 9:305-314. [PMID: 30482800 PMCID: PMC6325915 DOI: 10.1534/g3.118.200815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022]
Abstract
Ohno's hypothesis predicts that the expression of the single X chromosome in males needs compensatory upregulation to balance its dosage with that of the diploid autosomes. Additionally, X chromosome inactivation ensures that quadruple expression of the two X chromosomes is avoided in females. These mechanisms have been actively studied in mice and humans but lag behind in domestic species. Using RNA sequencing data, we analyzed the X chromosome upregulation in sheep fetal tissues from day 135 of gestation under control, over or restricted maternal diets (100%, 140% and 60% of National Research Council Total Digestible Nutrients), and in conceptuses, juvenile, and adult somatic tissues. By computing the mean expression ratio of all X-linked genes to all autosomal genes (X:A), we found that all samples displayed some levels of X chromosome upregulation. The degrees of X upregulation were not significant (P-value = 0.74) between ovine females and males in the same somatic tissues. Brain, however, displayed complete X upregulation. Interestingly, the male and female reproduction-related tissues exhibited divergent X dosage upregulation. Moreover, expression upregulation of the X chromosome in fetal tissues was not affected by maternal diets. Maternal nutrition, however, did change expression levels of several X-linked genes, such as sex determination genes SOX3 and NR0B1 In summary, our results showed that X chromosome upregulation occurred in nearly all sheep somatic tissues analyzed, thus support Ohno's hypothesis in a new species. However, the levels of upregulation differed by different subgroups of genes such as those that are house-keeping and "dosage-sensitive".
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Affiliation(s)
| | | | - Nathanial Jue
- School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93955
| | - Mingyuan Zhang
- Department of Animal Science
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China
| | | | - Sahar Al Seesi
- Smith College Department of Computer Science, Northampton, MA 01063
- Department of Computer Science
| | | | | | | | - Rachel O'Neill
- Department of Molecular and Cell Biology, and University of Connecticut, Storrs, CT, 06269
| | | | | | | | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China, and
| | - Zongliang Carl Jiang
- Department of Animal Science
- School of Animal Science, Louisiana State University, Baton Rouge, LA 70803
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46
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Duan JE, Shi W, Jue NK, Jiang Z, Kuo L, O'Neill R, Wolf E, Dong H, Zheng X, Chen J, Tian XC. Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos, and Somatic Tissues. Genome Biol Evol 2019; 11:242-252. [PMID: 30566637 PMCID: PMC6354180 DOI: 10.1093/gbe/evy270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression ratio of X- and A-linked genes has been relatively well studied in humans and mice, despite controversial results over the existence of upregulation of X-linked genes. Here we report the first comprehensive test of Ohno’s hypothesis in bovine preattachment embryos, germline, and somatic tissues. Overall an incomplete dosage compensation (0.5 < X:A < 1) of expressed genes and an excess X dosage compensation (X:A > 1) of ubiquitously expressed “dosage-sensitive” genes were seen. No significant differences in X:A ratios were observed between bovine female and male somatic tissues, further supporting Ohno’s hypothesis. Interestingly, preimplantation embryos manifested a unique pattern of X dosage compensation dynamics. Specifically, X dosage decreased after fertilization, indicating that the sperm brings in an inactive X to the matured oocyte. Subsequently, the activation of the bovine embryonic genome enhanced expression of X-linked genes and increased the X dosage. As a result, an excess compensation was exhibited from the 8-cell stage to the compact morula stage. The X dosage peaked at the 16-cell stage and stabilized after the blastocyst stage. Together, our findings confirm Ohno’s hypothesis of X dosage compensation in the bovine and extend it by showing incomplete and over-compensation for expressed and “dosage-sensitive” genes, respectively.
