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Aghaieabiane N, Koutis I. SGCP: a spectral self-learning method for clustering genes in co-expression networks. BMC Bioinformatics 2024; 25:230. [PMID: 38956463 PMCID: PMC11221046 DOI: 10.1186/s12859-024-05848-w] [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: 04/26/2023] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND A widely used approach for extracting information from gene expression data employs the construction of a gene co-expression network and the subsequent computational detection of gene clusters, called modules. WGCNA and related methods are the de facto standard for module detection. The purpose of this work is to investigate the applicability of more sophisticated algorithms toward the design of an alternative method with enhanced potential for extracting biologically meaningful modules. RESULTS We present self-learning gene clustering pipeline (SGCP), a spectral method for detecting modules in gene co-expression networks. SGCP incorporates multiple features that differentiate it from previous work, including a novel step that leverages gene ontology (GO) information in a self-leaning step. Compared with widely used existing frameworks on 12 real gene expression datasets, we show that SGCP yields modules with higher GO enrichment. Moreover, SGCP assigns highest statistical importance to GO terms that are mostly different from those reported by the baselines. CONCLUSION Existing frameworks for discovering clusters of genes in gene co-expression networks are based on relatively simple algorithmic components. SGCP relies on newer algorithmic techniques that enable the computation of highly enriched modules with distinctive characteristics, thus contributing a novel alternative tool for gene co-expression analysis.
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Affiliation(s)
- Niloofar Aghaieabiane
- Computer Science Department, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Ioannis Koutis
- Computer Science Department, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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2
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Lauria Sneideman MP, Meller VH. Master regulator of a mosquito X chromosome discovered. Nature 2023; 623:34-35. [PMID: 37770657 DOI: 10.1038/d41586-023-02972-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
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3
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AlSiraj Y, Thatcher SE, Blalock E, Saintilnord WN, Daugherty A, Lu HS, Luo W, Shen YH, LeMaire SA, Arnold AP, Cassis LA. Monosomy X in Female Mice Influences the Regional Formation and Augments the Severity of Angiotensin II-Induced Aortopathies. Arterioscler Thromb Vasc Biol 2021; 41:269-283. [PMID: 33054396 PMCID: PMC8259710 DOI: 10.1161/atvbaha.120.314407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Turner syndrome women (monosomy X) have high risk of aortopathies consistent with a role for sex chromosomes in disease development. We demonstrated that sex chromosomes influence regional development of Ang II (angiotensin II)-induced aortopathies in mice. In this study, we determined if the number of X chromosomes regulates regional development of Ang II-induced aortopathies. Approach and Results: We used females with varying numbers of X chromosomes (XX female mice [XXF] or XO female mice [XOF]) on an C57BL/6J (ascending aortopathies) or low-density lipoprotein receptor deficient (Ldlr-/-) background (descending and abdominal aortopathies) compared with XY males (XYM). To induce aortopathies, mice were infused with Ang II. XOF (C57BL/6J) exhibited larger percent increases in ascending aortic lumen diameters than Ang II-infused XXF or XYM. Ang II-infused XOF (Ldlr-/-) exhibited similar incidences of thoracic (XOF, 50%; XYM, 71%) and abdominal aortopathies (XOF, 83%; XYM, 71%) as XYM, which were greater than XXF (XXF, 0%). Abdominal aortic lumen diameters and maximal external diameters were similar between XOF and XYM but greater than XXF, and these effects persisted with extended Ang II infusions. Larger aortic lumen diameters, abdominal aortopathy incidence (XXF, 20%; XOF, 75%), and maximal aneurysm diameters (XXF, 1.02±0.17; XOF, 1.96±0.32 mm; P=0.027) persisted in ovariectomized Ang II-infused XOF mice. Data from RNA-seq demonstrated that X chromosome genes that escape X-inactivation (histone lysine demethylases Kdm5c and Kdm6a) exhibited lower mRNA abundance in aortas of XOF than XXF (P=0.033 and 0.024, respectively). Conversely, DNA methylation was higher in aortas of XOF than XXF (P=0.038). CONCLUSIONS The absence of a second X chromosome promotes diffuse Ang II-induced aortopathies in females.