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Affiliation(s)
| | - Wei Shi
- Department of Statistics, University of Connecticut, Storrs, CT
| | - Nathaniel K Jue
- School of Natural Sciences, California State University, Monterey Bay, CA
| | - Zongliang Jiang
- School of Animal Science, Louisiana State University, Agricultural Center, Baton Rouge, LA
| | - Lynn Kuo
- Department of Statistics, University of Connecticut, Storrs, CT
| | - Rachel O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT
| | - Eckhard Wolf
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität Muünchen, Germany
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, P.R. China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, P.R. China
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, P.R. China
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Hou J, Shi X, Chen C, Islam MS, Johnson AF, Kanno T, Huettel B, Yen MR, Hsu FM, Ji T, Chen PY, Matzke M, Matzke AJM, Cheng J, Birchler JA. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proc Natl Acad Sci U S A 2018; 115:E11321-E11330. [PMID: 30429332 PMCID: PMC6275517 DOI: 10.1073/pnas.1807796115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
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Affiliation(s)
- Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Md Soliman Islam
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Adam F Johnson
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam 550000
| | - Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding, Cologne, Germany 50829
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Fei-Man Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO 65211
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211;
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48
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Muyle A, Zemp N, Fruchard C, Cegan R, Vrana J, Deschamps C, Tavares R, Hobza R, Picard F, Widmer A, Marais GAB. Genomic imprinting mediates dosage compensation in a young plant XY system. NATURE PLANTS 2018; 4:677-680. [PMID: 30104649 DOI: 10.1038/s41477-018-0221-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/16/2018] [Indexed: 05/06/2023]
Abstract
Sex chromosomes have repeatedly evolved from a pair of autosomes. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced expression and eventual loss of Y genes1. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes. A diverse set of dosage compensating mechanisms that alleviates these negative effects has been described in animals2-4. However, the early steps in the evolution of dosage compensation remain unknown, and dosage compensation is poorly understood in plants5. Here, we describe a dosage compensation mechanism in the evolutionarily young XY sex determination system of the plant Silene latifolia. Genomic imprinting results in higher expression from the maternal X chromosome in both males and females. This compensates for reduced Y expression in males, but results in X overexpression in females and may be detrimental. It could represent a transient early stage in the evolution of dosage compensation. Our finding has striking resemblance to the first stage proposed by Ohno6 for the evolution of X inactivation in mammals.
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Affiliation(s)
- Aline Muyle
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France.
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Cécile Fruchard
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
| | - Radim Cegan
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Vrana
- Institute of Experimental Botany, Center of the Hana Region for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Raquel Tavares
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
| | - Roman Hobza
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Institute of Experimental Botany, Center of the Hana Region for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Franck Picard
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Gabriel A B Marais
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
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49
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Wei X, Zhang J. On the Origin of Compositional Features of Ribosomes. Genome Biol Evol 2018; 10:2010-2016. [PMID: 30059996 PMCID: PMC6097593 DOI: 10.1093/gbe/evy169] [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] [Accepted: 07/28/2018] [Indexed: 01/08/2023] Open
Abstract
Ribosomes are highly abundant in cells and comprise, besides RNAs of varying lengths, 55–80 similarly sized, short proteins. This seemingly unusual composition is thought to have resulted from selection for rapid autocatalytic ribosome production. Here, we demonstrate that ribosomal protein-splitting mutations cannot accelerate ribosome production. The autocatalytic explanation is also unnecessary, because protein lengths generally decline with expression levels. Although ribosomal proteins are shorter than expected from their expression levels, they are not outliers among members of large protein complexes in mean protein length or coefficient of variation. These observations are explainable because 1) shortening proteins lowers their synthetic cost and reduces the waste from mistranslation-induced protein dysfunction and degradation, 2) such benefits rise with expression levels, and 3) members of large complexes participate in more protein–protein interactions so are less tolerant to mistranslation. These and other considerations suggest that the compositional features of ribosomes originate from cellular energy economics.
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Affiliation(s)
- Xinzhu Wei
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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50
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Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding CG, Couté Y, Vicoso B. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife 2018; 7:e35684. [PMID: 30044216 PMCID: PMC6089595 DOI: 10.7554/elife.35684] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/16/2018] [Indexed: 12/05/2022] Open
Abstract
XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno's classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes.
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Affiliation(s)
| | - Celine Cosseau
- University of Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University MontpellierPerpignanFrance
| | - Sabrina Ferré
- Université Grenoble Alpes, CEA, Inserm, BIG-BGEGrenobleFrance
| | - Thomas Quack
- Institute for Parasitology, Biomedical Research Center SeltersbergJustus-Liebig-UniversityGiessenGermany
| | - Christoph G Grevelding
- Institute for Parasitology, Biomedical Research Center SeltersbergJustus-Liebig-UniversityGiessenGermany
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BIG-BGEGrenobleFrance
| | - Beatriz Vicoso
- Institute of Science and Technology AustriaKlosterneuburgAustria
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