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MESH Headings
- Angiotensin II
- Animals
- Aorta, Abdominal/metabolism
- Aorta, Abdominal/pathology
- Aorta, Thoracic/metabolism
- Aorta, Thoracic/pathology
- Aortic Aneurysm, Abdominal/chemically induced
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/metabolism
- Aortic Aneurysm, Abdominal/pathology
- Aortic Aneurysm, Thoracic/chemically induced
- Aortic Aneurysm, Thoracic/genetics
- Aortic Aneurysm, Thoracic/metabolism
- Aortic Aneurysm, Thoracic/pathology
- DNA Methylation
- Disease Models, Animal
- Female
- Histone Demethylases/genetics
- Histone Demethylases/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Ovariectomy
- Receptors, LDL/deficiency
- Receptors, LDL/genetics
- Severity of Illness Index
- Turner Syndrome/complications
- Turner Syndrome/genetics
- Mice
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Affiliation(s)
- Yasir AlSiraj
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
| | - Sean E. Thatcher
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
| | - Eric Blalock
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
| | - Wesley N. Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY
| | - Alan Daugherty
- Department of Physiology, University of Kentucky, Lexington KY
- Saha Cardiovascular Research Center, University of Kentucky, Lexington KY
| | - Hong S. Lu
- Department of Physiology, University of Kentucky, Lexington KY
- Saha Cardiovascular Research Center, University of Kentucky, Lexington KY
| | - Wei Luo
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, and Department of Cardiovascular Surgery, Texas Heart Institute, Houston TX
| | - Ying H. Shen
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, and Department of Cardiovascular Surgery, Texas Heart Institute, Houston TX
| | - Scott A. LeMaire
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, and Department of Cardiovascular Surgery, Texas Heart Institute, Houston TX
| | - Arthur P. Arnold
- Integrative Biology and Physiology, University of California, Los Angeles CA
| | - Lisa A. Cassis
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
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4
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Santos-Rebouças CB, Boy R, Vianna EQ, Gonçalves AP, Piergiorge RM, Abdala BB, Dos Santos JM, Calassara V, Machado FB, Medina-Acosta E, Pimentel MMG. Skewed X-Chromosome Inactivation and Compensatory Upregulation of Escape Genes Precludes Major Clinical Symptoms in a Female With a Large Xq Deletion. Front Genet 2020; 11:101. [PMID: 32194616 PMCID: PMC7064548 DOI: 10.3389/fgene.2020.00101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/29/2020] [Indexed: 11/13/2022] Open
Abstract
In mammalian females, X-chromosome inactivation (XCI) acts as a dosage compensation mechanism that equalizes X-linked genes expression between homo- and heterogametic sexes. However, approximately 12–23% of X-linked genes escape from XCI, being bi-allelic expressed. Herein, we report on genetic and functional data from an asymptomatic female of a Fragile X syndrome family, who harbors a large deletion on the X-chromosome. Array-CGH uncovered that the de novo, terminal, paternally originated 32 Mb deletion on Xq25-q28 spans 598 RefSeq genes, including escape and variable escape genes. Androgen receptor (AR) and retinitis pigmentosa 2 (RP2) methylation assays showed extreme skewed XCI ratios from both peripheral blood and buccal mucosa, silencing the abnormal X-chromosome. Surprisingly, transcriptome-wide analysis revealed that escape and variable escape genes spanning the deletion are mostly upregulated on the active X-chromosome, precluding major clinical/cognitive phenotypes in the female. Metaphase high count, hemizygosity concordance for microsatellite markers, and monoallelic expression of genes within the deletion suggest the absence of mosaicism in both blood and buccal mucosa. Taken together, our data suggest that an additional protective gene-by-gene mechanism occurs at the transcriptional level in the active X-chromosome to counterbalance detrimental phenotype effects of large Xq deletions.
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Affiliation(s)
- Cíntia B Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Boy
- Pedro Ernesto University Hospital, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evelyn Q Vianna
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andressa P Gonçalves
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael M Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca B Abdala
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jussara M Dos Santos
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Veluma Calassara
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe B Machado
- Department of Biological Sciences, Minas Gerais State University, Ubá, Brazil
| | - Enrique Medina-Acosta
- Laboratory of Biotechnology, State University of Northern Rio de Janeiro Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Márcia M G Pimentel
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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5
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Chen L, Wang L, Cheng Q, Tu YX, Yang Z, Li RZ, Luo ZH, Chen ZX. Anti-masculinization induced by aromatase inhibitors in adult female zebrafish. BMC Genomics 2020; 21:22. [PMID: 31910818 PMCID: PMC6947999 DOI: 10.1186/s12864-019-6437-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/29/2019] [Indexed: 01/03/2023] Open
Abstract
Background Early sex differentiation genes of zebrafish remain an unsolved mystery due to the difficulty to distinguish the sex of juvenile zebrafish. However, aromatase inhibitors (AIs) could direct juvenile zebrafish sex differentiation to male and even induce ovary-to-testis reversal in adult zebrafish. Results In order to determine the transcriptomic changes of sex differentiation in juvenile zebrafish and early sex-reversal in adult zebrafish, we sequenced the transcriptomes of juvenile and adult zebrafish treated with AI exemestane (EM) for 32 days, when juvenile zebrafish sex differentiation finished. EM treatment in females up-regulated the expression of genes involved in estrogen metabolic process, female gamete generation and oogenesis, including gsdf, macf1a and paqr5a, while down-regulated the expression of vitellogenin (vtg) genes, including vtg6, vtg2, vtg4, and vtg7 due to the lower level of Estradiol (E2). Furthermore, EM-juveniles showed up-regulation in genes related to cell death and apoptosis, such as bcl2l16 and anax1c, while the control-juveniles exhibited up-regulation of genes involved in positive regulation of reproductive process and oocyte differentiation such as zar1 and zpcx. Moreover, EM-females showed higher enrichment than control females in genes involved in VEGF signaling pathway, glycosaminoglycan degradation, hedgehog signaling pathway, GnRH signaling pathway and steroid hormone biosynthesis. Conclusions Our study shows anti-masculinization in EM-treated adult females but not in EM-treated juveniles. This may be responsible for the lower sex plasticity in adults than juveniles.
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Affiliation(s)
- Lu Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Li Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Qiwei Cheng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yi-Xuan Tu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Zhuang Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Run-Ze Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Zhi-Hui Luo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Zhen-Xia Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
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6
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Bhardwaj V, Semplicio G, Erdogdu NU, Manke T, Akhtar A. MAPCap allows high-resolution detection and differential expression analysis of transcription start sites. Nat Commun 2019; 10:3219. [PMID: 31363093 PMCID: PMC6667505 DOI: 10.1038/s41467-019-11115-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/20/2019] [Indexed: 01/06/2023] Open
Abstract
The position, shape and number of transcription start sites (TSS) are critical determinants of gene regulation. Most methods developed to detect TSSs and study promoter usage are, however, of limited use in studies that demand quantification of expression changes between two or more groups. In this study, we combine high-resolution detection of transcription start sites and differential expression analysis using a simplified TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with the software icetea. Applying MAPCap on developing Drosophila melanogaster embryos and larvae, we detected stage and sex-specific promoter and enhancer activity and quantify the effect of mutants of maleless (MLE) helicase at X-chromosomal promoters. We observe that MLE mutation leads to a median 1.9 fold drop in expression of X-chromosome promoters and affects the expression of several TSSs with a sexually dimorphic expression on autosomes. Our results provide quantitative insights into promoter activity during dosage compensation. The position, shape and number of transcription start sites (TSS) regulate gene expression. Here authors present MAPCap, a method for high-resolution detection and differential expression analysis of TSS, and apply MAPCap to early fly development, detecting stage and sex-specific promoter and enhancer activity.
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Affiliation(s)
- Vivek Bhardwaj
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Giuseppe Semplicio
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.
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7
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Malacrinò A, Kimber CM, Brengdahl M, Friberg U. Heightened condition-dependence of the sexual transcriptome as a function of genetic quality in Drosophila melanogaster head tissue. Proc Biol Sci 2019; 286:20190819. [PMID: 31288700 DOI: 10.1098/rspb.2019.0819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Theory suggests sexual traits should show heightened condition-dependent expression. This prediction has been tested extensively in experiments where condition has been manipulated through environmental quality. Condition-dependence as a function of genetic quality has, however, only rarely been addressed, despite its central importance in evolutionary theory. To address the effect of genetic quality on expression of sexual and non-sexual traits, we here compare gene expression in Drosophila melanogaster head tissue between flies with intact genomes (high condition) and flies carrying a major deleterious mutation (low condition). We find that sex-biased genes show heightened condition-dependent expression in both sexes, and that expression in low condition males and females regresses towards a more similar expression profile. As predicted, sex-biased expression was more sensitive to condition in males compared to females, but surprisingly female-biased, rather than male-biased, genes show higher sensitivity to condition in both sexes. Our results thus support the fundamental predictions of the theory of condition-dependence when condition is a function of genetic quality.
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Affiliation(s)
- Antonino Malacrinò
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden.,2 Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210 , USA
| | - Christopher M Kimber
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden
| | - Martin Brengdahl
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden
| | - Urban Friberg
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden
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8
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Kim M, Faucillion ML, Larsson J. RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation. PLoS Genet 2018; 14:e1007842. [PMID: 30532158 PMCID: PMC6301720 DOI: 10.1371/journal.pgen.1007842] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/20/2018] [Accepted: 11/20/2018] [Indexed: 02/03/2023] Open
Abstract
In Drosophila melanogaster, the male-specific lethal (MSL) complex plays a key role in dosage compensation by stimulating expression of male X-chromosome genes. It consists of MSL proteins and two long noncoding RNAs, roX1 and roX2, that are required for spreading of the complex on the chromosome and are redundant in the sense that loss of either does not affect male viability. However, despite rapid evolution, both roX species are present in diverse Drosophilidae species, raising doubts about their full functional redundancy. Thus, we have investigated consequences of deleting roX1 and/or roX2 to probe their specific roles and redundancies in D. melanogaster. We have created a new mutant allele of roX2 and show that roX1 and roX2 have partly separable functions in dosage compensation. In larvae, roX1 is the most abundant variant and the only variant present in the MSL complex when the complex is transmitted (physically associated with the X-chromosome) in mitosis. Loss of roX1 results in reduced expression of the genes on the X-chromosome, while loss of roX2 leads to MSL-independent upregulation of genes with male-biased testis-specific transcription. In roX1 roX2 mutant, gene expression is strongly reduced in a manner that is not related to proximity to high-affinity sites. Our results suggest that high tolerance of mis-expression of the X-chromosome has evolved. We propose that this may be a common property of sex-chromosomes, that dosage compensation is a stochastic process and its precision for each individual gene is regulated by the density of high-affinity sites in the locus.
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Affiliation(s)
- Maria Kim
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | - Jan Larsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- * E-mail:
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9
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Lee H, Oliver B. Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains. Epigenetics Chromatin 2018; 11:62. [PMID: 30355339 PMCID: PMC6199721 DOI: 10.1186/s13072-018-0232-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/15/2018] [Indexed: 12/20/2022] Open
Abstract
Background In animals with XY sex chromosomes, X-linked genes from a single X chromosome in males are imbalanced relative to autosomal genes. To minimize the impact of genic imbalance in male Drosophila, there is a dosage compensation complex (MSL) that equilibrates X-linked gene expression with the autosomes. There are other potential contributions to dosage compensation. Hemizygous autosomal genes located in repressive chromatin domains are often derepressed. If this homolog-dependent repression occurs on the X, which has no pairing partner, then derepression could contribute to male dosage compensation. Results We asked whether different chromatin states or topological associations correlate with X chromosome dosage compensation, especially in regions with little MSL occupancy. Our analyses demonstrated that male X chromosome genes that are located in repressive chromatin states are depleted of MSL occupancy; however, they show dosage compensation. The genes in these repressive regions were also less sensitive to knockdown of MSL components. Conclusions Our results suggest that this non-canonical dosage compensation is due to the same transacting derepression that occurs on autosomes. This mechanism would facilitate immediate compensation during the evolution of sex chromosomes from autosomes. This mechanism is similar to that of C. elegans, where enhanced recruitment of X chromosomes to the nuclear lamina dampens X chromosome expression as part of the dosage compensation response in XX individuals. Electronic supplementary material The online version of this article (10.1186/s13072-018-0232-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hangnoh Lee
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, USA. .,Section on Cell Cycle Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, USA
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10
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Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome. G3-GENES GENOMES GENETICS 2018; 8:587-598. [PMID: 29242386 PMCID: PMC5919722 DOI: 10.1534/g3.117.300400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA copy number variation is associated with many high phenotypic heterogeneity disorders. We systematically examined the impact of Drosophila melanogaster deletions on gene expression profiles to ask whether increased expression variability owing to reduced gene dose might underlie this phenotypic heterogeneity. Indeed, we found that one-dose genes have higher gene expression variability relative to two-dose genes. We then asked whether this increase in variability could be explained by intrinsic noise within cells due to stochastic biochemical events, or whether expression variability is due to extrinsic noise arising from more complex interactions. Our modeling showed that intrinsic gene expression noise averages at the organism level and thus cannot explain increased variation in one-dose gene expression. Interestingly, expression variability was related to the magnitude of expression compensation, suggesting that regulation, induced by gene dose reduction, is noisy. In a remarkable exception to this rule, the single X chromosome of males showed reduced expression variability, even compared with two-dose genes. Analysis of sex-transformed flies indicates that X expression variability is independent of the male differentiation program. Instead, we uncovered a correlation between occupancy of the chromatin-modifying protein encoded by males absent on the first (mof) and expression variability, linking noise suppression to the specialized X chromosome dosage compensation system. MOF occupancy on autosomes in both sexes also lowered transcriptional noise. Our results demonstrate that gene dose reduction can lead to heterogeneous responses, which are often noisy. This has implications for understanding gene network regulatory interactions and phenotypic heterogeneity. Additionally, chromatin modification appears to play a role in dampening transcriptional noise.
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11
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Dosage Compensation in Drosophila-a Model for the Coordinate Regulation of Transcription. Genetics 2017; 204:435-450. [PMID: 27729494 DOI: 10.1534/genetics.115.185108] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 12/20/2022] Open
Abstract
The sex chromosomes have special significance in the history of genetics. The chromosomal basis of inheritance was firmly established when Calvin Bridges demonstrated that exceptions to Mendel's laws of segregation were accompanied at the cytological level by exceptional sex chromosome segregation. The morphological differences between X and Y exploited in Bridges' experiments arose as a consequence of the evolution of the sex chromosomes. Originally a homologous chromosome pair, the degeneration of the Y chromosome has been accompanied by a requirement for increased expression of the single X chromosome in males. Drosophila has been a model for the study of this dosage compensation and has brought key strengths, including classical genetics, the exceptional cytology of polytene chromosomes, and more recently, comprehensive genomics. The impact of these studies goes beyond sex chromosome regulation, providing valuable insights into mechanisms for the establishment and maintenance of chromatin domains, and for the coordinate regulation of transcription.
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12
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Lee H, Cho DY, Whitworth C, Eisman R, Phelps M, Roote J, Kaufman T, Cook K, Russell S, Przytycka T, Oliver B. Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PLoS Genet 2016; 12:e1006295. [PMID: 27599372 PMCID: PMC5012587 DOI: 10.1371/journal.pgen.1006295] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 08/10/2016] [Indexed: 11/18/2022] Open
Abstract
Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are rare. These rare cases include trans de-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100bp) or in the gene body. Effects of deficiencies genome-wide are in genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds.
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Affiliation(s)
- Hangnoh Lee
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dong-Yeon Cho
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cale Whitworth
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Robert Eisman
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Melissa Phelps
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - John Roote
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Kaufman
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Kevin Cook
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Steven Russell
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Teresa Przytycka
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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13
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Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans. Genetics 2016; 204:355-69. [PMID: 27356611 DOI: 10.1534/genetics.116.190298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/27/2016] [Indexed: 01/31/2023] Open
Abstract
Dosage compensation mechanisms equalize the level of X chromosome expression between sexes. Yet the X chromosome is often enriched for genes exhibiting sex-biased, i.e., imbalanced expression. The relationship between X chromosome dosage compensation and sex-biased gene expression remains largely unexplored. Most studies determine sex-biased gene expression without distinguishing between contributions from X chromosome copy number (dose) and the animal's sex. Here, we uncoupled X chromosome dose from sex-specific gene regulation in Caenorhabditis elegans to determine the effect of each on X expression. In early embryogenesis, when dosage compensation is not yet fully active, X chromosome dose drives the hermaphrodite-biased expression of many X-linked genes, including several genes that were shown to be responsible for hermaphrodite fate. A similar effect is seen in the C. elegans germline, where X chromosome dose contributes to higher hermaphrodite X expression, suggesting that lack of dosage compensation in the germline may have a role in supporting higher expression of X chromosomal genes with female-biased functions in the gonad. In the soma, dosage compensation effectively balances X expression between the sexes. As a result, somatic sex-biased expression is almost entirely due to sex-specific gene regulation. These results suggest that lack of dosage compensation in different tissues and developmental stages allow X chromosome copy number to contribute to sex-biased gene expression and function.
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14
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Disteche CM. Dosage compensation of the sex chromosomes and autosomes. Semin Cell Dev Biol 2016; 56:9-18. [PMID: 27112542 DOI: 10.1016/j.semcdb.2016.04.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/16/2022]
Abstract
Males are XY and females are XX in most mammalian species. Other species such as birds have a different sex chromosome make-up: ZZ in males and ZW in females. In both types of organisms one of the sex chromosomes, Y or W, has degenerated due to lack of recombination with its respective homolog X or Z. Since autosomes are present in two copies in diploid organisms the heterogametic sex has become a natural "aneuploid" with haploinsufficiency for X- or Z-linked genes. Specific mechanisms have evolved to restore a balance between critical gene products throughout the genome and between males and females. Some of these mechanisms were co-opted from and/or added to compensatory processes that alleviate autosomal aneuploidy. Surprisingly, several modes of dosage compensation have evolved. In this review we will consider the evidence for dosage compensation and the molecular mechanisms implicated.
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Affiliation(s)
- Christine M Disteche
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA; Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA.
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15
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Arnold AP, Reue K, Eghbali M, Vilain E, Chen X, Ghahramani N, Itoh Y, Li J, Link JC, Ngun T, Williams-Burris SM. The importance of having two X chromosomes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150113. [PMID: 26833834 DOI: 10.1098/rstb.2015.0113] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2015] [Indexed: 12/14/2022] Open
Abstract
Historically, it was thought that the number of X chromosomes plays little role in causing sex differences in traits. Recently, selected mouse models have been used increasingly to compare mice with the same type of gonad but with one versus two copies of the X chromosome. Study of these models demonstrates that mice with one X chromosome can be strikingly different from those with two X chromosomes, when the differences are not attributable to confounding group differences in gonadal hormones. The number of X chromosomes affects adiposity and metabolic disease, cardiovascular ischaemia/reperfusion injury and behaviour. The effects of X chromosome number are likely the result of inherent differences in expression of X genes that escape inactivation, and are therefore expressed from both X chromosomes in XX mice, resulting in a higher level of expression when two X chromosomes are present. The effects of X chromosome number contribute to sex differences in disease phenotypes, and may explain some features of X chromosome aneuploidies such as in Turner and Klinefelter syndromes.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA Laboratory of Neuroendocrinology, UCLA Brain Research Institute, Los Angeles, CA, USA
| | - Karen Reue
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Eric Vilain
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Xuqi Chen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA Laboratory of Neuroendocrinology, UCLA Brain Research Institute, Los Angeles, CA, USA
| | - Negar Ghahramani
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA Laboratory of Neuroendocrinology, UCLA Brain Research Institute, Los Angeles, CA, USA
| | - Yuichiro Itoh
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA Laboratory of Neuroendocrinology, UCLA Brain Research Institute, Los Angeles, CA, USA
| | - Jingyuan Li
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jenny C Link
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Tuck Ngun
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA Laboratory of Neuroendocrinology, UCLA Brain Research Institute, Los Angeles, CA, USA
| | - Shayna M Williams-Burris
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA Interdepartmental Program for Neuroscience, University of California, Los Angeles, Los Angeles, CA, USA Laboratory of Neuroendocrinology, UCLA Brain Research Institute, Los Angeles, CA, USA
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16
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Primary Sex Determination in Drosophila melanogaster Does Not Rely on the Male-Specific Lethal Complex. Genetics 2015; 202:541-9. [PMID: 26614741 DOI: 10.1534/genetics.115.182931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/21/2015] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that the Male Specific Lethal (MSL) complex is active in Drosophila melanogaster embryos of both sexes prior to the maternal-to-zygotic transition. Elevated gene expression from the two X chromosomes of female embryos is proposed to facilitate the stable establishment of Sex-lethal (Sxl) expression, which determines sex and represses further activity of the MSL complex, leaving it active only in males. Important supporting data included female-lethal genetic interactions between the seven msl genes and either Sxl or scute and sisterlessA, two of the X-signal elements (XSE) that regulate early Sxl expression. Here I report contrary findings that there are no female-lethal genetic interactions between the msl genes and Sxl or its XSE regulators. Fly stocks containing the msl3(1) allele were found to exhibit a maternal-effect interaction with Sxl, scute, and sisterlessA mutations, but genetic complementation experiments showed that msl3 is neither necessary nor sufficient for the female-lethal interactions, which appear to be due to an unidentified maternal regulator of Sxl. Published data cited as evidence for an early function of the MSL complex in females, including a maternal effect of msl2, have been reevaluated and found not to support a maternal, or other effect, of the MSL complex in sex determination. These findings suggest that the MSL complex is not involved in primary sex determination or in X chromosome dosage compensation prior to the maternal-to-zygotic transition.
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